Dynamic Event Tree Analysis Through RAVEN

Energy Technology Data Exchange (ETDEWEB)

A. Alfonsi; C. Rabiti; D. Mandelli; J. Cogliati; R. A. Kinoshita; A. Naviglio

2013-09-01

Conventional Event-Tree (ET) based methodologies are extensively used as tools to perform reliability and safety assessment of complex and critical engineering systems. One of the disadvantages of these methods is that timing/sequencing of events and system dynamics is not explicitly accounted for in the analysis. In order to overcome these limitations several techniques, also know as Dynamic Probabilistic Risk Assessment (D-PRA), have been developed. Monte-Carlo (MC) and Dynamic Event Tree (DET) are two of the most widely used D-PRA methodologies to perform safety assessment of Nuclear Power Plants (NPP). In the past two years, the Idaho National Laboratory (INL) has developed its own tool to perform Dynamic PRA: RAVEN (Reactor Analysis and Virtual control ENvironment). RAVEN has been designed in a high modular and pluggable way in order to enable easy integration of different programming languages (i.e., C++, Python) and coupling with other application including the ones based on the MOOSE framework, developed by INL as well. RAVEN performs two main tasks: 1) control logic driver for the new Thermo-Hydraulic code RELAP-7 and 2) post-processing tool. In the first task, RAVEN acts as a deterministic controller in which the set of control logic laws (user defined) monitors the RELAP-7 simulation and controls the activation of specific systems. Moreover, RAVEN also models stochastic events, such as components failures, and performs uncertainty quantification. Such stochastic modeling is employed by using both MC and DET algorithms. In the second task, RAVEN processes the large amount of data generated by RELAP-7 using data-mining based algorithms. This paper focuses on the first task and shows how it is possible to perform the analysis of dynamic stochastic systems using the newly developed RAVEN DET capability. As an example, the Dynamic PRA analysis, using Dynamic Event Tree, of a simplified pressurized water reactor for a Station Black-Out scenario is presented.

Software infrastructure progress in the RAVEN code

Energy Technology Data Exchange (ETDEWEB)

Cogliati, Joshua J. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Permann, Cody J. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-03-01

The milestones have been achieved. RAVEN has been migrated to Gitlab which adds new abilities for code review and management. Standalone RAVEN framework packages have been created for OSX and two Linux distributions.

Reciprocity of agonistic support in ravens.

Science.gov (United States)

Fraser, Orlaith N; Bugnyar, Thomas

2012-01-01

Cooperative behaviour through reciprocation or interchange of valuable services in primates has received considerable attention, especially regarding the timeframe of reciprocation and its ensuing cognitive implications. Much less, however, is known about reciprocity in other animals, particularly birds. We investigated patterns of agonistic support (defined as a third party intervening in an ongoing conflict to attack one of the conflict participants, thus supporting the other) in a group of 13 captive ravens, Corvus corax. We found support for long-term, but not short-term, reciprocation of agonistic support. Ravens were more likely to support individuals who preened them, kin and dominant group members. These results suggest that ravens do not reciprocate on a calculated tit-for-tat basis, but aid individuals from whom reciprocated support would be most useful and those with whom they share a good relationship. Additionally, dyadic levels of agonistic support and consolation (postconflict affiliation from a bystander to the victim) correlated strongly with each other, but we found no evidence to suggest that receiving agonistic support influences the victim's likelihood of receiving support (consolation) after the conflict ends. Our findings are consistent with an emotionally mediated form of reciprocity in ravens and provide additional support for convergent cognitive evolution in birds and mammals.

Partner Choice in Raven (Corvus corax) Cooperation.

Science.gov (United States)

Asakawa-Haas, Kenji; Schiestl, Martina; Bugnyar, Thomas; Massen, Jorg J M

2016-01-01

Although social animals frequently make decisions about when or with whom to cooperate, little is known about the underlying mechanisms of partner choice. Most previous studies compared different dyads' performances, though did not allow an actual choice among partners. We tested eleven ravens, Corvus corax, in triads, giving them first the choice to cooperate with either a highly familiar or a rather unfamiliar partner and, second, with either a friend or a non-friend using a cooperative string-pulling task. In either test, the ravens had a second choice and could cooperate with the other partner, given that this one had not pulled the string in the meantime. We show that during the experiments, these partner ravens indeed learn to wait and inhibit pulling, respectively. Moreover, the results of these two experiments show that ravens' preferences for a specific cooperation partner are not based on familiarity. In contrast, the ravens did show a preference based on relationship quality, as they did choose to cooperate significantly more with friends than with non-friends and they were also more proficient when cooperating with a friend. In order to further identify the proximate mechanism of this preference, we designed an open-choice experiment for the whole group where all birds were free to cooperate on two separate apparatuses. This set-up allowed us to distinguish between preferences for close proximity and preferences to cooperate. The results revealed that friends preferred staying close to each other, but did not necessarily cooperate with one another, suggesting that tolerance of proximity and not relationship quality as a whole may be the driving force behind partner choice in raven cooperation. Consequently, we stress the importance of experiments that allow such titrations and, suggest that these results have important implications for the interpretations of cooperation studies that did not include open partner choice.

FrankenRaven: A New Platform for Remote Sensing

Science.gov (United States)

Dahlgren, R. P.; Fladeland, M. M.; Pinsker, E. A.; Jasionowicz, J. P.; Jones, L. L.; Mosser, C. D.; Pscheid, M. J.; Weidow, N. L.; Kelly, P. J.; Kern, C.; Werner, C. A.; Johnson, M. S.

2016-12-01

Small, modular aircraft are an emerging technology with a goal to maximize flexibility and enable multi-mission support. This reports the progress of an unmanned aerial system (UAS) project conducted at the NASA Ames Research Center (ARC) in 2016. This interdisciplinary effort builds upon the success of the 2014 FrankenEye project to apply rapid prototyping techniques to UAS, to develop a variety of platforms to host remote sensing instruments. In 2016, ARC received AeroVironment RQ-11A and RQ-11B Raven UAS from the US Department of the Interior, Office of Aviation Services. These aircraft have electric propulsion, a wingspan of roughly 1.3m, and have demonstrated reliability in challenging environments. The Raven airframe is an ideal foundation to construct more complex aircraft, and student interns using 3D printing were able to graft multiple Raven wings and fuselages into "FrankenRaven" aircraft. Aeronautical analysis shows that the new configuration has enhanced flight time, payload capacity, and distance compared to the original Raven. The FrankenRaven avionics architecture replaces the mil-spec avionics with COTS technology based upon the 3DR Pixhawk PX4 autopilot with a safety multiplexer for failsafe handoff to 2.4 GHz RC control and 915 MHz telemetry. This project demonstrates how design reuse, rapid prototyping, and modular subcomponents can be leveraged into flexible airborne platforms that can host a variety of remote sensing payloads and even multiple payloads. Modularity advances a new paradigm: mass-customization of aircraft around given payload(s). Multi-fuselage designs are currently under development to host a wide variety of payloads including a zenith-pointing spectrometer, a magnetometer, a multi-spectral camera, and a RGB camera. After airworthiness certification, flight readiness review, and test flights are performed at Crows Landing airfield in central California, field data will be taken at Kilauea volcano in Hawaii and other locations.

Enhancements to the RAVEN code in FY16

International Nuclear Information System (INIS)

Alfonsi, Andrea; Rabiti, Cristian; Maljovec, Daniel Patrick; Mandelli, Diego; Smith, Curtis Lee

2016-01-01

The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN has currently reached a good level of maturity in terms of deployed state-of-art and advanced capabilities. The main subject of this report is to show the activities that have been recently accomplished: • Implementation of ensemble modeling for time-series, and • initial implementation of model validation for surrogate models, and • advanced visualization capability for topology based data analysis The development of ensemble modeling for time-series has been performed in order to begin tackling the needs of those RISMC applications that need to communicate 1-Dimensional information (e.g. power histories, etc.) among different models. In this document the implementation details and an application example is reported. The second subject of this report is about the initial development of methods, within the RAVEN framework, to assess the validity of the predictive capabilities of surrogate models. Indeed, after the construction of a surrogate tight to a certain physical model, it is crucial to assess the goodness of its representation, in order to be confident with its prediction. In this initial activity, a cross-validation technique has been employed. This report will highlight the implementation details and proof its correct implementation by an application example. The final subject of this report is about the implementation of advanced visualization capability in RAVEN, for interactive data analysis. Indeed, RAVEN offers several post-processing capabilities that can structurally decompose data extracted from experimental results offering both data clustering/partitioning and dimensionality reduction techniques. A disadvantage of the workflow available in

Enhancements to the RAVEN code in FY16

Energy Technology Data Exchange (ETDEWEB)

Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Maljovec, Daniel Patrick [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Smith, Curtis Lee [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-09-01

The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN has currently reached a good level of maturity in terms of deployed state-of-art and advanced capabilities. The main subject of this report is to show the activities that have been recently accomplished: • Implementation of ensemble modeling for time-series, and • initial implementation of model validation for surrogate models, and • advanced visualization capability for topology based data analysis The development of ensemble modeling for time-series has been performed in order to begin tackling the needs of those RISMC applications that need to communicate 1-Dimensional information (e.g. power histories, etc.) among different models. In this document the implementation details and an application example is reported. The second subject of this report is about the initial development of methods, within the RAVEN framework, to assess the validity of the predictive capabilities of surrogate models. Indeed, after the construction of a surrogate tight to a certain physical model, it is crucial to assess the goodness of its representation, in order to be confident with its prediction. In this initial activity, a cross-validation technique has been employed. This report will highlight the implementation details and proof its correct implementation by an application example. The final subject of this report is about the implementation of advanced visualization capability in RAVEN, for interactive data analysis. Indeed, RAVEN offers several post-processing capabilities that can structurally decompose data extracted from experimental results offering both data clustering/partitioning and dimensionality reduction techniques. A disadvantage of the workflow available in

Performing Probabilistic Risk Assessment Through RAVEN

Energy Technology Data Exchange (ETDEWEB)

A. Alfonsi; C. Rabiti; D. Mandelli; J. Cogliati; R. Kinoshita

2013-06-01

The Reactor Analysis and Virtual control ENviroment (RAVEN) code is a software tool that acts as the control logic driver and post-processing engine for the newly developed Thermal-Hydraulic code RELAP-7. RAVEN is now a multi-purpose Probabilistic Risk Assessment (PRA) software framework that allows dispatching different functionalities: Derive and actuate the control logic required to simulate the plant control system and operator actions (guided procedures), allowing on-line monitoring/controlling in the Phase Space Perform both Monte-Carlo sampling of random distributed events and Dynamic Event Tree based analysis Facilitate the input/output handling through a Graphical User Interface (GUI) and a post-processing data mining module

Raven-II: an open platform for surgical robotics research.

Science.gov (United States)

Hannaford, Blake; Rosen, Jacob; Friedman, Diana W; King, Hawkeye; Roan, Phillip; Cheng, Lei; Glozman, Daniel; Ma, Ji; Kosari, Sina Nia; White, Lee

2013-04-01

The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven universities have begun research using this platform. The Raven-II system has two 3-DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechanism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.

RAVEN. Dynamic Event Tree Approach Level III Milestone

Energy Technology Data Exchange (ETDEWEB)

Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cogliati, Joshua [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2014-07-01

Conventional Event-Tree (ET) based methodologies are extensively used as tools to perform reliability and safety assessment of complex and critical engineering systems. One of the disadvantages of these methods is that timing/sequencing of events and system dynamics are not explicitly accounted for in the analysis. In order to overcome these limitations several techniques, also know as Dynamic Probabilistic Risk Assessment (DPRA), have been developed. Monte-Carlo (MC) and Dynamic Event Tree (DET) are two of the most widely used D-PRA methodologies to perform safety assessment of Nuclear Power Plants (NPP). In the past two years, the Idaho National Laboratory (INL) has developed its own tool to perform Dynamic PRA: RAVEN (Reactor Analysis and Virtual control ENvironment). RAVEN has been designed to perform two main tasks: 1) control logic driver for the new Thermo-Hydraulic code RELAP-7 and 2) post-processing tool. In the first task, RAVEN acts as a deterministic controller in which the set of control logic laws (user defined) monitors the RELAP-7 simulation and controls the activation of specific systems. Moreover, the control logic infrastructure is used to model stochastic events, such as components failures, and perform uncertainty propagation. Such stochastic modeling is deployed using both MC and DET algorithms. In the second task, RAVEN processes the large amount of data generated by RELAP-7 using data-mining based algorithms. This report focuses on the analysis of dynamic stochastic systems using the newly developed RAVEN DET capability. As an example, a DPRA analysis, using DET, of a simplified pressurized water reactor for a Station Black-Out (SBO) scenario is presented.

RAVEN: Dynamic Event Tree Approach Level III Milestone

Energy Technology Data Exchange (ETDEWEB)

Andrea Alfonsi; Cristian Rabiti; Diego Mandelli; Joshua Cogliati; Robert Kinoshita

2013-07-01

Conventional Event-Tree (ET) based methodologies are extensively used as tools to perform reliability and safety assessment of complex and critical engineering systems. One of the disadvantages of these methods is that timing/sequencing of events and system dynamics are not explicitly accounted for in the analysis. In order to overcome these limitations several techniques, also know as Dynamic Probabilistic Risk Assessment (DPRA), have been developed. Monte-Carlo (MC) and Dynamic Event Tree (DET) are two of the most widely used D-PRA methodologies to perform safety assessment of Nuclear Power Plants (NPP). In the past two years, the Idaho National Laboratory (INL) has developed its own tool to perform Dynamic PRA: RAVEN (Reactor Analysis and Virtual control ENvironment). RAVEN has been designed to perform two main tasks: 1) control logic driver for the new Thermo-Hydraulic code RELAP-7 and 2) post-processing tool. In the first task, RAVEN acts as a deterministic controller in which the set of control logic laws (user defined) monitors the RELAP-7 simulation and controls the activation of specific systems. Moreover, the control logic infrastructure is used to model stochastic events, such as components failures, and perform uncertainty propagation. Such stochastic modeling is deployed using both MC and DET algorithms. In the second task, RAVEN processes the large amount of data generated by RELAP-7 using data-mining based algorithms. This report focuses on the analysis of dynamic stochastic systems using the newly developed RAVEN DET capability. As an example, a DPRA analysis, using DET, of a simplified pressurized water reactor for a Station Black-Out (SBO) scenario is presented.

Item and Error Analysis on Raven's Coloured Progressive Matrices in Williams Syndrome

Science.gov (United States)

Van Herwegen, Jo; Farran, Emily; Annaz, Dagmara

2011-01-01

Raven's Coloured Progressive Matrices (RCPM) is a standardised test that is commonly used to obtain a non-verbal reasoning score for children. As the RCPM involves the matching of a target to a pattern it is also considered to be a visuo-spatial perception task. RCPM is therefore frequently used in studies in Williams Syndrome (WS), in order to…

Social networks predict selective observation and information spread in ravens

Science.gov (United States)

Rubenstein, Daniel I.; Bugnyar, Thomas; Hoppitt, William; Mikus, Nace; Schwab, Christine

2016-01-01

Animals are predicted to selectively observe and learn from the conspecifics with whom they share social connections. Yet, hardly anything is known about the role of different connections in observation and learning. To address the relationships between social connections, observation and learning, we investigated transmission of information in two raven (Corvus corax) groups. First, we quantified social connections in each group by constructing networks on affiliative interactions, aggressive interactions and proximity. We then seeded novel information by training one group member on a novel task and allowing others to observe. In each group, an observation network based on who observed whose task-solving behaviour was strongly correlated with networks based on affiliative interactions and proximity. Ravens with high social centrality (strength, eigenvector, information centrality) in the affiliative interaction network were also central in the observation network, possibly as a result of solving the task sooner. Network-based diffusion analysis revealed that the order that ravens first solved the task was best predicted by connections in the affiliative interaction network in a group of subadult ravens, and by social rank and kinship (which influenced affiliative interactions) in a group of juvenile ravens. Our results demonstrate that not all social connections are equally effective at predicting the patterns of selective observation and information transmission. PMID:27493780

System Reliability Analysis Capability and Surrogate Model Application in RAVEN

Energy Technology Data Exchange (ETDEWEB)

Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Huang, Dongli [Idaho National Lab. (INL), Idaho Falls, ID (United States); Gleicher, Frederick [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Bei [Idaho National Lab. (INL), Idaho Falls, ID (United States); Adbel-Khalik, Hany S. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pascucci, Valerio [Idaho National Lab. (INL), Idaho Falls, ID (United States); Smith, Curtis L. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-11-01

This report collect the effort performed to improve the reliability analysis capabilities of the RAVEN code and explore new opportunity in the usage of surrogate model by extending the current RAVEN capabilities to multi physics surrogate models and construction of surrogate models for high dimensionality fields.

"The raven", by Machado de Assis "The raven", by Machado de Assis

Directory of Open Access Journals (Sweden)

Sérgio Luiz Prado Bellei

2008-04-01

Full Text Available The Brazilian critic José Guilherme Merquior once claimed that Machado de Assis's translation of "The Raven" should not be considered inferior to the well known translation of the Portuguese poet Fernando Pessoa. 1 Unfortunately Merquior does not seem to find necessary to give reasons for this evaluation. And yet even the most cursory reading of the two translations will show that some sort of explanation is necessary because Machado and Pessoa are obviously doing something radically different with Poe's poem. Consider, for example, the two renderings of the first stanza in relation to Poe's original: The Brazilian critic José Guilherme Merquior once claimed that Machado de Assis's translation of "The Raven" should not be considered inferior to the well known translation of the Portuguese poet Fernando Pessoa. 1 Unfortunately Merquior does not seem to find necessary to give reasons for this evaluation. And yet even the most cursory reading of the two translations will show that some sort of explanation is necessary because Machado and Pessoa are obviously doing something radically different with Poe's poem. Consider, for example, the two renderings of the first stanza in relation to Poe's original:

Craving Ravens: Individual ‘haa’ Call Rates at Feeding Sites as Cues to Personality and Levels of Fission-Fusion Dynamics?

Directory of Open Access Journals (Sweden)

Georgine Szipl

2014-08-01

Full Text Available Common ravens aggregate in large non-breeder flocks for roosting and foraging until they achieve the status of territorial breeders. When discovering food, they produce far-reaching yells or ‘haa’ calls, which attract conspecifics. Due to the high levels of fission-fusion dynamics in non-breeders’ flocks, assemblies of feeding ravens were long thought to represent anonymous aggregations. Yet, non-breeders vary in their degree of vagrancy, and ‘haa’ calls convey individually distinct acoustic features, which are perceived by conspecifics. These findings give rise to the assumption that raven societies are based on differential social relationships on an individual level. We investigated the occurrence of ‘haa’ calling and individual call rates in a group of individually marked free-ranging ravens. Calling mainly occurred in subadult and adult females, which showed low levels of vagrancy. Call rates differed significantly between individuals and with residency status, and were correlated with calling frequency and landing frequency. Local ravens called more often and at higher rates, and were less likely to land at the feeding site than vagrant birds. The results are discussed with respect to individual degrees of vagrancy, which may have an impact on social knowledge and communication in this species.

Working Memory Capacity and Fluid Abilities: Examining the Correlation between Operation Span and Raven

Science.gov (United States)

Unsworth, N.; Engle, R.W.

2005-01-01

The correlation between a measure of working memory capacity (WMC) (Operation Span) and a measure of fluid abilities (Raven Advanced Progressive Matrices) was examined. Specifically, performance on Raven problems was decomposed by difficulty, memory load, and rule type. The results suggest that the relation between Operation Span and Raven is…

Developing and Implementing the Data Mining Algorithms in RAVEN

International Nuclear Information System (INIS)

Sen, Ramazan Sonat; Maljovec, Daniel Patrick; Alfonsi, Andrea; Rabiti, Cristian

2015-01-01

The RAVEN code is becoming a comprehensive tool to perform probabilistic risk assessment, uncertainty quantification, and verification and validation. The RAVEN code is being developed to support many programs and to provide a set of methodologies and algorithms for advanced analysis. Scientific computer codes can generate enormous amounts of data. To post-process and analyze such data might, in some cases, take longer than the initial software runtime. Data mining algorithms/methods help in recognizing and understanding patterns in the data, and thus discover knowledge in databases. The methodologies used in the dynamic probabilistic risk assessment or in uncertainty and error quantification analysis couple system/physics codes with simulation controller codes, such as RAVEN. RAVEN introduces both deterministic and stochastic elements into the simulation while the system/physics code model the dynamics deterministically. A typical analysis is performed by sampling values of a set of parameter values. A major challenge in using dynamic probabilistic risk assessment or uncertainty and error quantification analysis for a complex system is to analyze the large number of scenarios generated. Data mining techniques are typically used to better organize and understand data, i.e. recognizing patterns in the data. This report focuses on development and implementation of Application Programming Interfaces (APIs) for different data mining algorithms, and the application of these algorithms to different databases.

Developing and Implementing the Data Mining Algorithms in RAVEN

Energy Technology Data Exchange (ETDEWEB)

Sen, Ramazan Sonat [Idaho National Lab. (INL), Idaho Falls, ID (United States); Maljovec, Daniel Patrick [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-09-01

The RAVEN code is becoming a comprehensive tool to perform probabilistic risk assessment, uncertainty quantification, and verification and validation. The RAVEN code is being developed to support many programs and to provide a set of methodologies and algorithms for advanced analysis. Scientific computer codes can generate enormous amounts of data. To post-process and analyze such data might, in some cases, take longer than the initial software runtime. Data mining algorithms/methods help in recognizing and understanding patterns in the data, and thus discover knowledge in databases. The methodologies used in the dynamic probabilistic risk assessment or in uncertainty and error quantification analysis couple system/physics codes with simulation controller codes, such as RAVEN. RAVEN introduces both deterministic and stochastic elements into the simulation while the system/physics code model the dynamics deterministically. A typical analysis is performed by sampling values of a set of parameter values. A major challenge in using dynamic probabilistic risk assessment or uncertainty and error quantification analysis for a complex system is to analyze the large number of scenarios generated. Data mining techniques are typically used to better organize and understand data, i.e. recognizing patterns in the data. This report focuses on development and implementation of Application Programming Interfaces (APIs) for different data mining algorithms, and the application of these algorithms to different databases.

Raven surgical robot training in preparation for da vinci.

Science.gov (United States)

Glassman, Deanna; White, Lee; Lewis, Andrew; King, Hawkeye; Clarke, Alicia; Glassman, Thomas; Comstock, Bryan; Hannaford, Blake; Lendvay, Thomas S

2014-01-01

The rapid adoption of robotic assisted surgery challenges the pace at which adequate robotic training can occur due to access limitations to the da Vinci robot. Thirty medical students completed a randomized controlled trial evaluating whether the Raven robot could be used as an alternative training tool for the Fundamentals of Laparoscopic Surgery (FLS) block transfer task on the da Vinci robot. Two groups, one trained on the da Vinci and one trained on the Raven, were tested on a criterion FLS block transfer task on the da Vinci. After robotic FLS block transfer proficiency training there was no statistically significant difference between path length (p=0.39) and economy of motion scores (p=0.06) between the two groups, but those trained on the da Vinci did have faster task times (p=0.01). These results provide evidence for the value of using the Raven robot for training prior to using the da Vinci surgical system for similar tasks.

Brains, tools, innovation and biogeography in crows and ravens

DEFF Research Database (Denmark)

Jønsson, Knud Andreas; Fabre, Pierre-Henri Fréderic; Irestedt, Martin

2012-01-01

BACKGROUND:Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative....... Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.......BACKGROUND:Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative...... Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success...

The Effects of Site Characterization Activities on the Abundance of Ravens (Corvus corax) in the Yucca Mountain Area

Energy Technology Data Exchange (ETDEWEB)

P.E. Lederle

1998-05-08

In response to the Nuclear Waste Policy Act of 1982 and the Nuclear Waste Policy Amendments Act of 1987, the U.S. Department of Energy (DOE) developed and is implementing the Yucca Mountain Site Characterization Project. Raven abundance was measured from August 1991 through August 1995 along treatment and control routes to evaluate whether site characterization activities resulted in increased raven abundance at Yucca Mountain. This study fulfills the requirement set forth in the incidental take provisions of the Biological Opinion that DOE monitor the abundance of ravens at Yucca Mountain. Ravens were more abundant at Yucca Mountain than in the control area, and raven abundance in both areas increased over time. However, the magnitude of differences between Yucca Mountain and control surveys did not change over time, indicating that the increase in raven abundance observed during this study was not related to site characterization activities. Increases over time on both Yucca Mountain and control routes are consistent with increases in raven abundance in the Mojave Desert reported by the annual Breeding Bird Survey of the US. Fish and Wildlife Service. Evidence from the Desert Tortoise Monitoring Program at Yucca Mountain suggests that ravens are not a significant predator of small tortoises in this locale. Carcasses of small tortoises (less than 110 mm in length) collected during the study showed little evidence of raven predation, and 59 radiomarked hatchlings that were monitored on a regular basis were not preyed upon by ravens. Overall, no direct evidence of raven predation on tortoises was observed during this study. Small tortoises are probably encountered so infrequently by ravens that they are rarely exploited as a food source. This is likely due to the relatively low abundance of both desert tortoises and ravens in the Yucca Mountain area.

The Effects of Site Characterization Activities on the Abundance of Ravens (Corvus corax) in the Yucca Mountain Area

International Nuclear Information System (INIS)

P.E. Lederle

1998-01-01

In response to the Nuclear Waste Policy Act of 1982 and the Nuclear Waste Policy Amendments Act of 1987, the U.S. Department of Energy (DOE) developed and is implementing the Yucca Mountain Site Characterization Project. Raven abundance was measured from August 1991 through August 1995 along treatment and control routes to evaluate whether site characterization activities resulted in increased raven abundance at Yucca Mountain. This study fulfills the requirement set forth in the incidental take provisions of the Biological Opinion that DOE monitor the abundance of ravens at Yucca Mountain. Ravens were more abundant at Yucca Mountain than in the control area, and raven abundance in both areas increased over time. However, the magnitude of differences between Yucca Mountain and control surveys did not change over time, indicating that the increase in raven abundance observed during this study was not related to site characterization activities. Increases over time on both Yucca Mountain and control routes are consistent with increases in raven abundance in the Mojave Desert reported by the annual Breeding Bird Survey of the US. Fish and Wildlife Service. Evidence from the Desert Tortoise Monitoring Program at Yucca Mountain suggests that ravens are not a significant predator of small tortoises in this locale. Carcasses of small tortoises (less than 110 mm in length) collected during the study showed little evidence of raven predation, and 59 radiomarked hatchlings that were monitored on a regular basis were not preyed upon by ravens. Overall, no direct evidence of raven predation on tortoises was observed during this study. Small tortoises are probably encountered so infrequently by ravens that they are rarely exploited as a food source. This is likely due to the relatively low abundance of both desert tortoises and ravens in the Yucca Mountain area

Ravens notice dominance reversals among conspecifics within and outside their social group.

Science.gov (United States)

Massen, Jorg J M; Pašukonis, Andrius; Schmidt, Judith; Bugnyar, Thomas

2014-04-22

A core feature of social intelligence is the understanding of third-party relations, which has been experimentally demonstrated in primates. Whether other social animals also have this capacity, and whether they can use this capacity flexibly to, for example, also assess the relations of neighbouring conspecifics, remains unknown. Here we show that ravens react differently to playbacks of dominance interactions that either confirm or violate the current rank hierarchy of members in their own social group and of ravens in a neighbouring group. Therefore, ravens understand third-party relations and may deduce those not only via physical interactions but also by observation.

Ravens intervene in others' bonding attempts.

Science.gov (United States)

Massen, Jorg J M; Szipl, Georgine; Spreafico, Michela; Bugnyar, Thomas

2014-11-17

The competition for power in a complex social world is hypothesized to be a driving force in the evolution of intelligence. More specifically, power may be obtained not only by brute force but also by social strategies resembling human politics. Most empirical evidence comes from primate studies that report unprovoked aggression by dominants to maintain power by spreading fear and third-party interventions in conflicts. Coalitionary support has also been described in other animals and is often linked to social bonding. As coalitions can lead to a gain in power and fitness benefits, individuals may try to prevent coalitionary support or indirectly prevent others from forming social bonds that might lead to coalitions. Although there is some empirical evidence that coalitionary support can be manipulated, little is known about the indirect strategy. We show here that wild ravens (Corvus corax) regularly intervene in affiliative interactions of others even though such interventions are potentially risky and without immediate benefits. Moreover, the identities of both interveners and intervened pairs are not randomly distributed. Ravens with existing ties initiate most interventions, and ravens that are creating new ties are most likely to be the targets of interventions. These patterns are consistent with the idea that interventions function to prevent others from forming alliances and consequently becoming future competitors. We thus show previously undescribed social maneuvers in the struggle for power. These maneuvers are likely to be of importance in other social species as well. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Estudio sobre la pertinencia del uso de las normas disponibles del Raven en adultos mayores chilenos Estudo sobre a pertinência da utilização das normas disponíveis de Raven em idosos chilenos Study on the relevance of using available norms Raven in Chileans older adults

OpenAIRE

Cristina Alarcón Paz; Vanessa Díaz Valenzuela; Jacqueline Hernández Rosales; Claudia Estrada Goic

2012-01-01

La evaluación de la inteligencia en población adulto mayor ha aumentado su relevancia debido al incremento de la esperanza de vida. Este estudio centra su interés en la pertinencia de normas disponibles para el Test de Matrices Progresivas de Raven para dicha población. Se utilizaron normas de Colchester (1942, en Raven, Court y Raven, 2008), las más completas existentes. Participaron 102 adultos mayores voluntarios (más de 60 años). El diseño fue no experimental transversal correlacional. Lo...

RAVEN-2: Around-The-World UAV Project

National Research Council Canada - National Science Library

Burleigh, Chris

2003-01-01

The Raven around-the-world UAV project is part of an on-going effort to build up a significant European capability in the design, construction and operation of large UAVs and manned reconnaissance aircraft...

Subadult ravens generally don’t transfer valuable tokens to conspecifics when there is nothing to gain for themselves.

Directory of Open Access Journals (Sweden)

Jorg J.M. Massen

2015-06-01

Full Text Available The extent to which humans help each other is extraordinary in itself, and difficult to explain from an evolutionary perspective. Therefore, there has been a recent surge in studies investigating the evolution of prosocial behavior using a comparative approach. Nevertheless, most of these studies have focused on primates only, and little is known about other animal orders. In a previous study, common ravens (Corvus corax have been shown to be indifferent to the gains of conspecifics. However, this may have been due to the experimental set-up, as many studies that use different set-ups report conflicting results within the same species. We therefore tested ravens’ prosocial tendencies in a different set-up; i.e., we tested whether sub-adult ravens would transfer a token to a partner and, thereby, provide the partner with the opportunity to exchange a token for a reward. To control and test for effects of partner identity, we tested 8 individuals both in a dyadic and in a group setting. Our results show that in general the ravens in our experiment did not show other-regarding preferences. However, some acts of helping did occur spontaneously. We discuss what could be the causes for those sporadic instances, and why in general prosocial tendencies were found to be almost lacking among the ravens in this set-up.

NH11B-1726: FrankenRaven: A New Platform for Remote Sensing

Science.gov (United States)

Dahlgren, Robert; Fladeland, Matthew M.; Pinsker, Ethan A.; Jasionowicz, John P.; Jones, Lowell L.; Pscheid, Matthew J.

2016-01-01

Small, modular aircraft are an emerging technology with a goal to maximize flexibility and enable multi-mission support. This reports the progress of an unmanned aerial system (UAS) project conducted at the NASA Ames Research Center (ARC) in 2016. This interdisciplinary effort builds upon the success of the 2014 FrankenEye project to apply rapid prototyping techniques to UAS, to develop a variety of platforms to host remote sensing instruments. In 2016, ARC received AeroVironment RQ-11A and RQ-11B Raven UAS from the US Department of the Interior, Office of Aviation Services. These aircraft have electric propulsion, a wingspan of roughly 1.3m, and have demonstrated reliability in challenging environments. The Raven airframe is an ideal foundation to construct more complex aircraft, and student interns using 3D printing were able to graft multiple Raven wings and fuselages into FrankenRaven aircraft. Aeronautical analysis shows that the new configuration has enhanced flight time, payload capacity, and distance compared to the original Raven. The FrankenRaven avionics architecture replaces the mil-spec avionics with COTS technology based upon the 3DR Pixhawk PX4 autopilot with a safety multiplexer for failsafe handoff to 2.4 GHz RC control and 915 MHz telemetry. This project demonstrates how design reuse, rapid prototyping, and modular subcomponents can be leveraged into flexible airborne platforms that can host a variety of remote sensing payloads and even multiple payloads. Modularity advances a new paradigm: mass-customization of aircraft around given payload(s). Multi-fuselage designs are currently under development to host a wide variety of payloads including a zenith-pointing spectrometer, a magnetometer, a multi-spectral camera, and a RGB camera. After airworthiness certification, flight readiness review, and test flights are performed at Crows Landing airfield in central California, field data will be taken at Kilauea volcano in Hawaii and other locations.

Time Dependent Data Mining in RAVEN

Energy Technology Data Exchange (ETDEWEB)

Cogliati, Joshua Joseph [Idaho National Lab. (INL), Idaho Falls, ID (United States); Chen, Jun [Idaho National Lab. (INL), Idaho Falls, ID (United States); Patel, Japan Ketan [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Maljovec, Daniel Patrick [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Talbot, Paul William [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-09-01

RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The goal of this type of analyses is to understand the response of such systems in particular with respect their probabilistic behavior, to understand their predictability and drivers or lack of thereof. Data mining capabilities are the cornerstones to perform such deep learning of system responses. For this reason static data mining capabilities were added last fiscal year (FY 15). In real applications, when dealing with complex multi-scale, multi-physics systems it seems natural that, during transients, the relevance of the different scales, and physics, would evolve over time. For these reasons the data mining capabilities have been extended allowing their application over time. In this writing it is reported a description of the new RAVEN capabilities implemented with several simple analytical tests to explain their application and highlight the proper implementation. The report concludes with the application of those newly implemented capabilities to the analysis of a simulation performed with the Bison code.

Generation speed in Raven's Progressive Matrices Test

NARCIS (Netherlands)

Verguts, T.; Boeck, P. De; Maris, E.G.G.

1999-01-01

In this paper, we investigate the role of response fluency on a well-known intelligence test, Raven's (1962) Advanced Progressive Matrices (APM) test. Critical in solving this test is finding rules that govern the items. Response fluency is conceptualized as generation speed or the speed at which a

RavenDB 2.x beginner's guide

CERN Document Server

Tannir, Khaled

2013-01-01

Written in a friendly, example-driven Beginner's Guide format, there are plenty of step-by-step instructions and examples that are designed to help you get started with RavenDB. If you are a .NET developer, new to document-oriented databases, and you wish to learn how to build applications using NoSQL databases, then this book is for you. Experience with relational database systems will be helpful, but not necessary.

Estudio sobre la pertinencia del uso de las normas disponibles del Raven en adultos mayores chilenos

OpenAIRE

Alarcón Paz,Cristina; Díaz Valenzuela,Vanessa; Hernández Rosales,Jacqueline; Estrada Goic,Claudia

2012-01-01

La evaluación de la inteligencia en población adulto mayor ha aumentado su relevancia debido al incremento de la esperanza de vida. Este estudio centra su interés en la pertinencia de normas disponibles para el Test de Matrices Progresivas de Raven para dicha población. Se utilizaron normas de Colchester (1942, en Raven, Court y Raven, 2008), las más completas existentes. Participaron 102 adultos mayores voluntarios (más de 60 años). El diseño fue no experimental transversal correlacional. Lo...

Estudio sobre la pertinencia del uso de las normas disponibles del Raven en adultos mayores chilenos Estudo sobre a pertinência da utilização das normas disponíveis de Raven em idosos chilenos Study on the relevance of using available norms Raven in Chileans older adults

Directory of Open Access Journals (Sweden)

Cristina Alarcón Paz

2012-12-01

Full Text Available La evaluación de la inteligencia en población adulto mayor ha aumentado su relevancia debido al incremento de la esperanza de vida. Este estudio centra su interés en la pertinencia de normas disponibles para el Test de Matrices Progresivas de Raven para dicha población. Se utilizaron normas de Colchester (1942, en Raven, Court y Raven, 2008, las más completas existentes. Participaron 102 adultos mayores voluntarios (más de 60 años. El diseño fue no experimental transversal correlacional. Los resultados indican que las normas resultan poco exigentes para ese grupo y que existen diferencias significativas entre los adultos de la tercera y cuarta edad, privilegiando a los del primer grupo. El índice de discrepancia mostró alta sensibilidad, indicando que la distribución de puntajes esperados no se corresponde al de la población general. Se discuten los resultados en torno a la necesidad de actualización de las normas y la consideración de las nuevas características de este periodo vital.A avaliação da inteligência na população idosa tem aumentado sua importância devido ao aumento da expectativa de vida. Este estudo está centrado na relevância das normas disponíveis para o teste de Matrizes Progressivas de Raven para essa população. Foram utilizadas as normas de Colchester (1942, citado por Raven, Court y Raven, 2008, as mais completas disponíveis. Participaram 102 idosos voluntários (com idade superior a 60 anos. O desenho do estudo foi não experimental transversal correlacional. Os resultados indicam que as normas são pouco exigentes para esse grupo e que existem diferenças significativas entre os adultos da terceira e quarta idade, privilegiando o primeiro grupo. O índice de discrepância mostrou alta sensibilidade, indicando que a distribuição de pontuações esperadas não corresponde a da população em geral. Os resultados são discutidos em relação à necessidade de atualização das normas e da considera

Raven's Test Performance of Sub-Saharan Africans: Average Performance, Psychometric Properties, and the Flynn Effect

Science.gov (United States)

Wicherts, Jelte M.; Dolan, Conor V.; Carlson, Jerry S.; van der Maas, Han L. J.

2010-01-01

This paper presents a systematic review of published data on the performance of sub-Saharan Africans on Raven's Progressive Matrices. The specific goals were to estimate the average level of performance, to study the Flynn Effect in African samples, and to examine the psychometric meaning of Raven's test scores as measures of general intelligence.…

The Shortened Raven Standard Progressive Matrices: Item Response Theory-Based Psychometric Analyses and Normative Data

Science.gov (United States)

Van der Elst, Wim; Ouwehand, Carolijn; van Rijn, Peter; Lee, Nikki; Van Boxtel, Martin; Jolles, Jelle

2013-01-01

The purpose of the present study was to evaluate the psychometric properties of a shortened version of the Raven Standard Progressive Matrices (SPM) under an item response theory framework (the one- and two-parameter logistic models). The shortened Raven SPM was administered to N = 453 cognitively healthy adults aged between 24 and 83 years. The…

Application of hierarchical genetic models to Raven and WAIS subtests: a Dutch twin study.

Science.gov (United States)

Rijsdijk, Frühling V; Vernon, P A; Boomsma, Dorret I

2002-05-01

Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a genetic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard Progressive test score, collected in 194 18-year-old Dutch twin pairs. We investigated whether first-order group factors possess genetic and environmental variance independent of the higher-order general factor and whether the hierarchical structure is significant for all sources of variance. A hierarchical model with the 3 Cohen group-factors (verbal comprehension, perceptual organisation and freedom-from-distractibility) and a higher-order g factor showed the best fit to the phenotypic data and to additive genetic influences (A), whereas the unique environmental source of variance (E) could be modeled by a single general factor and specifics. There was no evidence for common environmental influences. The covariation among the WAIS group factors and the covariation between the group factors and the Raven is predominantly influenced by a second-order genetic factor and strongly support the notion of a biological basis of g.

Learning of Three-Term Contingencies Correlates with Raven Scores, but Not with Measures of Cognitive Processing

Science.gov (United States)

Williams, Ben A.; Pearlberg, Stephen L.

2006-01-01

College undergraduates learned word lists involving three-term contingencies (stimulus-response-outcome). Learning rate was correlated approximately 0.5 with scores on Raven's Advanced Progressive Matrices (Raven) but did not correlate significantly with several tasks (inspection time, card-sorting, trail-making, PASAT) shown to be associated with…

RAVEN AS A TOOL FOR DYNAMIC PROBABILISTIC RISK ASSESSMENT: SOFTWARE OVERVIEW

Energy Technology Data Exchange (ETDEWEB)

Alfonsi Andrea; Mandelli Diego; Rabiti Cristian; Joshua Cogliati; Robert Kinoshita

2013-05-01

RAVEN is a software tool under development at the Idaho National Laboratory (INL) that acts as the control logic driver and post-processing tool for the newly developed Thermo-Hydraylic code RELAP- 7. The scope of this paper is to show the software structure of RAVEN and its utilization in connection with RELAP-7. A short overview of the mathematical framework behind the code is presented along with its main capabilities such as on-line controlling/monitoring and Monte-Carlo sampling. A demo of a Station Black Out PRA analysis of a simplified Pressurized Water Reactor (PWR) model is shown in order to demonstrate the Monte-Carlo and clustering capabilities.

Sediment accumulation and water volume in Loch Raven Reservoir, Baltimore County, Maryland

Science.gov (United States)

Banks, William S.L.; LaMotte, Andrew E.

1999-01-01

Baltimore City and its metropolitan area are supplied with water from three reservoirs, Liberty Reservoir, Prettyboy Reservoir, and Loch Raven Reservoir. Prettyboy and Loch Raven Reservoirs are located on the Gunpowder Falls (figure 1). The many uses of the reservoir system necessitate coordination and communication among resource managers. The 1996 Amendment to the Safe Drinking Water Act require States to complete source-water assessments for public drinking-water supplies. As part of an ongoing effort to provide safe drinking water and as a direct result of these laws, the City of Baltimore and the Maryland Department of the Environment (MDE), in cooperation with other State and local agencies, are studying the Gunpowder Falls Basin and its role as a source of water supply to the Baltimore area. As a part of this study, the U.S. Geological Survey (USGS), in cooperation with the Maryland Geological Survey (MGS), with funding provided by the City of Baltimore and MDE, is examining sediment accumulation in Loch Raven Reservoir. The Baltimore City Department of Public Works periodically determines the amount of water that can be stored in its reservoirs. To make this determination, field crews measure the water depth along predetermined transects or ranges. These transects provide consistent locations where water depth, or bathymetric, measurements can be made. Range surveys are repeated to provide a record of the change in storage capacity due to sediment accumulation over time. Previous bathymetric surveys of Loch Raven Reservoir were performed in 1943, 1961, 1972, and 1985. Errors in data-collection and analysis methods have been assessed and documented (Baltimore City Department of Public Works, 1989). Few comparisons can be made among survey results because of changing data-collection techniques and analysis methods.

Psychometric Investigation of the Raven's Colored Progressive Matrices Test in a Sample of Preschool Children.

Science.gov (United States)

Lúcio, Patrícia Silva; Cogo-Moreira, Hugo; Puglisi, Marina; Polanczyk, Guilherme Vanoni; Little, Todd D

2017-11-01

The present study investigated the psychometric properties of the Raven's Colored Progressive Matrices (CPM) test in a sample of preschoolers from Brazil ( n = 582; age: mean = 57 months, SD = 7 months; 46% female). We investigated the plausibility of unidimensionality of the items (confirmatory factor analysis) and differential item functioning (DIF) for sex and age (multiple indicators multiple causes method). We tested four unidimensional models and the one with the best-fit index was a reduced form of the Raven's CPM. The DIF analysis was carried out with the reduced form of the test. A few items presented DIF (two for sex and one for age), confirming that the Raven's CPM items are mostly measurement invariant. There was no effect of sex on the general factor, but increasing age was associated with higher values of the g factor. Future research should indicate if the reduced form is suitable for evaluating the general ability of preschoolers.

UAV-UGV collaboration with a PackBot UGV and Raven SUAV for pursuit and tracking of a dynamic target

Science.gov (United States)

Cheung, Carol; Grocholsky, Benjamin

2008-04-01

Fielded military unmanned systems are currently extending the reach of the U.S. forces in surveillance and reconnaissance missions. Providing long-range eyes on enemy operations, unmanned aerial vehicles (UAVs), such as the AeroVironment Raven, have proven themselves indispensable without risking soldiers' lives. Meanwhile, unmanned ground vehicles (UGVs), such as the iRobot PackBot, are quickly joining ranks in Explosive Ordnance Disposal (EOD) missions to identify and dispose of ordnance or to clear roads and buildings. UAV-UGV collaboration and the benefit of force multiplication is increasingly more tangible. iRobot Corporation and CMU Robotics Institute are developing the capability to simultaneously control the Raven small UAV (SUAV) and PackBot UGV from a single operator control unit (OCU) via waypoint navigation. Techniques to support autonomous collaboration for pursuing and tracking a dismounted soldier will be developed and integrated on a Raven-PackBot team. The Raven will survey an area and geolocate an operator-selected target. The Raven will share this target location with the PackBot and together they will collaboratively pursue the target intelligently to maintain track on the target. We will accomplish this goal by implementing a decentralized control and data fusion software architecture. The PackBot will be equipped with on-board waypoint navigation algorithms, a Navigator Payload containing a stereo-vision system, GPS, and a high-accuracy IMU. The Raven will have two on-board cameras, a side-looking and a forward-looking optical camera. The Supervisor OCU will act as the central mission planner, allowing the operator to monitor mission events and override vehicle tasks.

Raven's matrices and working memory: a dual-task approach.

Science.gov (United States)

Rao, K Venkata; Baddeley, Alan

2013-01-01

Raven's Matrices Test was developed as a "pure" measure of Spearman's concept of general intelligence, g. Subsequent research has attempted to specify the processes underpinning performance, some relating it to the concept of working memory and proposing a crucial role for the central executive, with the nature of other components currently unclear. Up to this point, virtually all work has been based on correlational analysis of number of correct solutions, sometimes related to possible strategies. We explore the application to this problem of the concurrent task methodology used widely in developing the concept of multicomponent working memory. Participants attempted to solve problems from the matrices under baseline conditions, or accompanied by backward counting or verbal repetition tasks, assumed to disrupt the central executive and phonological loop components of working memory, respectively. As in other uses of this method, number of items correct showed little effect, while solution time measures gave very clear evidence of an important role for the central executive, but no evidence for phonological loop involvement. We conclude that this and related concurrent task techniques hold considerable promise for the analysis of Raven's matrices and potentially for other established psychometric tests.

So Young and Already Victims of Stereotype Threat: Socio-Economic Status and Performance of 6 to 9 Years Old Children on Raven's Progressive Matrices

Science.gov (United States)

Desert, Michel; Preaux, Marie; Jund, Robin

2009-01-01

The aim of this study was to verify whether children from low socio-economic status (SES) are victims of stereotype threat. Children in first grade (6 to 7 years old) and third grade (8 to 9 years old) performed Raven's progressive matrices, an intellectual ability test commonly used by psychologists. The test was presented either with the…

Expression and purification of sea raven type II antifreeze protein from Drosophila melanogaster S2 cells.

Science.gov (United States)

Scotter, Andrew J; Kuntz, Douglas A; Saul, Michelle; Graham, Laurie A; Davies, Peter L; Rose, David R

2006-06-01

We present a system for the expression and purification of recombinant sea raven type II antifreeze protein, a cysteine-rich, C-type lectin-like globular protein that has proved to be a difficult target for recombinant expression and purification. The cDNAs encoding the pro- and mature forms of the sea raven protein were cloned into a modified pMT Drosophila expression vector. These constructs produced N-terminally His(6)-tagged pro- and mature forms of the type II antifreeze protein under the control of a metallothionein promoter when transfected into Drosophila melanogaster S2 cells. Upon induction of stable cell lines the two proteins were expressed at high levels and secreted into the medium. The proteins were then purified from the cell medium in a simple and rapid protocol using immobilized metal affinity chromatography and specific protease cleavage by tobacco etch virus protease. The proteins demonstrated antifreeze activity indistinguishable from that of wild-type sea raven antifreeze protein purified from serum as illustrated by ice affinity purification, ice crystal morphology, and their ability to inhibit ice crystal growth. This expression and purification system gave yields of 95 mg/L of fully active mature sea raven type II AFP and 9.6 mg/L of the proprotein. This surpasses all previous attempts to express this protein in Escherichia coli, baculovirus-infected fall armyworm cells and Pichia pastoris and will provide sufficient protein for structural analysis.

GPS tracking of non-breeding ravens reveals the importance of anthropogenic food sources during their dispersal in the Eastern Alps.

Science.gov (United States)

Loretto, Matthias-Claudio; Schuster, Richard; Bugnyar, Thomas

2016-08-01

In many songbirds, the space use of breeders is well studied but poorly understood for non-breeders. In common ravens, some studies of non-breeders indicate high vagrancy with large individual differences in home range size, whereas others show that up to 40% of marked non-breeders can be regularly observed at the same anthropogenic food source over months to years. The aim of this study was to provide new insights on ravens' behavior during dispersal in the Eastern Alps. We deployed Global Positioning System (GPS) loggers on 10 individuals to gather accurate spatial and temporal information on their movements to quantify: 1) the dimension of the birds' space use (home range size with seasonal effects and daily/long-term travel distances), 2) how long they stayed in a dispersal stage of wandering as opposed to settling temporarily, and 3) their destination of movements. We recorded movements of up to 40 km per hour, more than 160 km within 1 day and more than 11,000 km within 20 months, indicating high vagrancy. Switching frequently between temporarily settling and travelling large distances in short time intervals leads to extensive home ranges, which also explains and combines the different findings in the literature. The destinations are rich anthropogenic food sources, where the birds spent on average 75% of their time. We discuss how ravens may find these "feeding hot spots" and which factors may influence their decision to stay/leave a site. The strong dependence on anthropogenic resources found in this population may have implications for site management and conservation issues.

Solving the Raven Progressive Matrices by Adults with Intellectual Disability with/without Down Syndrome: Different Cognitive Patterns as Indicated by Eye-Movements

Science.gov (United States)

Vakil, Eli; Lifshitz-Zehavi, Hefziba

2012-01-01

Raven matrices are used for assessing fluid intelligence and the intellectual level of groups with low intelligence. Our study addresses qualitative analysis of information processing in Raven matrices performance among individuals with intellectual disability with that of their typically developed (TD) counterparts. Twenty-three adults with…

In silico detection of sequence variations modifying transcriptional regulation.

Directory of Open Access Journals (Sweden)

Malin C Andersen

2008-01-01

Full Text Available Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers. The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation.

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

Science.gov (United States)

Andersen, Malin C; Engström, Pär G; Lithwick, Stuart; Arenillas, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W; Odeberg, Jacob

2008-01-01

Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation. PMID:18208319

Initial Probabilistic Evaluation of Reactor Pressure Vessel Fracture with Grizzly and Raven

Energy Technology Data Exchange (ETDEWEB)

Spencer, Benjamin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hoffman, William [Univ. of Idaho, Moscow, ID (United States); Sen, Sonat [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Dickson, Terry [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bass, Richard [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-10-01

The Grizzly code is being developed with the goal of creating a general tool that can be applied to study a variety of degradation mechanisms in nuclear power plant components. The first application of Grizzly has been to study fracture in embrittled reactor pressure vessels (RPVs). Grizzly can be used to model the thermal/mechanical response of an RPV under transient conditions that would be observed in a pressurized thermal shock (PTS) scenario. The global response of the vessel provides boundary conditions for local models of the material in the vicinity of a flaw. Fracture domain integrals are computed to obtain stress intensity factors, which can in turn be used to assess whether a fracture would initiate at a pre-existing flaw. These capabilities have been demonstrated previously. A typical RPV is likely to contain a large population of pre-existing flaws introduced during the manufacturing process. This flaw population is characterized stastistically through probability density functions of the flaw distributions. The use of probabilistic techniques is necessary to assess the likelihood of crack initiation during a transient event. This report documents initial work to perform probabilistic analysis of RPV fracture during a PTS event using a combination of the RAVEN risk analysis code and Grizzly. This work is limited in scope, considering only a single flaw with deterministic geometry, but with uncertainty introduced in the parameters that influence fracture toughness. These results are benchmarked against equivalent models run in the FAVOR code. When fully developed, the RAVEN/Grizzly methodology for modeling probabilistic fracture in RPVs will provide a general capability that can be used to consider a wider variety of vessel and flaw conditions that are difficult to consider with current tools. In addition, this will provide access to advanced probabilistic techniques provided by RAVEN, including adaptive sampling and parallelism, which can dramatically

Application of hierarchical genetic models to Raven and WAIS subtests: a Dutch twin study

NARCIS (Netherlands)

Rijsdijk, F.V.; Vernon, P.A.; Boomsma, D.I.

2002-01-01

Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a genetic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard

Development of Abbreviated Nine-Item Forms of the Raven's Standard Progressive Matrices Test

Science.gov (United States)

Bilker, Warren B.; Hansen, John A.; Brensinger, Colleen M.; Richard, Jan; Gur, Raquel E.; Gur, Ruben C.

2012-01-01

The Raven's Standard Progressive Matrices (RSPM) is a 60-item test for measuring abstract reasoning, considered a nonverbal estimate of fluid intelligence, and often included in clinical assessment batteries and research on patients with cognitive deficits. The goal was to develop and apply a predictive model approach to reduce the number of items…

RAVEN: a GUI and an Artificial Intelligence Engine in a Dynamic PRA Framework

Energy Technology Data Exchange (ETDEWEB)

C. Rabiti; D. Mandelli; A. Alfonsi; J. Cogliati; R. Kinoshita; D. Gaston; R. Martineau; C. Curtis

2013-06-01

Increases in computational power and pressure for more accurate simulations and estimations of accident scenario consequences are driving the need for Dynamic Probabilistic Risk Assessment (PRA) [1] of very complex models. While more sophisticated algorithms and computational power address the back end of this challenge, the front end is still handled by engineers that need to extract meaningful information from the large amount of data and build these complex models. Compounding this problem is the difficulty in knowledge transfer and retention, and the increasing speed of software development. The above-described issues would have negatively impacted deployment of the new high fidelity plant simulator RELAP-7 (Reactor Excursion and Leak Analysis Program) at Idaho National Laboratory. Therefore, RAVEN that was initially focused to be the plant controller for RELAP-7 will help mitigate future RELAP-7 software engineering risks. In order to accomplish this task, Reactor Analysis and Virtual Control Environment (RAVEN) has been designed to provide an easy to use Graphical User Interface (GUI) for building plant models and to leverage artificial intelligence algorithms in order to reduce computational time, improve results, and help the user to identify the behavioral pattern of the Nuclear Power Plants (NPPs). In this paper we will present the GUI implementation and its current capability status. We will also introduce the support vector machine algorithms and show our evaluation of their potentiality in increasing the accuracy and reducing the computational costs of PRA analysis. In this evaluation we will refer to preliminary studies performed under the Risk Informed Safety Margins Characterization (RISMC) project of the Light Water Reactors Sustainability (LWRS) campaign [3]. RISMC simulation needs and algorithm testing are currently used as a guidance to prioritize RAVEN developments relevant to PRA.

Analysis of the Raven CPM Subtest Scores for a Sample of Gifted Children.

Science.gov (United States)

Kluever, Raymond C.; Green, Kathy E.

The inter-subject/intra-subject subtest patterns (profiles) of the same sample of gifted children were examined based on factors found in a previous study of the Raven Coloured Progressive Matrices Test (CPM) that investigated structural properties with specific application to a sample of gifted children. The sample consisted of 166 children (78…

Relaciones entre los testes de Bender y Matrizes Progressivas Coloridas de Raven en la evaluación de la inteligencia

OpenAIRE

Fermino Fernandes Sisto; Daniel Bartholomeu; Fabián Javier Marín Rueda; Acácia Aparecida Angeli dos Santos; Ana Paula Porto Noronha

2008-01-01

Esta pesquisa estudou as relações entre o Teste Gestaltico Visomotor de Bender avaliado conforme o Sistema de Pontuação Gradual (B-SPG) e as Matrizes Progressivas Coloridas de Raven. Participaram desta pesquisa 280 sujeitos com idades variando de sete a 10 anos com média de oito anos (DP=1,11) de ambos os sexos. Os testes foram aplicados coletivamente. Dentre os resultados, encontraram-se correlações negativas e significativas entre a medida do Bender e das séries do Raven, bem como com seu t...

Variation and Commonality in Phenomenographic Research Methods

Science.gov (United States)

Akerlind, Gerlese S.

2012-01-01

This paper focuses on the data analysis stage of phenomenographic research, elucidating what is involved in terms of both commonality and variation in accepted practice. The analysis stage of phenomenographic research is often not well understood. This paper helps to clarify the process, initially by collecting together in one location the more…

Análise da Produção Científica Brasileira sobre o Teste das Matrizes Progressivas de Raven

OpenAIRE

Cardoso, Lucila Moraes; Lopes, Érica Ive Xavier; Oliveira, Jamille Cavalcante de; Braga, Aline Pinheiro

2017-01-01

Resumo O Teste das Matrizes Progressivas de Raven é um instrumento não verbal para avaliação da inteligência. As pesquisas sobre ele, no Brasil, iniciaram-se na década de 1950 e continuaram a desenvolver-se com o passar dos anos, em maior ou menor escala de acordo com o período. O presente estudo objetivou quantificar e analisar a produção científica brasileira de artigos a respeito do Teste das Matrizes Progressivas de Raven, disponíveis nas bases de dados Scientific Electronic Library Onlin...

Brains, tools, innovation and biogeography in crows and ravens

Science.gov (United States)

2012-01-01

Background Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. Results This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. Conclusions Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances

New Rule Use Drives the Relation between Working Memory Capacity and Raven's Advanced Progressive Matrices

Science.gov (United States)

Wiley, Jennifer; Jarosz, Andrew F.; Cushen, Patrick J.; Colflesh, Gregory J. H.

2011-01-01

The correlation between individual differences in working memory capacity and performance on the Raven's Advanced Progressive Matrices (RAPM) is well documented yet poorly understood. The present work proposes a new explanation: that the need to use a new combination of rules on RAPM problems drives the relation between performance and working…

Exploration of the Raven APM-National Adult Reading Test discrepancy as a measure of intellectual decline in older persons.

Science.gov (United States)

van den Berg, Esther; Nys, Gudrun M S; Brands, Augustina M A; Ruis, Carla; van Zandvoort, Martine J E; Kessels, Roy P C

2013-01-01

Previous studies have shown that the discrepancy between performance on "fluid" and "crystallized" intelligence measures may serve as an indicator for intellectual decline. The validity of this procedure in older persons is unknown. The present study developed a multiple regression equation, to predict the Raven Advanced Progressive Matrices (APM) score from the National Adult Reading Test (NART) score and demographic variables in a large sample of healthy older persons (n = 270). The discrepancy between the predicted and observed Raven APM scores was transformed into a percentile distribution as an indicator of intellectual decline, which can be used in clinical practice. The validity of the procedure was further examined by comparing the proportion of persons with a significant decline (at the -1 and -1.65 SD level) between two older patient samples (87 patients with cerebral stroke and 387 patients with diabetes mellitus) by means of χ(2) tests. There was a significantly higher rate of intellectual decline at the -1 SD ("below average") and -1.65 SD ("impaired") cutoff levels for patients with stroke compared with patients with diabetes (stroke, 34% and 14%; diabetes, 16% and 5%, p Raven APM-NART discrepancy may be a useful measure of intellectual decline in older persons.

Use of the Remote Access Virtual Environment Network (RAVEN) for coordinated IVA-EVA astronaut training and evaluation.

Science.gov (United States)

Cater, J P; Huffman, S D

1995-01-01

This paper presents a unique virtual reality training and assessment tool developed under a NASA grant, "Research in Human Factors Aspects of Enhanced Virtual Environments for Extravehicular Activity (EVA) Training and Simulation." The Remote Access Virtual Environment Network (RAVEN) was created to train and evaluate the verbal, mental and physical coordination required between the intravehicular (IVA) astronaut operating the Remote Manipulator System (RMS) arm and the EVA astronaut standing in foot restraints on the end of the RMS. The RAVEN system currently allows the EVA astronaut to approach the Hubble Space Telescope (HST) under control of the IVA astronaut and grasp, remove, and replace the Wide Field Planetary Camera drawer from its location in the HST. Two viewpoints, one stereoscopic and one monoscopic, were created all linked by Ethernet, that provided the two trainees with the appropriate training environments.

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones

Science.gov (United States)

Fuller, Trevon L.; Thomassen, Henri A.; Peralvo, Manuel; Buermann, Wolfgang; Milá, Borja; Kieswetter, Charles M.; Jarrín-V, Pablo; Devitt, Susan E. Cameron; Mason, Eliza; Schweizer, Rena M.; Schlunegger, Jasmin; Chan, Janice; Wang, Ophelia; Schneider, Christopher J.; Pollinger, John P.; Saatchi, Sassan; Graham, Catherine H.; Wayne, Robert K.; Smith, Thomas B.

2013-01-01

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible. PMID:23595273

Matrizes progressivas coloridas de Raven - escala especial: normas para Porto Alegre, RS The Raven's coloured progressive matrices: norms for Porto Alegre, RS

Directory of Open Access Journals (Sweden)

Denise Ruschel Bandeira

2004-12-01

Full Text Available O Teste das Matrizes Progressivas Coloridas de Raven destina-se à avaliação do desenvolvimento intelectual de crianças de 5 a 11 anos de idade. O presente trabalho teve como objetivo estabelecer normas para as crianças de Porto Alegre - RS. A amostra foi composta por 779 crianças matriculadas em escolas estaduais, de 4 anos e 9 meses a 11 anos e 9 meses. Foi constatado aumento progressivo nas médias de pontos com o aumento da idade e não foram encontradas diferenças entre meninos e meninas. Na comparação com as crianças de escolas públicas de São Paulo, as médias das crianças de Porto Alegre foram mais altas, mas em geral foram inferiores às das escolas particulares de São Paulo. Foram estabelecidas as normas em percentis para cada faixa etária. Os resultados reforçam a necessidade do estabelecimento de normas distintas para as diferentes regiões do Brasil, principalmente em relação aos testes de inteligência.The Raven's Coloured Progressive Matrices was proposed standards to Porto Alegre (RS children. The sample was composed by 779 children from Porto Alegre state public schools, aged from 4 years and 9 months to 11 years and 9 months. It was found a progressive increase in average scores as age increased and it was not verified differences between boys and girls. Comparing average scores between children from São Paulo and Porto Alegre public schools we found that the average scores from Porto Alegre children was higher, but they were lower than the scores from São Paulo private schools children. Percentile ranks were obtained to each age level with range of six months. Research results show the need to establish specific norms to different Brazilian regions, mainly concerning intelligence tests.

CLUSTER GLIMPSES WITH RAVEN: AO-CORRECTED NEAR AND MID-INFRARED IMAGES OF GLIMPSE C01 AND GLIMPSE C02

Energy Technology Data Exchange (ETDEWEB)

Davidge, T. J.; Andersen, D. R. [Dominion Astrophysical Observatory, National Research Council of Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Lardière, O., E-mail: tim.davidge@nrc.ca, E-mail: david.andersen@nrc.ca, E-mail: lardiere@uvic.ca [Department of Mechanical Engineering, University of Victoria, Victoria, BC V8W 3P2 (Canada); and others

2016-12-01

We discuss images of the star clusters GLIMPSE C01 (GC01) and GLIMPSE C02 (GC02) that were recorded with the Subaru IRCS. Distortions in the wavefront were corrected with the RAVEN adaptive optics (AO) science demonstrator, allowing individual stars in the central regions of both clusters—where the fractional contamination from non-cluster objects is lowest—to be imaged. In addition to J , H , and K ′ images, both clusters were observed through a narrow-band filter centered near 3.05 μ m; GC01 was also observed through two other narrow-band filters that sample longer wavelengths. Stars in the narrow-band images have an FWHM that is close to the telescope diffraction limit, demonstrating that open-loop AO systems like RAVEN can deliver exceptional image quality. The near-infrared color–magnitude diagram of GC01 is smeared by non-uniform extinction with a 1 σ dispersion Δ A{sub K}  = ±0.13 mag. Spatial variations in A{sub K} are not related in a systematic way to location in the field. The Red Clump is identified in the K luminosity function (LF) of GC01, and a distance modulus of 13.6 is found. The K LF of GC01 is consistent with a system that is dominated by stars with an age >1 Gyr. As for GC02, the K LF is flat for K  > 16, and the absence of a sub-giant branch argues against an old age if the cluster is at a distance of ∼7 kpc. Archival SPITZER [3.6] and [4.5] images of the clusters are also examined, and the red giant branch-tip is identified. It is demonstrated in the Appendix that the [3.6] surface brightness profiles of both clusters can be traced out to radii of at least 100 arcsec.

A decorated raven bone from the Zaskalnaya VI (Kolosovskaya) Neanderthal site, Crimea

Science.gov (United States)

Evans, Sarah; Stepanchuk, Vadim; Tsvelykh, Alexander; d’Errico, Francesco

2017-01-01

We analyze a radius bone fragment of a raven (Corvus corax) from Zaskalnaya VI rock shelter, Crimea. The object bears seven notches and comes from an archaeological level attributed to a Micoquian industry dated to between 38 and 43 cal kyr BP. Our study aims to examine the degree of regularity and intentionality of this set of notches through their technological and morphometric analysis, complemented by comparative experimental work. Microscopic analysis of the notches indicate that they were produced by the to-and-fro movement of a lithic cutting edge and that two notches were added to fill in the gap left between previously cut notches, probably to increase the visual consistency of the pattern. Multivariate analysis of morphometric data recorded on the archaeological notches and sets of notches cut by nine modern experimenters on radii of domestic turkeys shows that the variations recorded on the Zaskalnaya set are comparable to experimental sets made with the aim of producing similar, parallel, equidistant notches. Identification of the Weber Fraction, the constant that accounts for error in human perception, for equidistant notches cut on bone rods and its application to the Zaskalnaya set of notches and thirty-six sets of notches incised on seventeen Upper Palaeolithic bone objects from seven sites indicate that the Zaskalnaya set falls within the range of variation of regularly spaced experimental and Upper Palaeolithic sets of notches. This suggests that even if the production of the notches may have had a utilitarian reason the notches were made with the goal of producing a visually consistent pattern. This object represents the first instance of a bird bone from a Neanderthal site bearing modifications that cannot be explained as the result of butchery activities and for which a symbolic argument can be built on direct rather than circumstantial evidence. PMID:28355292

A decorated raven bone from the Zaskalnaya VI (Kolosovskaya) Neanderthal site, Crimea.

Science.gov (United States)

Majkić, Ana; Evans, Sarah; Stepanchuk, Vadim; Tsvelykh, Alexander; d'Errico, Francesco

2017-01-01

We analyze a radius bone fragment of a raven (Corvus corax) from Zaskalnaya VI rock shelter, Crimea. The object bears seven notches and comes from an archaeological level attributed to a Micoquian industry dated to between 38 and 43 cal kyr BP. Our study aims to examine the degree of regularity and intentionality of this set of notches through their technological and morphometric analysis, complemented by comparative experimental work. Microscopic analysis of the notches indicate that they were produced by the to-and-fro movement of a lithic cutting edge and that two notches were added to fill in the gap left between previously cut notches, probably to increase the visual consistency of the pattern. Multivariate analysis of morphometric data recorded on the archaeological notches and sets of notches cut by nine modern experimenters on radii of domestic turkeys shows that the variations recorded on the Zaskalnaya set are comparable to experimental sets made with the aim of producing similar, parallel, equidistant notches. Identification of the Weber Fraction, the constant that accounts for error in human perception, for equidistant notches cut on bone rods and its application to the Zaskalnaya set of notches and thirty-six sets of notches incised on seventeen Upper Palaeolithic bone objects from seven sites indicate that the Zaskalnaya set falls within the range of variation of regularly spaced experimental and Upper Palaeolithic sets of notches. This suggests that even if the production of the notches may have had a utilitarian reason the notches were made with the goal of producing a visually consistent pattern. This object represents the first instance of a bird bone from a Neanderthal site bearing modifications that cannot be explained as the result of butchery activities and for which a symbolic argument can be built on direct rather than circumstantial evidence.

SU-F-T-287: A Preliminary Study On Patient Specific VMAT Verification Using a Phosphor-Screen Based Geometric QA System (Raven QA)

International Nuclear Information System (INIS)

Lee, M; Yi, B; Wong, J; Ding, K

2016-01-01

Purpose: The RavenQA system (LAP Laser, Germany) is a QA device with a phosphor screen detector for performing the QA tasks of TG-142. This study tested if it is feasible to use the system for the patient specific QA of the Volumetric Modulated Arc Therapy (VMAT). Methods: Water equivalent material (5cm) is attached to the front of the detector plate of the RavenQA for dosimetry purpose. Then the plate is attached to the gantry to synchronize the movement between the detector and the gantry. Since the detector moves together with gantry, The ’Reset gantry to 0’ function of the Eclipse planning system (Varian, CA) is used to simulate the measurement situation when calculating dose of the detector plate. The same gantry setup is used when delivering the treatment beam for feasibility test purposes. Cumulative dose is acquired for each arc. The optical scatter component of each captured image from the CCD camera is corrected by deconvolving the 2D spatial invariant optical scatter kernel (OSK). We assume that the OSK is a 2D isotropic point spread function with inverse-squared decrease as a function of radius from the center. Results: Three cases of VMAT plans including head & neck, whole pelvis and abdomen-pelvis are tested. Setup time for measurements was less than 5 minutes. Passing rates of absolute gamma were 99.3, 98.2, 95.9 respectively for 3%/3mm criteria and 96.2, 97.1, 86.4 for 2%/2mm criteria. The abdomen-pelvis field has long treatment fields, 37cm, which are longer than the detector plate (25cm). This plan showed relatively lower passing rate than other plans. Conclusion: An algorithm for IMRT/VMAT verification using the RavenQA has been developed and tested. The model of spatially invariant OSK works well for deconvolution purpose. It is proved that the RavenQA can be used for the patient specific verification of VMAT. This work is funded in part by a Maryland Industrial Partnership Program grant to University of Maryland and to JPLC who owns the

Modeling stimulus variation in three common implicit attitude tasks.

Science.gov (United States)

Wolsiefer, Katie; Westfall, Jacob; Judd, Charles M

2017-08-01

We explored the consequences of ignoring the sampling variation due to stimuli in the domain of implicit attitudes. A large literature in psycholinguistics has examined the statistical treatment of random stimulus materials, but the recommendations from this literature have not been applied to the social psychological literature on implicit attitudes. This is partly because of inherent complications in applying crossed random-effect models to some of the most common implicit attitude tasks, and partly because no work to date has demonstrated that random stimulus variation is in fact consequential in implicit attitude measurement. We addressed this problem by laying out statistically appropriate and practically feasible crossed random-effect models for three of the most commonly used implicit attitude measures-the Implicit Association Test, affect misattribution procedure, and evaluative priming task-and then applying these models to large datasets (average N = 3,206) that assess participants' implicit attitudes toward race, politics, and self-esteem. We showed that the test statistics from the traditional analyses are substantially (about 60 %) inflated relative to the more-appropriate analyses that incorporate stimulus variation. Because all three tasks used the same stimulus words and faces, we could also meaningfully compare the relative contributions of stimulus variation across the tasks. In an appendix, we give syntax in R, SAS, and SPSS for fitting the recommended crossed random-effects models to data from all three tasks, as well as instructions on how to structure the data file.

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Science.gov (United States)

Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

2013-01-01

We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production. PMID:23555215

Variation in diagnosis and management of common foot problems by GPs

NARCIS (Netherlands)

Gorter, K; de Melker, R; Kuyvenhoven, M; de Poel, S.

2001-01-01

Background. There are indications that the diagnosis and management of common foot problems vary widely in general practice. Objectives. Our aim was to explore the variation of GPs' diagnosis and management of common foot problems and the possible correlation between GPs' characteristics and their

Canada: variations on a common theme

Directory of Open Access Journals (Sweden)

Raisa B. Deber

2010-12-01

Full Text Available Canada faces health care challenges common to all industrialized countries – how to ensure timely access to high quality care, close to home, at an affordable cost. Addressing these challenges is complicated by interjurisdictional variation in both how health care is managed and delivered, and in health outcomes. Canada can be described as a non-system of 10 provincial and three territorial health insurance plans which mandate publicly-funded coverage for medically necessary hospital and physician services, based upon common principles and shaped by a federal governance structure that affords substantial power and autonomy to the provinces/territories over matters of health and health care. This article first examines the structural context of the health care system in Canada, including the range of services publicly funded, the public-private mix, and the complexities of current governance arrangements. It then discusses several issues affecting health policy reform: costs versus access; questions of sustainability, quality, and performance; human resources capacity; and the provision of public and population health services.

The Power of Perspective in The Raven Cycle

Directory of Open Access Journals (Sweden)

Andrea Dumančić

2017-07-01

Full Text Available Beginning with the discussion of the terms narration and narrative, the paper asserts the difference between point of view, which is defined as “who” tells a story, and perspective, which shows “how” a narrator / a character perceives the events making up the story. To show the power of perspective in a literary work, the paper focuses on the young adult novel series The Raven Cycle by Maggie Stiefvater. The five main characters – Blue Sargent, Richard Gansey III, Adam Parrish, Ronan Lynch, and Noah Czerny – have been given unique perspectives that are unveiled through their separate character arcs. Blue’s perspective is clad with assumptions; Gansey’s is a clash between the perceived and the perceiving; Adam’s comes to light only when compared to other characters’ perspectives; Ronan’s is postponed and contrary to expectations; Noah’s is absent until the very end of the series.

Evidências de validade das Matrizes Progressivas Avançadas de Raven em universitários Validity Evidence of Raven's Advanced Progressive Matrices in university students

Directory of Open Access Journals (Sweden)

Milena Oliveira Rosseti

2009-08-01

Full Text Available O objetivo do estudo foi encontrar evidências de validade das Matrizes Progressivas Avançadas de Raven em universitários. Participaram 369 universitários de duas universidades privadas do estado de São Paulo, sendo 104 (28,2% do sexo masculino e 265 (71,8% do feminino. Em relação aos cursos, 167 (45,3% são de Psicologia, 111 (30,1% de Administração de Empresas, 54 (14,6% de Gestão de Recursos Humanos e 37 (10% de Pedagogia. Os resultados demonstraram que houve diferença significativa com relação ao gênero, com um melhor desempenho do sexo masculino (t=4,21 e pThe aim of the study was to find validity evidence of Raven's Advanced Progressive Matrices in university students. The sample consisted of 369 university students from two private universities in the state of Sao Paulo, being a 104 (28,2% of the masculine and 265 (71,8% of the feminine. Regarding the courses, 167 (45,3% is of Psychology, 111 (30,1% is of Business Administration, 54 (14,6 % is of Management of Human Resources and 37 (10% is of Pedagogy. The results showed statistically significant difference of sex, with males having better performance in the instrument (t=4.21; p<0.01. The analysis of variance (ANOVA showed significant difference between averages of the courses (F=13,8; p<0,00, and the courses that are differentiated in accordance with the test ad-hoc of Tukey were Administration and Psychology that obtained scores bigger than the others courses. The results demonstrated what the used instrument showed precisely to value aspects of the general intelligence at university students.

Integrating common and rare genetic variation in diverse human populations.

Science.gov (United States)

Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Dermitzakis, Emmanouil; Schaffner, Stephen F; Yu, Fuli; Peltonen, Leena; Dermitzakis, Emmanouil; Bonnen, Penelope E; Altshuler, David M; Gibbs, Richard A; de Bakker, Paul I W; Deloukas, Panos; Gabriel, Stacey B; Gwilliam, Rhian; Hunt, Sarah; Inouye, Michael; Jia, Xiaoming; Palotie, Aarno; Parkin, Melissa; Whittaker, Pamela; Yu, Fuli; Chang, Kyle; Hawes, Alicia; Lewis, Lora R; Ren, Yanru; Wheeler, David; Gibbs, Richard A; Muzny, Donna Marie; Barnes, Chris; Darvishi, Katayoon; Hurles, Matthew; Korn, Joshua M; Kristiansson, Kati; Lee, Charles; McCarrol, Steven A; Nemesh, James; Dermitzakis, Emmanouil; Keinan, Alon; Montgomery, Stephen B; Pollack, Samuela; Price, Alkes L; Soranzo, Nicole; Bonnen, Penelope E; Gibbs, Richard A; Gonzaga-Jauregui, Claudia; Keinan, Alon; Price, Alkes L; Yu, Fuli; Anttila, Verneri; Brodeur, Wendy; Daly, Mark J; Leslie, Stephen; McVean, Gil; Moutsianas, Loukas; Nguyen, Huy; Schaffner, Stephen F; Zhang, Qingrun; Ghori, Mohammed J R; McGinnis, Ralph; McLaren, William; Pollack, Samuela; Price, Alkes L; Schaffner, Stephen F; Takeuchi, Fumihiko; Grossman, Sharon R; Shlyakhter, Ilya; Hostetter, Elizabeth B; Sabeti, Pardis C; Adebamowo, Clement A; Foster, Morris W; Gordon, Deborah R; Licinio, Julio; Manca, Maria Cristina; Marshall, Patricia A; Matsuda, Ichiro; Ngare, Duncan; Wang, Vivian Ota; Reddy, Deepa; Rotimi, Charles N; Royal, Charmaine D; Sharp, Richard R; Zeng, Changqing; Brooks, Lisa D; McEwen, Jean E

2010-09-02

Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

Comparison of Individual Performance in Intelligence Tests WAIS III and RPM (Raven's Progressive Matrices)

OpenAIRE

Petrů, Vít

2017-01-01

This thesis deals with replacement of performative scale of Wechsler Adult Intelligence Scale (3rd revision) through Raven's Standard Progressive Matrices and Advanced Progressive Matrices. In the theoretical part introduces the concepts of intelligence, approaches to its exploration and intelligence tests. The theoretical part is also devoted to the description of the used methods and presents an overview of the research on a similar theme as this work. In the empirical part of the thesis is...

Seasonal variation and food deprivation in common vampire bats (Chiroptera: Phyllostomidae

Directory of Open Access Journals (Sweden)

M. B. Freitas

Full Text Available The aim of this study was to investigate the effects of seasonal variation and fasting on fat reserves of the common vampire bat Desmodus rotundus. Plasma free fatty acids (FFA, along with lipid content of the liver and muscles, and fatty acids from the carcass were obtained from bats fed bovine blood and from whom food was subsequently withheld for 24 and 48 h. Animals were caught during both dry and rainy seasons. In general, fat tissue stores were not significantly influenced by seasonal variation. Lipid content of liver, muscles, and carcass decreased during some food deprivation periods, although the concomitant increase expected in plasma FFA was not observed. Lipid metabolism is hypothesized as being continued by the tissues themselves. In addition, free access to food sources (e.g., domestic livestock throughout the year is believed to contribute to the low seasonal variations in fat reserves observed in the common vampire bat.

Blue Tigers, Black Tapirs, & the Pied Raven of the Faroe Islands: Teaching Genetic Drift Using Real-Life Animal Examples

Science.gov (United States)

Robischon, Marcel

2015-01-01

Genetic drift is a concept of population genetics that is central to understanding evolutionary processes and aspects of conservation biology. It is frequently taught using rather abstract representations. I introduce three real-life zoological examples, based on historical and recent color morphs of tigers, tapirs, and ravens, that can complement…

Propriedades psicométricas do Raven Geral no contexto de Minas Gerais

Directory of Open Access Journals (Sweden)

Carmen Flores-Mendoza

2014-08-01

Full Text Available The psychometric parameters of the Standard Progressive Matrices of Raven (SPM test for Minas Gerais state were investigated. 1956 people aged between 07 and 65 were the participants. The analysis of the items through the Item Response Theory, Model 2P, showed appropriate levels of difficulty and discrimination of all items except for item E12, which was extremely difficult. The test information function indicated that the SPM test was relatively easily to carry out by the sample of Minas Gerais. The Flynn effect, or cognitive gains of generation, may be the factor responsible. However, the prediction of school performance (criterion validity using the SPM test is still possible. Implications for professional use are discussed.

Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study.

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Kasperaviciūte, Dalia; Catarino, Claudia B; Heinzen, Erin L; Depondt, Chantal; Cavalleri, Gianpiero L; Caboclo, Luis O; Tate, Sarah K; Jamnadas-Khoda, Jenny; Chinthapalli, Krishna; Clayton, Lisa M S; Shianna, Kevin V; Radtke, Rodney A; Mikati, Mohamad A; Gallentine, William B; Husain, Aatif M; Alhusaini, Saud; Leppert, David; Middleton, Lefkos T; Gibson, Rachel A; Johnson, Michael R; Matthews, Paul M; Hosford, David; Heuser, Kjell; Amos, Leslie; Ortega, Marcos; Zumsteg, Dominik; Wieser, Heinz-Gregor; Steinhoff, Bernhard J; Krämer, Günter; Hansen, Jörg; Dorn, Thomas; Kantanen, Anne-Mari; Gjerstad, Leif; Peuralinna, Terhi; Hernandez, Dena G; Eriksson, Kai J; Kälviäinen, Reetta K; Doherty, Colin P; Wood, Nicholas W; Pandolfo, Massimo; Duncan, John S; Sander, Josemir W; Delanty, Norman; Goldstein, David B; Sisodiya, Sanjay M

2010-07-01

Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully revealed common variants associated with disease risk, the role of common variation in partial epilepsies has not yet been explored in a well-powered study. We undertook a genome-wide association-study to identify common variants which influence risk for epilepsy shared amongst partial epilepsy syndromes, in 3445 patients and 6935 controls of European ancestry. We did not identify any genome-wide significant association. A few single nucleotide polymorphisms may warrant further investigation. We exclude common genetic variants with effect sizes above a modest 1.3 odds ratio for a single variant as contributors to genetic susceptibility shared across the partial epilepsies. We show that, at best, common genetic variation can only have a modest role in predisposition to the partial epilepsies when considered across syndromes in Europeans. The genetic architecture of the partial epilepsies is likely to be very complex, reflecting genotypic and phenotypic heterogeneity. Larger meta-analyses are required to identify variants of smaller effect sizes (odds ratio<1.3) or syndrome-specific variants. Further, our results suggest research efforts should also be directed towards identifying the multiple rare variants likely to account for at least part of the heritability of the partial epilepsies. Data emerging from genome-wide association-studies will be valuable during the next serious challenge of interpreting all the genetic variation emerging from whole-genome sequencing studies.

Original article Temperamental variation in learned irrelevance in humans

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Aleksandra Gruszka

2015-07-01

Full Text Available Background Learned irrelevance (LIRR represents one of the mechanisms of attentional set-shifting and refers to the inability to attend to, or to learn about, any aspect of a stimulus previously experienced as irrelevant. Although it has been extensively studied in the context of clinical populations, not much is known about LIRR effects in relation to normal variation in individual differences. The present study was designed to assess how temperamental factors may modulate LIRR. Participants and procedures Sixty-eight healthy volunteers performed a visual discrimination learning task modelled after Wisconsin Card Sorting Test. To test the susceptibility to learned irrelevance, participants were expected to shift their attention either to a dimension that prior to the extra-dimensional shift was completely irrelevant, or to a dimension that was previously partly correlated with reinforcement. Temperamental traits were assessed using the Formal Characteristics of Behaviour-Temperament Inventory (Zawadzki & Strelau, 1997. Intelligence level was stratified according to Raven’s Advanced Progressive Matrices (Raven, Raven, & Court, 2003. Results Low level of Briskness and high level of Perseverance were related to enhanced susceptibility to LIRR. High levels of Activity and Emotional Reactivity were related to the poorer performance on the extra-dimensional set-shifting. No effects of other temperament characteristics or intelligence on LIRR were observed. Conclusions The results confirm a strong variation in LIRR related to individual differences in temperament, which appears to be unrelated to DA function. Our results highlight the importance of considering individual differences in studies on cognitive control.

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

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Lv, Weihua; Zheng, Xianhu; Kuang, Youyi; Cao, Dingchen; Yan, Yunqin; Sun, Xiaowen

2016-05-05

Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs

Variations in Nutrients Composition of Most Commonly Consumed Cassava (Manihot esculenta Mixed Dishes in South-Eastern Nigeria

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G. I. Davidson

2017-01-01

Full Text Available Variations in nutrient composition of most commonly consumed cassava (Manihot esculenta mixed dishes in South-eastern Nigeria were determined. Four communities were randomly selected from each of the five states in the South-east. Focus group discussions (FGD were conducted in each of the communities to determine commonly consumed foods and variations in recipes. 24-Hour dietary recall was conducted using 50 randomly selected households in those communities. Recipes collected during the FGD were standardized, prepared, and chemically analysed using standard methods. Data were analysed using descriptive statistics. Cassava-based dishes were the most commonly consumed in South-eastern Nigeria. Ninety-two percent of the study population ate cassava either in form of “fufu” (fermented cassava meal/garri (fermented and roasted cassava meal with soup or as “abacha” (tapioca salad. Commonly consumed soups were melon (Citrullus vulgaris seeds, “ora” (Pterocarpus soyauxii, and vegetable soups. Seven melon seed, six “ora,” and four vegetable soups and five “abacha” variations were identified. Except for vegetable soup, coefficient of variation for moisture was <10%, while large variations (19–71% were observed for energy and nutrients. These variations in cassava-based dishes need to be reflected in the country-specific food composition database to enable nutrient intake assessment or provision of dietary guidance using such food composition database as a reference material to be more effective.

Improving Limit Surface Search Algorithms in RAVEN Using Acceleration Schemes: Level II Milestone

Energy Technology Data Exchange (ETDEWEB)

Alfonsi, Andrea [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Cogliati, Joshua Joseph [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Sen, Ramazan Sonat [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Smith, Curtis Lee [Idaho National Laboratory (INL), Idaho Falls, ID (United States)

2015-07-01

The RAVEN code is becoming a comprehensive tool to perform Probabilistic Risk Assessment (PRA); Uncertainty Quantification (UQ) and Propagation; and Verification and Validation (V&V). The RAVEN code is being developed to support the Risk-Informed Safety Margin Characterization (RISMC) pathway by developing an advanced set of methodologies and algorithms for use in advanced risk analysis. The RISMC approach uses system simulator codes applied to stochastic analysis tools. The fundamental idea behind this coupling approach to perturb (by employing sampling strategies) timing and sequencing of events, internal parameters of the system codes (i.e., uncertain parameters of the physics model) and initial conditions to estimate values ranges and associated probabilities of figures of merit of interest for engineering and safety (e.g. core damage probability, etc.). This approach applied to complex systems such as nuclear power plants requires performing a series of computationally expensive simulation runs. The large computational burden is caused by the large set of (uncertain) parameters characterizing those systems. Consequently, exploring the uncertain/parametric domain, with a good level of confidence, is generally not affordable, considering the limited computational resources that are currently available. In addition, the recent tendency to develop newer tools, characterized by higher accuracy and larger computational resources (if compared with the presently used legacy codes, that have been developed decades ago), has made this issue even more compelling. In order to overcome to these limitations, the strategy for the exploration of the uncertain/parametric space needs to use at best the computational resources focusing the computational effort in those regions of the uncertain/parametric space that are “interesting” (e.g., risk-significant regions of the input space) with respect the targeted Figures Of Merit (FOM): for example, the failure of the system

Crop physiological analysis of seed quality variation in common bean (Phaseolus vulgaris L.)

NARCIS (Netherlands)

Muasya, R.M.

2001-01-01

Keywords : Physiological maturity, harvest maturity, earliness, common bean, Phaseolus vulgaris L., morphological markers, variation, moisture content, dry weight, viability, vigour, electrical conductivity, tetrazolium, seed lot, seed

The Quest for Item Types Based on Information Processing: An Analysis of Raven's Advanced Progressive Matrices, with a Consideration of Gender Differences

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Vigneau, Francois; Bors, Douglas A.

2008-01-01

Various taxonomies of Raven's Advanced Progressive Matrices (APM) items have been proposed in the literature to account for performance on the test. In the present article, three such taxonomies based on information processing, namely Carpenter, Just and Shell's [Carpenter, P.A., Just, M.A., & Shell, P., (1990). What one intelligence test…

Distinct neural substrates of visuospatial and verbal-analytic reasoning as assessed by Raven's Advanced Progressive Matrices.

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Chen, Zhencai; De Beuckelaer, Alain; Wang, Xu; Liu, Jia

2017-11-24

Recent studies revealed spontaneous neural activity to be associated with fluid intelligence (gF) which is commonly assessed by Raven's Advanced Progressive Matrices, and embeds two types of reasoning: visuospatial and verbal-analytic reasoning. With resting-state fMRI data, using global brain connectivity (GBC) analysis which averages functional connectivity of a voxel in relation to all other voxels in the brain, distinct neural correlates of these two reasoning types were found. For visuospatial reasoning, negative correlations were observed in both the primary visual cortex (PVC) and the precuneus, and positive correlations were observed in the temporal lobe. For verbal-analytic reasoning, negative correlations were observed in the right inferior frontal gyrus (rIFG), dorsal anterior cingulate cortex and temporoparietal junction, and positive correlations were observed in the angular gyrus. Furthermore, an interaction between GBC value and type of reasoning was found in the PVC, rIFG and the temporal lobe. These findings suggest that visuospatial reasoning benefits more from elaborate perception to stimulus features, whereas verbal-analytic reasoning benefits more from feature integration and hypothesis testing. In sum, the present study offers, for different types of reasoning in gF, first empirical evidence of separate neural substrates in the resting brain.

Common variation in ISL1 confers genetic susceptibility for human congenital heart disease.

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Kristen N Stevens

Full Text Available Congenital heart disease (CHD is the most common birth abnormality and the etiology is unknown in the overwhelming majority of cases. ISLET1 (ISL1 is a transcription factor that marks cardiac progenitor cells and generates diverse multipotent cardiovascular cell lineages. The fundamental role of ISL1 in cardiac morphogenesis makes this an exceptional candidate gene to consider as a cause of complex congenital heart disease. We evaluated whether genetic variation in ISL1 fits the common variant-common disease hypothesis. A 2-stage case-control study examined 27 polymorphisms mapping to the ISL1 locus in 300 patients with complex congenital heart disease and 2,201 healthy pediatric controls. Eight genic and flanking ISL1 SNPs were significantly associated with complex congenital heart disease. A replication study analyzed these candidate SNPs in 1,044 new cases and 3,934 independent controls and confirmed that genetic variation in ISL1 is associated with risk of non-syndromic congenital heart disease. Our results demonstrate that two different ISL1 haplotypes contribute to risk of CHD in white and black/African American populations.

Genetic variation of common walnut (Juglans regia in Piedmont, Northwestern Italy

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Ferrazzini D

2007-12-01

Full Text Available The European or common walnut is a large tree prized as a multipurpose species: it provides valuable timber and produces a high-quality edible nut. The diffusion of the species in Italy has been largely influenced by the human activity, mainly through germplasm movement, selection of genotypes most suited for wood or fruit production and adaptation induced on fruit crop reproductive materials. As a consequence, genetic variability has been reduced, so that programs aimed at its preservation appear of the utmost importance. 104 walnut plants growing in Piedmont, northwestern Italy, were investigated through genetic variation scored at RAPD loci, yielded by PCR amplification of 10 decamer primers. Among the 101 studied loci, only 53 were polymorphic, showing a low level of genetic variation within the studied material. Genetic differentiation was estimated both at individual and geographical area level. Only in few cases trees growing in the same area showed to be genetically similar, while the differentiation between areas accounted for about 10% of the total variation, according to AMOVA. No significant correlation was found between genetic and geographic distances. The results of the study showed that also in Piedmont (such as it was already demonstrated in other parts of Italy the distribution of common walnut is a direct consequence of the human activity. The selection of individual trees, to be used as basic materials for seed supply, should therefore be based mainly on phenotypic traits, rather than ecological features of the location: in species characterized by artificial diffusion, the adoption of Region of Provenance has a scarce significance and prominence should be given to the phenotype selection.

Genetic variation of piperidine alkaloids in Pinus ponderosa: a common garden study.

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Gerson, Elizabeth A; Kelsey, Rick G; St Clair, J Bradley

2009-02-01

Previous measurements of conifer alkaloids have revealed significant variation attributable to many sources, environmental and genetic. The present study takes a complementary and intensive, common garden approach to examine genetic variation in Pinus ponderosa var. ponderosa alkaloid production. Additionally, this study investigates the potential trade-off between seedling growth and alkaloid production, and associations between topographic/climatic variables and alkaloid production. Piperidine alkaloids were quantified in foliage of 501 nursery seedlings grown from seed sources in west-central Washington, Oregon and California, roughly covering the western half of the native range of ponderosa pine. A nested mixed model was used to test differences among broad-scale regions and among families within regions. Alkaloid concentrations were regressed on seedling growth measurements to test metabolite allocation theory. Likewise, climate characteristics at the seed sources were also considered as explanatory variables. Quantitative variation from seedling to seedling was high, and regional variation exceeded variation among families. Regions along the western margin of the species range exhibited the highest alkaloid concentrations, while those further east had relatively low alkaloid levels. Qualitative variation in alkaloid profiles was low. All measures of seedling growth related negatively to alkaloid concentrations on a natural log scale; however, coefficients of determination were low. At best, annual height increment explained 19.4 % of the variation in ln(total alkaloids). Among the climate variables, temperature range showed a negative, linear association that explained 41.8 % of the variation. Given the wide geographic scope of the seed sources and the uniformity of resources in the seedlings' environment, observed differences in alkaloid concentrations are evidence for genetic regulation of alkaloid secondary metabolism in ponderosa pine. The theoretical

Ravens reconcile after aggressive conflicts with valuable partners.

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Fraser, Orlaith N; Bugnyar, Thomas

2011-03-25

Reconciliation, a post-conflict affiliative interaction between former opponents, is an important mechanism for reducing the costs of aggressive conflict in primates and some other mammals as it may repair the opponents' relationship and reduce post-conflict distress. Opponents who share a valuable relationship are expected to be more likely to reconcile as for such partners the benefits of relationship repair should outweigh the risk of renewed aggression. In birds, however, post-conflict behavior has thus far been marked by an apparent absence of reconciliation, suggested to result either from differing avian and mammalian strategies or because birds may not share valuable relationships with partners with whom they engage in aggressive conflict. Here, we demonstrate the occurrence of reconciliation in a group of captive subadult ravens (Corvus corax) and show that it is more likely to occur after conflicts between partners who share a valuable relationship. Furthermore, former opponents were less likely to engage in renewed aggression following reconciliation, suggesting that reconciliation repairs damage caused to their relationship by the preceding conflict. Our findings suggest not only that primate-like valuable relationships exist outside the pair bond in birds, but that such partners may employ the same mechanisms in birds as in primates to ensure that the benefits afforded by their relationships are maintained even when conflicts of interest escalate into aggression. These results provide further support for a convergent evolution of social strategies in avian and mammalian species.

Visual/Verbal-Analytic Reasoning Bias as a Function of Self-Reported Autistic-Like Traits: A Study of Typically Developing Individuals Solving Raven's Advanced Progressive Matrices

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Fugard, Andrew J. B.; Stewart, Mary E.; Stenning, Keith

2011-01-01

People with autism spectrum condition (ASC) perform well on Raven's matrices, a test which loads highly on the general factor in intelligence. However, the mechanisms supporting enhanced performance on the test are poorly understood. Evidence is accumulating that milder variants of the ASC phenotype are present in typically developing individuals,…

Common variations in ALG9 are not associated with bipolar I disorder: a family-based study

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Bacanu Silviu-Alin

2006-07-01

Full Text Available Abstract Background A mannosyltransferase gene (ALG9, DIBD1 at chromosome band 11q23 was previously identified to be disrupted by a balanced chromosomal translocation t(9;11(p24;q23 co-segregating with bipolar affective disorder in a small family. Inborn ALG9 deficiency (congenital disorders of glycosylation type IL is associated with progressive microcephaly, seizures, developmental delay, and hepatomegaly. It is unknown whether common variations of ALG9 predispose to bipolar affective disorder. Methods We tested five polymorphic markers spanning ALG9 (three intragenic and one upstream microsatellite repeats and one common missense variation, V289I (rs10502151 for their association with bipolar I disorder in two pedigree series. The NIMH (National Institute of Mental Health pedigrees had a total of 166 families showing transmissions to 250 affected offspring, whereas The PITT (The University of Pittsburgh pedigrees had a total of 129 families showing transmissions to 135 cases. We used transmission disequilibrium test for the association analyses. Results We identified three common and distinct haplotypes spanning the ALG9 gene. We found no statistically-significant evidence of transmission disequilibrium of marker alleles or multi-marker haplotypes to the affected offspring with bipolar I disorder. Conclusion These results suggest that common variations in ALG9 do not play a major role in predisposition to bipolar affective disorder.

Fast Kalman Filtering for Relative Spacecraft Position and Attitude Estimation for the Raven ISS Hosted Payload

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Galante, Joseph M.; Van Eepoel, John; D'Souza, Chris; Patrick, Bryan

2016-01-01

The Raven ISS Hosted Payload will feature several pose measurement sensors on a pan/tilt gimbal which will be used to autonomously track resupply vehicles as they approach and depart the International Space Station. This paper discusses the derivation of a Relative Navigation Filter (RNF) to fuse measurements from the different pose measurement sensors to produce relative position and attitude estimates. The RNF relies on relative translation and orientation kinematics and careful pose sensor modeling to eliminate dependence on orbital position information and associated orbital dynamics models. The filter state is augmented with sensor biases to provide a mechanism for the filter to estimate and mitigate the offset between the measurements from different pose sensors

Variations of the aortic arch - a study on the most common branching patterns

International Nuclear Information System (INIS)

Muller, Marguerite; Schmitz, Bernd L; Schick, Melanie; Schloetzer, Wiebke; Pauls, Sandra; Roehrer, Stefan; Kapapa, Thomas

2011-01-01

Background: Anatomical variants of the aortic arch and its branching patterns often appear as an incidental finding during routine computed tomography (CT) scanning. These variations can be of relevance when performing angiography or endovascular interventions and may cause symptoms such as dysphagia. Purpose: To analyze common anatomical variations found within the arteries originating from the aortic arch in patients using contrast CT imaging techniques. Material and Methods: A total of 2033 contrast CT scans were analyzed. To obtain a truly representative sample, cases were chosen from different hospital departments without previous knowledge of the patient history. Results: The total percentage of variations within the analyzed patients was 13.3%. In 8.0% a truncus bicaroticus was found. 4.2% of the patients showed a left vertebral artery originating directly from the aortic arch, mostly proximal, and in 1 case distal to the left subclavian artery. In 1.0% we found an aberrant right subclavian artery. We also found a single case of a right descending aortic arch. Conclusion: Variations of the aortic arch and its branching are frequently found, mostly as an incidental finding during routine diagnostic scanning. A contrast-enhanced CT scan is a good method with which to study the aortic arch and its associated branching pattern

Variations of the aortic arch - a study on the most common branching patterns

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Muller, Marguerite; Schmitz, Bernd L; Schick, Melanie; Schloetzer, Wiebke (Dept. of Diagnostic and Interventional Radiology, Section Neuroradiology, Univ. Ulm (Germany)), email: marguerite.mueller@uni-ulm.de; Pauls, Sandra (Dept. of Diagnostic and Interventional Radiology, Univ. Ulm (Germany)); Roehrer, Stefan; Kapapa, Thomas (Dept. of Neurosurgery, Univ. Ulm (Germany))

2011-09-15

Background: Anatomical variants of the aortic arch and its branching patterns often appear as an incidental finding during routine computed tomography (CT) scanning. These variations can be of relevance when performing angiography or endovascular interventions and may cause symptoms such as dysphagia. Purpose: To analyze common anatomical variations found within the arteries originating from the aortic arch in patients using contrast CT imaging techniques. Material and Methods: A total of 2033 contrast CT scans were analyzed. To obtain a truly representative sample, cases were chosen from different hospital departments without previous knowledge of the patient history. Results: The total percentage of variations within the analyzed patients was 13.3%. In 8.0% a truncus bicaroticus was found. 4.2% of the patients showed a left vertebral artery originating directly from the aortic arch, mostly proximal, and in 1 case distal to the left subclavian artery. In 1.0% we found an aberrant right subclavian artery. We also found a single case of a right descending aortic arch. Conclusion: Variations of the aortic arch and its branching are frequently found, mostly as an incidental finding during routine diagnostic scanning. A contrast-enhanced CT scan is a good method with which to study the aortic arch and its associated branching pattern

A common variation of the PTEN gene is associated with peripheral insulin resistance

DEFF Research Database (Denmark)

Grinder-Hansen, L; Ribel-Madsen, R; Wojtaszewski, Jørgen

2016-01-01

. RESULTS: The minor G allele of PTEN rs11202614 was associated with elevated fasting plasma insulin levels and a decreased peripheral glucose disposal rate, but not with the hepatic insulin resistance index or insulin secretion measured as the first-phase insulin response and disposition index. The single...... nucleotide polymorphism was not associated with either PI3K or Akt activities. CONCLUSION: A common PTEN variation is associated with peripheral insulin resistance and subsequent risk of developing T2D. However, the association with insulin resistance is not explained by decreased proximal insulin signalling......AIM: Phosphatase and tensin homologue (PTEN) reduces insulin sensitivity by inhibiting the phosphatidylinositol 3-kinase (PI3K)/v-akt murine thymoma viral oncogene homologue (Akt) pathway. This study investigated how a common single nucleotide polymorphism near PTEN, previously associated...

Common Variation in the DOPA Decarboxylase (DDC) Gene and Human Striatal DDC Activity In Vivo.

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Eisenberg, Daniel P; Kohn, Philip D; Hegarty, Catherine E; Ianni, Angela M; Kolachana, Bhaskar; Gregory, Michael D; Masdeu, Joseph C; Berman, Karen F

2016-08-01

The synthesis of multiple amine neurotransmitters, such as dopamine, norepinephrine, serotonin, and trace amines, relies in part on DOPA decarboxylase (DDC, AADC), an enzyme that is required for normative neural operations. Because rare, loss-of-function mutations in the DDC gene result in severe enzymatic deficiency and devastating autonomic, motor, and cognitive impairment, DDC common genetic polymorphisms have been proposed as a source of more moderate, but clinically important, alterations in DDC function that may contribute to risk, course, or treatment response in complex, heritable neuropsychiatric illnesses. However, a direct link between common genetic variation in DDC and DDC activity in the living human brain has never been established. We therefore tested for this association by conducting extensive genotyping across the DDC gene in a large cohort of 120 healthy individuals, for whom DDC activity was then quantified with [(18)F]-FDOPA positron emission tomography (PET). The specific uptake constant, Ki, a measure of DDC activity, was estimated for striatal regions of interest and found to be predicted by one of five tested haplotypes, particularly in the ventral striatum. These data provide evidence for cis-acting, functional common polymorphisms in the DDC gene and support future work to determine whether such variation might meaningfully contribute to DDC-mediated neural processes relevant to neuropsychiatric illness and treatment.

Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion

DEFF Research Database (Denmark)

Okello, John Bosco A.; Nyakaana, Silvester; Masembe, C.

2005-01-01

Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific....... A relatively low overall nucleotide diversity was observed ( =1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation...... was observed in the total data set (FST=0.138; P=0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (FCT=0.103; P=0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical...

Influence of common preanalytical variations on the metabolic profile of serum samples in biobanks

International Nuclear Information System (INIS)

Fliniaux, Ophélie; Gaillard, Gwenaelle; Lion, Antoine; Cailleu, Dominique; Mesnard, François; Betsou, Fotini

2011-01-01

A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4°C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4°C. Five or ten serum freeze–thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of human serum.

Influence of common preanalytical variations on the metabolic profile of serum samples in biobanks

Energy Technology Data Exchange (ETDEWEB)

Fliniaux, Ophelie [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Gaillard, Gwenaelle [Biobanque de Picardie (France); Lion, Antoine [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Cailleu, Dominique [Batiment Serres-Transfert, rue de Mai/rue Dallery, Plateforme Analytique (France); Mesnard, Francois, E-mail: francois.mesnard@u-picardie.fr [University of Picardie Jules Verne, Laboratoire de Phytotechnologie EA 3900-BioPI (France); Betsou, Fotini [Integrated Biobank of Luxembourg (Luxembourg)

2011-12-15

A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4 Degree-Sign C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4 Degree-Sign C. Five or ten serum freeze-thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of human serum.

Strategy use fully mediates the relationship between working memory capacity and performance on Raven's matrices.

Science.gov (United States)

Gonthier, Corentin; Thomassin, Noémylle

2015-10-01

Working memory capacity consistently correlates with fluid intelligence. It has been suggested that this relationship is partly attributable to strategy use: Participants with high working memory capacity would use more effective strategies, in turn leading to higher performance on fluid intelligence tasks. However, this idea has never been directly investigated. In 2 experiments, we tested this hypothesis by directly manipulating strategy use in a combined experimental-correlational approach (Experiment 1; N = 250) and by measuring strategy use with a self-report questionnaire (Experiment 2; N = 93). Inducing all participants to use an effective strategy in Raven's matrices decreased the correlation between working memory capacity and performance; the strategy use measure fully mediated the relationship between working memory capacity and performance on the matrices task. These findings indicate that individual differences in strategic behavior drive the predictive utility of working memory. We interpret the results within a theoretical framework integrating the multiple mediators of the relationship between working memory capacity and high-level cognition. (c) 2015 APA, all rights reserved).

Behavioral responses to inequity in reward distribution and working effort in crows and ravens.

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Claudia A F Wascher

Full Text Available Sensitivity to inequity is considered to be a crucial cognitive tool in the evolution of human cooperation. The ability has recently been shown also in primates and dogs, raising the question of an evolutionary basis of inequity aversion. We present first evidence that two bird species are sensitive to other individuals' efforts and payoffs. In a token exchange task we tested both behavioral responses to inequity in the quality of reward (preferred versus non-preferred food and to the absence of reward in the presence of a rewarded partner, in 5 pairs of corvids (6 crows, 4 ravens. Birds decreased their exchange performance when the experimental partner received the reward as a gift, which indicates that they are sensitive to other individuals' working effort. They also decreased their exchange performance in the inequity compared with the equity condition. Notably, corvids refused to take the reward after a successful exchange more often in the inequity compared with the other conditions. Our findings indicate that awareness to other individuals' efforts and payoffs may evolve independently of phylogeny in systems with a given degree of social complexity.

Common genetic variation and novel loci associated with volumetric mammographic density.

Science.gov (United States)

Brand, Judith S; Humphreys, Keith; Li, Jingmei; Karlsson, Robert; Hall, Per; Czene, Kamila

2018-04-17

Mammographic density (MD) is a strong and heritable intermediate phenotype of breast cancer, but much of its genetic variation remains unexplained. We conducted a genetic association study of volumetric MD in a Swedish mammography screening cohort (n = 9498) to identify novel MD loci. Associations with volumetric MD phenotypes (percent dense volume, absolute dense volume, and absolute nondense volume) were estimated using linear regression adjusting for age, body mass index, menopausal status, and six principal components. We also estimated the proportion of MD variance explained by additive contributions from single-nucleotide polymorphisms (SNP-based heritability [h 2 SNP ]) in 4948 participants of the cohort. In total, three novel MD loci were identified (at P associated with breast cancer in available meta-analysis data including 122,977 breast cancer cases and 105,974 control subjects (P < 0.05). h 2 SNP (SE) estimates for percent dense, absolute dense, and nondense volume were 0.29 (0.07), 0.31 (0.07), and 0.25 (0.07), respectively. Corresponding ratios of h 2 SNP to previously observed narrow-sense h 2 estimates in the same cohort were 0.46, 0.72, and 0.41, respectively. These findings provide new insights into the genetic basis of MD and biological mechanisms linking MD to breast cancer risk. Apart from identifying three novel loci, we demonstrate that at least 25% of the MD variance is explained by common genetic variation with h 2 SNP /h 2 ratios varying between dense and nondense MD components.

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

DEFF Research Database (Denmark)

Weiner, Daniel J; Wigdor, Emilie M; Ripke, Stephan

2017-01-01

Autism spectrum disorder (ASD) risk is influenced by common polygenic and de novo variation. We aimed to clarify the influence of polygenic risk for ASD and to identify subgroups of ASD cases, including those with strongly acting de novo variants, in which polygenic risk is relevant. Using a nove...

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

NARCIS (Netherlands)

Weiner, Daniel J.; Wigdor, Emilie M.; Ripke, Stephan; Walters, Raymond K.; Kosmicki, Jack A.; Grove, Jakob; Samocha, Kaitlin E.; Goldstein, Jacqueline I.; Okbay, Aysu; Bybjerg-Grauholm, Jonas; Werge, Thomas; Hougaard, David M.; Taylor, Jacob; Skuse, David; Devlin, Bernie; Anney, Richard; Sanders, Stephan J.; Bishop, Somer; Mortensen, Preben Bo; Børglum, Anders D.; Smith, George Davey; Daly, Mark J.; Robinson, Elise B.; Bækvad-Hansen, Marie; Dumont, Ashley; Hansen, Christine; Hansen, Thomas F.; Howrigan, Daniel; Mattheisen, Manuel; Moran, Jennifer; Mors, Ole; Nordentoft, Merete; Nørgaard-Pedersen, Bent; Poterba, Timothy; Poulsen, Jesper; Stevens, Christine; Anttila, Verneri; Holmans, Peter; Huang, Hailiang; Klei, Lambertus; Lee, Phil H.; Medland, Sarah E.; Neale, Benjamin; Weiss, Lauren A.; Zwaigenbaum, Lonnie; Yu, Timothy W.; Wittemeyer, Kerstin; Willsey, A. Jeremy; Wijsman, Ellen M.; Wassink, Thomas H.; Waltes, Regina; Walsh, Christopher A.; Wallace, Simon; Vorstman, Jacob A.S.; Vieland, Veronica J.; Vicente, Astrid M.; Van Engeland, Herman; Tsang, Kathryn; Thompson, Ann P.; Szatmari, Peter; Svantesson, Oscar; Steinberg, Stacy; Stefansson, Kari; Stefansson, Hreinn; State, Matthew W.; Soorya, Latha; Silagadze, Teimuraz; Scherer, Stephen W.; Schellenberg, Gerard D.; Sandin, Sven; Saemundsen, Evald; Rouleau, Guy A.; Rogé, Bernadette; Roeder, Kathryn; Roberts, Wendy; Reichert, Jennifer; Reichenberg, Abraham; Rehnström, Karola; Regan, Regina; Poustka, Fritz; Poultney, Christopher S.; Piven, Joseph; Pinto, Dalila; Pericak-Vance, Margaret A.; Pejovic-Milovancevic, Milica; Pedersen, Marianne G.; Pedersen, Carsten B.; Paterson, Andrew D.; Parr, Jeremy R.; Pagnamenta, Alistair T.; Oliveira, Guiomar; Nurnberger, John I.; Murtha, Michael T.; Mouga, Susana; Morrow, Eric M.; DeLuca, Daniel Moreno; Monaco, Anthony P.; Minshew, Nancy; Merikangas, Alison; McMahon, William M.; McGrew, Susan G.; Martsenkovsky, Igor; Martin, Donna M.; Mane, Shrikant M.; Magnusson, Pall; Magalhaes, Tiago; Maestrini, Elena; Lowe, Jennifer K.; Lord, Catherine; Levitt, Pat; Martin, Christa Lese; Ledbetter, David H.; Leboyer, Marion; LeCouteur, Ann S.; Ladd-Acosta, Christine; Kolevzon, Alexander; Klauck, Sabine M.; Jacob, Suma; Iliadou, Bozenna; Hultman, Christina M.; Hertz-Picciotto, Irva; Hendren, Robert; Hansen, Christine S.; Haines, Jonathan L.; Guter, Stephen J.; Grice, Dorothy E.; Green, Jonathan M.; Green, Andrew; Goldberg, Arthur P.; Gillberg, Christopher; Gilbert, John; Gallagher, Louise; Freitag, Christine M.; Fombonne, Eric; Folstein, Susan E.; Fernandez, Bridget; Fallin, M. Daniele; Ercan-Sencicek, A. Gulhan; Ennis, Sean; Duque, Frederico; Duketis, Eftichia; Delorme, Richard; DeRubeis, Silvia; DeJonge, Maretha V.; Dawson, Geraldine; Cuccaro, Michael L.; Correia, Catarina T.; Conroy, Judith; Conceição, Inês C.; Chiocchetti, Andreas G.; Celestino-Soper, Patrícia B.S.; Casey, Jillian; Cantor, Rita M.; Cafe, Cátia; Brennan, Sean; Bourgeron, Thomas; Bolton, Patrick F.; Bölte, Sven; Bolshakova, Nadia; Betancur, Catalina; Bernier, Raphael; Beaudet, Arthur L.; Battaglia, Agatino; Bal, Vanessa H.; Baird, Gillian; Bailey, Anthony J.; Bader, Joel S.; Bacchelli, Elena; Anagnostou, Evdokia; Amaral, David; Almeida, Joana; Buxbaum, Joseph D.; Chakravarti, Aravinda; Cook, Edwin H.; Coon, Hilary; Geschwind, Daniel H.; Gill, Michael; Hakonarson, Hakon; Hallmayer, Joachim; Palotie, Aarno; Santangelo, Susan; Sutcliffe, James S.; Arking, Dan E.

2017-01-01

Autism spectrum disorder (ASD) risk is influenced by common polygenic and de novo variation. We aimed to clarify the influence of polygenic risk for ASD and to identify subgroups of ASD cases, including those with strongly acting de novo variants, in which polygenic risk is relevant. Using a novel

Common variation near ROBO2 is associated with expressive vocabulary in infancy.

Science.gov (United States)

St Pourcain, Beate; Cents, Rolieke A M; Whitehouse, Andrew J O; Haworth, Claire M A; Davis, Oliver S P; O'Reilly, Paul F; Roulstone, Susan; Wren, Yvonne; Ang, Qi W; Velders, Fleur P; Evans, David M; Kemp, John P; Warrington, Nicole M; Miller, Laura; Timpson, Nicholas J; Ring, Susan M; Verhulst, Frank C; Hofman, Albert; Rivadeneira, Fernando; Meaburn, Emma L; Price, Thomas S; Dale, Philip S; Pillas, Demetris; Yliherva, Anneli; Rodriguez, Alina; Golding, Jean; Jaddoe, Vincent W V; Jarvelin, Marjo-Riitta; Plomin, Robert; Pennell, Craig E; Tiemeier, Henning; Davey Smith, George

2014-09-16

Twin studies suggest that expressive vocabulary at ~24 months is modestly heritable. However, the genes influencing this early linguistic phenotype are unknown. Here we conduct a genome-wide screen and follow-up study of expressive vocabulary in toddlers of European descent from up to four studies of the EArly Genetics and Lifecourse Epidemiology consortium, analysing an early (15-18 months, 'one-word stage', N(Total) = 8,889) and a later (24-30 months, 'two-word stage', N(Total)=10,819) phase of language acquisition. For the early phase, one single-nucleotide polymorphism (rs7642482) at 3p12.3 near ROBO2, encoding a conserved axon-binding receptor, reaches the genome-wide significance level (P=1.3 × 10(-8)) in the combined sample. This association links language-related common genetic variation in the general population to a potential autism susceptibility locus and a linkage region for dyslexia, speech-sound disorder and reading. The contribution of common genetic influences is, although modest, supported by genome-wide complex trait analysis (meta-GCTA h(2)(15-18-months) = 0.13, meta-GCTA h(2)(24-30-months) = 0.14) and in concordance with additional twin analysis (5,733 pairs of European descent, h(2)(24-months) = 0.20).

Rare and common regulatory variation in population-scale sequenced human genomes.

Directory of Open Access Journals (Sweden)

Stephen B Montgomery

2011-07-01

Full Text Available Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.

Fiber and nonstarch polysaccharide content and variation in common crops used in broiler diets

DEFF Research Database (Denmark)

Knudsen, Knud Erik Bach

2014-01-01

The current paper reviews content and variation in fiber and nonstarch polysaccharides (NSP) of common crops used in broiler diets. The cereal grain is a complex structure, and its cell walls (CW) differ in their composition and hence properties. Arabinoxylan (AX), mixed linkage (1→3; 1→4)-β...... AX, but β-glucan can also be present mainly in rye and wheat brans. The CW composition of seeds and grains of protein crops and feedstuffs are different from that of cereals. The main CW polymers are pectic substances (homogalacturonan, rhamnogalacturonan type I and II, xylogalacturonan...

Serum chemistry reference values for the common genet (Genetta genetta): variations associated with Leishmania infantum infection.

Science.gov (United States)

Millán, Javier; Chirife, Andrea D; Altet, Laura

2015-03-01

The role of wildlife in the epidemiology of leishmaniosis in under debate, and determining whether infection with Leishmania infantum causes illness in wild carnivores is important to determine its potential role as a reservoir. To provide for the first time serum biochemistry reference values for the common genet (Genetta genetta), and to determine variations associated with L. infantum infection. Twenty-five serum biochemistry parameters were determined in 22 wild-caught genets. Blood samples were analyzed for L. infantum DNA by means of real-time polymerase chain reaction (PCR). Two female genets were positive for L. infantum DNA but did not show any external clinical sign upon physical examination. Among other variations in the biochemistry values of these genets, one presented a higher concentration of gamma-globulins and cholesterol, whereas the other genet presented increased creatinine, bilirubin, and chloride levels when compared to uninfected females. Sex-related differences in some parameters were also reported. Infection with L. infantum may sometimes be accompanied by abnormal serum biochemistry in wild carnivores. Clinical disease may occur in L. infantum-infected wild carnivores. This has implications in the epidemiology of leishmaniosis. In addition, the data provided here would also be useful as reference values for researchers or rehabilitators working with the common genet.

Type 2 diabetes mellitus interacts with obesity and common variations in PLTP to affect plasma phospholipid transfer protein activity

NARCIS (Netherlands)

Dullaart, R. P. F.; Vergeer, M.; de Vries, R.; Kappelle, P. J. W. H.; Dallinga-Thie, G. M.

2012-01-01

Dullaart RPF, Vergeer M, de Vries R, Kappelle PJWH, Dallinga-Thie GM (University Medical Center Groningen, University of Groningen, Groningen; and Academic Medical Center Amsterdam, Amsterdam; The Netherlands). Type 2 diabetes mellitus interacts with obesity and common variations in PLTP to affect

Inter- and Intraspecific Variations in the Pectoral Muscles of Common Chimpanzees (Pan troglodytes), Bonobos (Pan paniscus), and Humans (Homo sapiens)

OpenAIRE

Potau, J. M.; Arias-Martorell, J.; Bello-Hellegouarch, G.; Casado, A.; Pastor, J. F.; de Paz, F.; Diogo, R.

2018-01-01

We have analyzed anatomic variations in the pectoralis major and pectoralis minor muscles of common chimpanzees (Pan\\ud troglodytes) and bonobos(Pan paniscus) and compared them to anatomic variations in these muscles in humans(Homo sapiens). We\\ud have macroscopically dissected these muscles in six adult Pan troglodytes, five Pan paniscus of ages ranging from fetus to adult, and\\ud five adult Homo sapiens. Although Pan troglodytes are thought to lack a separate pectoralis abdominis muscle, we...

The Role of Leaf Volatiles of Ludwigia octovalvis (Jacq.) Raven in the Attraction of Altica cyanea (Weber) (Coleoptera: Chrysomelidae).

Science.gov (United States)

Mitra, Saubhik; Karmakar, Amarnath; Mukherjee, Abhishek; Barik, Anandamay

2017-07-01

Larvae and adults of Altica cyanea (Weber) (Coleoptera: Chrysomelidae) feed on the rice-field weed Ludwigia octovalvis (Jacq.) Raven (Onagraceae), commonly known as willow primrose, which is considered a biocontrol agent of the weed. Volatile organic compounds from undamaged plants, plants after 4, 12, and 36 h of continuous feeding by A. cyanea larvae or adult females and after mechanical damaging were identified by GC-MS and GC-FID analyses. Twenty nine compounds were identified from undamaged plants. 2Z-Penten-1-ol, geraniol, and 1-tridecanol were present in all plants damaged by larvae. In contrast, feeding by adults caused the release of 2Z-penten-1-ol only after 12 and 36 h; whereas geraniol and 1-tridecanol appeared only after 36 h. Farnesyl acetone was detected after 12 and 36 h of feeding by larvae and after 36 h of feeding by adults. Farnesene was detected after 36 h of feeding by larvae and adults. Linalool was unique after 36 h of feeding by larvae. In Y-shaped glass tube olfactometer bioassays, A. cyanea females were attracted to volatiles after 36 h of feeding by larvae or adults compared to volatiles released by undamaged plants. The insects were attracted to five synthetic compounds: 3-hexanol, α-pinene, linalool oxide, geraniol, and phytol. Synthetic blends were more attractive than individual compounds. Compared to undamaged plants, volatiles released by plants, damaged by conspecific individuals, were more attractive to A. cyanea females, due to elevated emissions of 3-hexanol, α-pinene, linalool oxide, geraniol, and phytol.

Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort.

Science.gov (United States)

Moon, Sanghoon; Kim, Young Jin; Hong, Chang Bum; Kim, Dong-Joon; Lee, Jong-Young; Kim, Bong-Jo

2011-11-01

To date, hundreds of thousands of copy-number variation (CNV) data have been reported using various platforms. The proportion of Asians in these data is, however, relatively small as compared with that of other ethnic groups, such as Caucasians and Yorubas. Because of limitations in platform resolution and the high noise level in signal intensity, in most CNV studies (particularly those using single nucleotide polymorphism arrays), the average number of CNVs in an individual is less than the number of known CNVs. In this study, we ascertained reliable, common CNV regions (CNVRs) and identified actual frequency rates in the Korean population to provide more CNV information. We performed two-stage analyses for detecting structural variations with two platforms. We discovered 576 common CNVRs (88 CNV segments on average in an individual), and 87% (501 of 576) of these CNVRs overlapped by ≥1 bp with previously validated CNV events. Interestingly, from the frequency analysis of CNV profiles, 52 of 576 CNVRs had a frequency rate of population.

Change is good: variations in common biological mechanisms in the epsilonproteobacterial genera Campylobacter and Helicobacter.

Science.gov (United States)

Gilbreath, Jeremy J; Cody, William L; Merrell, D Scott; Hendrixson, David R

2011-03-01

Microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. The epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. Many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. Some epsilonproteobacteria, such as Campylobacter jejuni and Helicobacter pylori, are common pathogens of humans that inhabit specific regions of the gastrointestinal tract. As such, the biological processes of pathogenic Campylobacter and Helicobacter spp. are often modeled after those of common enteric pathogens such as Salmonella spp. and Escherichia coli. While many exquisite biological mechanisms involving biochemical processes, genetic regulatory pathways, and pathogenesis of disease have been elucidated from studies of Salmonella spp. and E. coli, these paradigms often do not apply to the same processes in the epsilonproteobacteria. Instead, these bacteria often display extensive variation in common biological mechanisms relative to those of other prototypical bacteria. In this review, five biological processes of commonly studied model bacterial species are compared to those of the epsilonproteobacteria C. jejuni and H. pylori. Distinct differences in the processes of flagellar biosynthesis, DNA uptake and recombination, iron homeostasis, interaction with epithelial cells, and protein glycosylation are highlighted. Collectively, these studies support a broader view of the vast repertoire of biological mechanisms employed by bacteria and suggest that future studies of the epsilonproteobacteria will continue to provide novel and interesting information regarding prokaryotic cellular biology.

Inter- and Intraspecific Variations in the Pectoral Muscles of Common Chimpanzees (Pan troglodytes), Bonobos (Pan paniscus), and Humans (Homo sapiens).

Science.gov (United States)

Potau, J M; Arias-Martorell, J; Bello-Hellegouarch, G; Casado, A; Pastor, J F; de Paz, F; Diogo, R

2018-01-01

We have analyzed anatomic variations in the pectoralis major and pectoralis minor muscles of common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) and compared them to anatomic variations in these muscles in humans (Homo sapiens) . We have macroscopically dissected these muscles in six adult Pan troglodytes , five Pan paniscus of ages ranging from fetus to adult, and five adult Homo sapiens . Although Pan troglodytes are thought to lack a separate pectoralis abdominis muscle, we have identified this muscle in three of the Pan troglodytes ; none of the Pan paniscus , however, had this muscle. We have also found deep supernumerary fascicles in the pectoralis major of two Pan troglodytes and all five Pan paniscus . In all six Pan troglodytes , the pectoralis minor was inserted at the supraspinatus tendon, while, in Pan paniscus and Homo sapiens , it was inserted at the coracoid process of the scapula. Some of the anatomic features and variations of these muscles in common chimpanzees and bonobos are similar to those found in humans, therefore enhancing our knowledge of primate comparative anatomy and evolution and also shedding light on several clinical issues.

Inter- and Intraspecific Variations in the Pectoral Muscles of Common Chimpanzees (Pan troglodytes, Bonobos (Pan paniscus, and Humans (Homo sapiens

Directory of Open Access Journals (Sweden)

J. M. Potau

2018-01-01

Full Text Available We have analyzed anatomic variations in the pectoralis major and pectoralis minor muscles of common chimpanzees (Pan troglodytes and bonobos (Pan paniscus and compared them to anatomic variations in these muscles in humans (Homo sapiens. We have macroscopically dissected these muscles in six adult Pan troglodytes, five Pan paniscus of ages ranging from fetus to adult, and five adult Homo sapiens. Although Pan troglodytes are thought to lack a separate pectoralis abdominis muscle, we have identified this muscle in three of the Pan troglodytes; none of the Pan paniscus, however, had this muscle. We have also found deep supernumerary fascicles in the pectoralis major of two Pan troglodytes and all five Pan paniscus. In all six Pan troglodytes, the pectoralis minor was inserted at the supraspinatus tendon, while, in Pan paniscus and Homo sapiens, it was inserted at the coracoid process of the scapula. Some of the anatomic features and variations of these muscles in common chimpanzees and bonobos are similar to those found in humans, therefore enhancing our knowledge of primate comparative anatomy and evolution and also shedding light on several clinical issues.

Unusual Congenital Aortic Anomaly with Rare Common Celiamesenteric Trunk Variation: MR Angiography and Digital Substraction Angiography Findings

International Nuclear Information System (INIS)

Tosun, Ozgur; Sanlidilek, Umman; Cetin, Huseyin; Ozdemir, Ozcan; Kurt, Aydin; Sakarya, Mehmet Emin; Tas, Ismet

2007-01-01

Magnetic resonance angiography and digital substraction angiography (DSA) findings in a case with a rare congenital thoracoabdominal aortic hypoplasia and common celiamesenteric trunk variation with occlusion of infrarenal abdominal aorta are described here. To our knowledge, this aortic anomaly has not been previously described in the English literature. DSA is the optimum imaging modality for determination of aortic hypoplasia, associated vascular malformations, collateral vessels, and direction of flow within vessels

Heritable Variation for Sex Ratio under Environmental Sex Determination in the Common Snapping Turtle (Chelydra Serpentina)

Science.gov (United States)

Janzen, F. J.

1992-01-01

The magnitude of quantitative genetic variation for primary sex ratio was measured in families extracted from a natural population of the common snapping turtle (Chelydra serpentina), which possesses temperature-dependent sex determination (TSD). Eggs were incubated at three temperatures that produced mixed sex ratios. This experimental design provided estimates of the heritability of sex ratio in multiple environments and a test of the hypothesis that genotype X environment (G X E) interactions may be maintaining genetic variation for sex ratio in this population of C. serpentina. Substantial quantitative genetic variation for primary sex ratio was detected in all experimental treatments. These results in conjunction with the occurrence of TSD in this species provide support for three critical assumptions of Fisher's theory for the microevolution of sex ratio. There were statistically significant effects of family and incubation temperature on sex ratio, but no significant interaction was observed. Estimates of the genetic correlations of sex ratio across environments were highly positive and essentially indistinguishable from +1. These latter two findings suggest that G X E interaction is not the mechanism maintaining genetic variation for sex ratio in this system. Finally, although substantial heritable variation exists for primary sex ratio of C. serpentina under constant temperatures, estimates of the effective heritability of primary sex ratio in nature are approximately an order of magnitude smaller. Small effective heritability and a long generation time in C. serpentina imply that evolution of sex ratios would be slow even in response to strong selection by, among other potential agents, any rapid and/or substantial shifts in local temperatures, including those produced by changes in the global climate. PMID:1592234

Vascular Variations Associated with Intracranial Aneurysms.

Science.gov (United States)

Orakdogen, Metin; Emon, Selin Tural; Somay, Hakan; Engin, Taner; Is, Merih; Hakan, Tayfun

2017-01-01

To investigate the vascular variations in patients with intracranial aneurysm in circle of Willis. We used the data on 128 consecutive intracranial aneurysm cases. Cerebral angiography images were analyzed retrospectively. Arteries were grouped as anterior cerebral arterial system (ACS), posterior cerebral arterial system (PCS) and middle cerebral arterial system (MCS) for grouping vascular variations. Lateralization, being single/multiple, gender; and also any connection with accompanying aneurysms" number, localization, dimension, whether bleeding/incidental aneurysm has been inspected. Variations were demonstrated in 57.8% of the cases. The most common variation was A1 variation (34.4%). The rate of variations was 36.7%, 24.2% and 10.2% respectively in ACS, PCS and MCS. MCS variations were significantly higher in males. Anterior communicating artery (ACoA) aneurysm observance rates were significantly higher and posterior communicating artery (PCoA) aneurysm and middle cerebral artery (MCA) aneurysm observance rates were significantly lower when compared to "no ACS variation detected" cases. In "PCS variation detected" cases, PCoA aneurysm observance rates and coexistence of multiple variations were significantly higher. The rate of vascular variations in patients with aneurysms was 57.8%. Arterial hypoplasia and aplasia were the most common variations. ACS was the most common region that variations were located in; they were mostly detected on the right side. Coexistence of ACoA aneurysm was higher than PCoA and MCA aneurysms. In the PCS variations group, PCoA aneurysms were the most common aneurysms that accompanying the variation and multiple variations were more common than in the other two groups. The variations in MCS were most common in males.

Longevity is independent of common variations in genes associated with cardiovascular risk

DEFF Research Database (Denmark)

Bladbjerg, E M; Andersen-Ranberg, K; Maat, M de

1999-01-01

Do extremely old persons have a genetically favourable profile which has protected them from cardiovascular death? We have tried to answer this question by measuring DNA polymorphisms of selected cardiovascular risk indicators [factor VII, FVII (R/Q353, intron 7 (37bp)n, and -323ins10), beta fibr......, ACE (intron 16 ins287), and angiotensinogen (M/T235)]. Blood was collected from 187 unselected Danish centenarians, and 201 healthy Danish blood donors, aged 20-64 years (mean age 42 years). Genomic DNA was amplified using PCR and the genotype was determined by RFLP methods or allele.......33; for ACE 0.52; and for angiotensinogen 0.36. Comparable frequencies were observed in the blood donors. Subgroup analysis of men and women separately gave similar results. The genotype frequencies in the centenarians and the blood donors were similar for all polymorphisms, and this study suggests...... that common variations in genes associated with cardiovascular risk do not contribute significantly to longevity....

Measuring spatial variation in secondary production and food quality using a common consumer approach in Lake Erie

Science.gov (United States)

Larson, James H.; Richardson, William B.; Evans, Mary Anne; Schaeffer, Jeff; Wynne, Timothy; Bartsch, Michelle; Bartsch, Lynn; Nelson, J. C.; Vallazza, Jon M.

2016-01-01

Lake Erie is a large lake straddling the border of the U.S. and Canada that has become increasingly eutrophic in recent years. Eutrophication is particularly focused in the shallow western basin. The western basin of Lake Erie is hydrodynamically similar to a large estuary, with riverine inputs from the Detroit and Maumee Rivers mixing together and creating gradients in chemical and physical conditions. This study was driven by two questions: How does secondary production and food quality for consumers vary across this large mixing zone? and Are there correlations between cyanobacterial abundance and secondary production or food quality for consumers? Measuring spatial and temporal variation in secondary production and food quality is difficult for a variety of logistical reasons, so here a common consumer approach was used. In a common consumer approach, individuals of a single species are raised under similar conditions until placed in the field across environmental gradients of interest. After some period of exposure, the response of that common consumer is measured to provide an index of spatial variation in conditions. Here, a freshwater mussel (Lampsilis siliquoidea) was deployed at 32 locations that spanned habitat types and a gradient in cyanobacterial abundance in the western basin of Lake Erie to measure spatial variation in growth (an index of secondary production) and fatty acid (FA) content (an index of food quality). We found secondary production was highest within the Maumee rivermouth and lowest in the open waters of the lake. Mussel tissues in the Maumee rivermouth also included more eicosapentaenoic and docosapentaenoic fatty acids (EPA and DPA, respectively), but fewer bacterial FAs, suggesting more algae at the base of the food web in the Maumee rivermouth compared to open lake sites. The satellite-derived estimate of cyanobacterial abundance was not correlated to secondary production, but was positively related to EPA and DPA content in the

Light Water Reactor Sustainability Program Support and Modeling for the Boiling Water Reactor Station Black Out Case Study Using RELAP and RAVEN

Energy Technology Data Exchange (ETDEWEB)

Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Smith, Curtis [Idaho National Lab. (INL), Idaho Falls, ID (United States); Riley, Thomas [Idaho National Lab. (INL), Idaho Falls, ID (United States); Schroeder, John [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alfonsi, Aldrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Nielsen, Joe [Idaho National Lab. (INL), Idaho Falls, ID (United States); Maljovec, Dan [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Bie [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pascucci, Valerio [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2013-09-01

The existing fleet of nuclear power plants is in the process of extending its lifetime and increasing the power generated. In order to evaluate the impact of these two factors on the safety of the plant, the Risk Informed Safety Margin Characterization (RISMC) project aims to provide insight to decision makers through a series of simulations of the plant dynamics for different initial conditions (e.g., probabilistic analysis and uncertainty quantification). This report focuses, in particular, on the impact of power uprate on the safety of a boiled water reactor system. The case study considered is a loss of off-site power followed by the loss of diesel generators, i.e., a station black out (SBO) event. Analysis is performed by using a thermo-hydraulic code, i.e. RELAP-5, and a stochastic analysis tool currently under development at INL, i.e. RAVEN. Starting from the event tree models contained in SAPHIRE, we built the input file for RELAP-5 that models in great detail system dynamics under SBO conditions. We also interfaced RAVEN with RELAP-5 so that it would be possible to run multiple RELAP-5 simulation runs by changing specific keywords of the input file. We both employed classical statistical tools, i.e. Monte-Carlo, and more advanced machine learning based algorithms to perform uncertainty quantification in order to quantify changes in system performance and limitations as a consequence of power uprate. We also employed advanced data analysis and visualization tools that helped us to correlate simulation outcome such as maximum core temperature with a set of input uncertain parameters. Results obtained gave a detailed overview of the issues associated to power uprate for a SBO accident scenario. We were able to quantify how timing of safety related events were impacted by a higher reactor core power. Such insights can provide useful material to the decision makers to perform risk-infomed safety margins management.

Plastic and heritable components of phenotypic variation in Nucella lapillus: an assessment using reciprocal transplant and common garden experiments.

Science.gov (United States)

Pascoal, Sonia; Carvalho, Gary; Creer, Simon; Rock, Jenny; Kawaii, Kei; Mendo, Sonia; Hughes, Roger

2012-01-01

Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F(2)s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F(1)s than F(2)s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal.

Plastic and heritable components of phenotypic variation in Nucella lapillus: an assessment using reciprocal transplant and common garden experiments.

Directory of Open Access Journals (Sweden)

Sonia Pascoal

Full Text Available Assessment of plastic and heritable components of phenotypic variation is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed the above in relation to adaptive shell morphology of the rocky intertidal snail Nucella lapillus by reciprocal transplantation of snails between two shores differing in wave action and rearing snails of the same provenance in a common garden. Results were compared with those reported for similar experiments conducted elsewhere. Microsatellite variation indicated limited gene flow between the populations. Intrinsic growth rate was greater in exposed-site than sheltered-site snails, but the reverse was true of absolute growth rate, suggesting heritable compensation for reduced foraging opportunity at the exposed site. Shell morphology of reciprocal transplants partially converged through plasticity toward that of native snails. Shell morphology of F(2s in the common garden partially retained characteristics of the P-generation, suggesting genetic control. A maternal effect was revealed by greater resemblance of F(1s than F(2s to the P-generation. The observed synergistic effects of plastic, maternal and genetic control of shell-shape may be expected to maximise fitness when environmental characteristics become unpredictable through dispersal.

Rule reversal: Ecogeographical patterns of body size variation in the common treeshrew (Mammalia, Scandentia)

Science.gov (United States)

Sargis, Eric J.; Millien, Virginie; Woodman, Neal; Olson, Link E.

2018-01-01

There are a number of ecogeographical “rules” that describe patterns of geographical variation among organisms. The island rule predicts that populations of larger mammals on islands evolve smaller mean body size than their mainland counterparts, whereas smaller‐bodied mammals evolve larger size. Bergmann's rule predicts that populations of a species in colder climates (generally at higher latitudes) have larger mean body sizes than conspecifics in warmer climates (at lower latitudes). These two rules are rarely tested together and neither has been rigorously tested in treeshrews, a clade of small‐bodied mammals in their own order (Scandentia) broadly distributed in mainland Southeast Asia and on islands throughout much of the Sunda Shelf. The common treeshrew, Tupaia glis, is an excellent candidate for study and was used to test these two rules simultaneously for the first time in treeshrews. This species is distributed on the Malay Peninsula and several offshore islands east, west, and south of the mainland. Using craniodental dimensions as a proxy for body size, we investigated how island size, distance from the mainland, and maximum sea depth between the mainland and the islands relate to body size of 13 insular T. glis populations while also controlling for latitude and correlation among variables. We found a strong negative effect of latitude on body size in the common treeshrew, indicating the inverse of Bergmann's rule. We did not detect any overall difference in body size between the island and mainland populations. However, there was an effect of island area and maximum sea depth on body size among island populations. Although there is a strong latitudinal effect on body size, neither Bergmann's rule nor the island rule applies to the common treeshrew. The results of our analyses demonstrate the necessity of assessing multiple variables simultaneously in studies of ecogeographical rules.

Normal variation of hepatic artery

International Nuclear Information System (INIS)

Kim, Inn; Nam, Myung Hyun; Rhim, Hyun Chul; Koh, Byung Hee; Seo, Heung Suk; Kim, Soon Yong

1987-01-01

This study was an analyses of blood supply of the liver in 125 patients who received hepatic arteriography and abdominal aortography from Jan. 1984 to Dec. 1986 at the Department of Radiology of Hanyang University Hospital. A. Variations in extrahepatic arteries: 1. The normal extrahepatic artery pattern occurred in 106 of 125 cases (84.8%) ; Right hepatic and left hepatic arteries arising from the hepatic artery proper and hepatic artery proper arising from the common hepatic artery. 2. The most common type of variation of extrahepatic artery was replaced right hepatic artery from superior mesenteric artery: 6 of 125 cases (4.8%). B. Variations in intrahepatic arteries: 1. The normal intrahepatic artery pattern occurred in 83 of 125 cases (66.4%). Right hepatic and left hepatic arteries arising from the hepatic artery proper and middle hepatic artery arising from lower portion of the umbilical point of left hepatic artery. 2. The most common variation of intrahepatic arteries was middle hepatic artery. 3. Among the variation of middle hepatic artery; Right, middle and left hepatic arteries arising from the same location at the hepatic artery proper was the most common type; 17 of 125 cases (13.6%)

Geographical variation in the prevalence of sensitization to common aeroallergens in adults

DEFF Research Database (Denmark)

Newson, R B; van Ree, R; Forsberg, B

2014-01-01

BACKGROUND: Geographical variation in the prevalence of sensitization to aeroallergens may reflect differences in exposure to risk factors such as having older siblings, being raised on a farm or other unidentified exposures. OBJECTIVE: We wanted to measure geographical variation in skin prick te...

On characterizing population commonalities and subject variations in brain networks.

Science.gov (United States)

Ghanbari, Yasser; Bloy, Luke; Tunc, Birkan; Shankar, Varsha; Roberts, Timothy P L; Edgar, J Christopher; Schultz, Robert T; Verma, Ragini

2017-05-01

Brain networks based on resting state connectivity as well as inter-regional anatomical pathways obtained using diffusion imaging have provided insight into pathology and development. Such work has underscored the need for methods that can extract sub-networks that can accurately capture the connectivity patterns of the underlying population while simultaneously describing the variation of sub-networks at the subject level. We have designed a multi-layer graph clustering method that extracts clusters of nodes, called 'network hubs', which display higher levels of connectivity within the cluster than to the rest of the brain. The method determines an atlas of network hubs that describes the population, as well as weights that characterize subject-wise variation in terms of within- and between-hub connectivity. This lowers the dimensionality of brain networks, thereby providing a representation amenable to statistical analyses. The applicability of the proposed technique is demonstrated by extracting an atlas of network hubs for a population of typically developing controls (TDCs) as well as children with autism spectrum disorder (ASD), and using the structural and functional networks of a population to determine the subject-level variation of these hubs and their inter-connectivity. These hubs are then used to compare ASD and TDCs. Our method is generalizable to any population whose connectivity (structural or functional) can be captured via non-negative network graphs. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of the taxonomic status of Allobates talamancae (Anura: Aromobatidae) and its interpopulation variation in Costa Rica

International Nuclear Information System (INIS)

Salazar Zuniga, Jose Andres

2014-01-01

The taxonomic status of the species Allobates talamancae is reevaluated. The morphology, morphometry and characteristics of the singing are compared between specimens from the type locality with other populations of the Caribe and Pacifico of Costa Rica. The species Allobates talamancae is redescribed using songs and specimens from the type locality. Possible variations in the spectral and temporal characteristics of the singing of notice of the males Allobates talamancae are examined between the type locality and other locations populations of the Caribe and Pacifico of Costa Rica. The temporal spectrum analysis of the characteristics of the singing is realized through the program Raven 1.2.1. Spectrograms were produced with a Fast Fourier transform using a window type Hann with a frequency resolution of 124 Hz and a temporal of 11,6 ms and an overlap of 50%. The degree of morphological and morphometric variation are determined among individuals of Allobates talamancae from the type locality with other populations of the Caribe and Pacifico of Costa Rica. The measurements to determine the morphometric analysis of each specimen collected is realized through digital photographs on a base of white background with a scale in millimeters. The morphological analysis is defined by the revision of 47 characteristics suggested in the literature [es

On the intraspecific variation in morphometry and shape of sagittal otoliths of common sardine, Strangomera bentincki, off central-southern Chile

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Sandra Curin-Osorio

2012-11-01

Full Text Available Size and shape of fish otoliths are species-specific, but some species also display intraspecific variations. The common sardine, Strangomera bentincki, is a small pelagic fish inhabiting a seasonal upwelling ecosystem off central-southern Chile, having two discrete spawning sites along its latitudinal distribution. Otoliths of specimens were collected from commercial catches in Talcahuano and Corral, representing the central and south spawning zones. On the basis of otolith images, size-based shape descriptors were used to detect ontogenetic variation, and morphometric variables (length, breadth, area, perimeter and weight were used to detect geographical differences in size and shape of otoliths. Outline analysis was studied on the basis of elliptic Fourier descriptors through multivariate statistical procedures. Size-based shape descriptors showed that otolith shape starts to be stable for fish larger than 12 cm total length, which keep an elliptical form. Morphometric variables for fish larger than 12 cm revealed intraspecific variation between central and south zones, which were associated with otolith weight and breadth. Outline analysis did not reveal significant spatial differences, but extreme intraspecific variation was due to the antirostrum, excisure, and posterior part of otoliths. Intraspecific variation in otolith size could be linked to differences in each spawning habitat and related to geographical origin, whose differences are not clearly identified. It is concluded that intraspecific variability in morphometric variables of sardine otoliths revealed geographic differences in size that are not attributable to allometric effects, and that otolith shape was similar between specimens from different geographic origin.

Common Genetic Variation and Haplotypes of the Anion Exchanger SLC4A2 in Primary Biliary Cirrhosis

Science.gov (United States)

Juran, Brian D.; Atkinson, Elizabeth J.; Larson, Joseph J.; Schlicht, Erik M.; Lazaridis, Konstantinos N.

2010-01-01

Objectives Deficiencies of the anion exchanger SLC4A2 are thought to play a pathogenic role in primary biliary cirrhosis (PBC), evidenced by decreased expression and activity in PBC patients and development of disease features in SLC4A2 knockout mice. We hypothesized that genetic variation in SLC4A2 might influence this pathogenic contribution. Thus, we aimed to perform a comprehensive assessment of SLC4A2 genetic variation in PBC using a linkage disequilibrium (LD)-based haplotype-tagging approach. Methods Twelve single nucleotide polymorphisms (SNPs) across SLC4A2 were genotyped in 409 PBC patients and 300 controls and evaluated for association with disease, as well as with prior orthotopic liver transplant and antimitochondrial antibody (AMA) status among the PBC patients, both individually and as inferred haplotypes, using logistic regression. Results All SNPs were in Hardy–Weinberg equilibrium. No associations with disease or liver transplantation were detected, but two variants, rs2303929 and rs3793336, were associated with negativity for antimitochondrial antibodies among the PBC patients. Conclusions The common genetic variation of SLC4A2 does not directly affect the risk of PBC or its clinical outcome. Whether the deficiency of SLC4A2 expression and activity observed earlier in PBC patients is an acquired epiphenomenon of underlying disease or is because of heritable factors in unappreciated regulatory regions remains uncertain. Of note, two SLC4A2 variants appear to influence AMA status among PBC patients. The mechanisms behind this finding are unclear. PMID:19491853

Pauses in Striatal Cholinergic Interneurons: What is Revealed by Their Common Themes and Variations?

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Yan-Feng Zhang

2017-10-01

Full Text Available Striatal cholinergic interneurons, the so-called tonically active neurons (TANs, pause their firing in response to sensory cues and rewards during classical conditioning and instrumental tasks. The respective pause responses observed can demonstrate many commonalities, such as constant latency and duration, synchronous occurrence in a population of cells, and coincidence with phasic activities of midbrain dopamine neurons (DANs that signal reward predictions and errors. Pauses can however also show divergent properties. Pause latencies and durations can differ in a given TAN between appetitive vs. aversive outcomes in classical conditioning, initial excitation can be present or absent, and a second pause can variably follow a rebound. Despite more than 20 years of study, the functions of these pause responses are still elusive. Our understanding of pause function is hindered by an incomplete understanding of how pauses are generated. In this mini-review article, we compare pause types, as well as current key hypotheses for inputs underlying pauses that include dopamine-induced inhibition through D2-receptors, a GABA input from ventral tegmental area, and a prolonged afterhyperpolarization induced by excitatory input from the cortex or from the thalamus. We review how each of these mechanisms alone explains some but not all aspects of pause responses. These mechanisms might need to operate in specific but variable sets of sequences to generate a full range of pause responses. Alternatively, these mechanisms might operate in conjunction with an underlying control mechanism within cholinergic interneurons which could potentially provide a framework to generate the common themes and variations seen amongst pause responses.

Bilateral renal artery variation

OpenAIRE

Üçerler, Hülya; Üzüm, Yusuf; İkiz, Z. Aslı Aktan

2014-01-01

Each kidney is supplied by a single renal artery, although renal artery variations are common. Variations of the renal arteryhave become important with the increasing number of renal transplantations. Numerous studies describe variations in renalartery anatomy. Especially the left renal artery is among the most critical arterial variations, because it is the referred side forresecting the donor kidney. During routine dissection in a formalin fixed male cadaver, we have found a bilateral renal...

Variations in the origin of inferior phrenic arteries and their relationship to celiac axis variations on CT angiography

Energy Technology Data Exchange (ETDEWEB)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal [Dept. of Radiology, Tepecik Training and Research Hospital, Izmir (Turkmenistan); Toka, Onur [Dept. of Statistics, Hacettepe University, Ankara (Turkmenistan)

2017-04-15

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18–94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

Variations in the origin of inferior phrenic arteries and their relationship to celiac axis variations on CT angiography

International Nuclear Information System (INIS)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal; Toka, Onur

2017-01-01

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18–94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation

Variations in the Origin of Inferior Phrenic Arteries and Their Relationship to Celiac Axis Variations on CT Angiography.

Science.gov (United States)

Aslaner, Ramazan; Pekcevik, Yeliz; Sahin, Hilal; Toka, Onur

2017-01-01

Knowing the origin of the inferior phrenic artery (IPA) is important prior to surgical interventions and interventional radiological procedures related to IPA. We aimed to identify variations in the origin of IPA and to investigate the relationship between the origin of IPA and celiac axis variations using computed tomography angiography (CTA). The CTA images of 1000 patients (737 male and 263 female, the mean age 60, range 18-94 years) were reviewed in an analysis of IPA and celiac axis variations. The origin of IPA was divided into two groups, those originating as a common trunk and those originating independently without a truncus. The relationship between the origin of IPA and celiac axis variation was analyzed using Pearson's chi-square test. Both IPAs originated from a common trunk in 295 (29.5%) patients. From which the majority of the common trunk originated from the aorta. Contrastingly, the inferior phrenic arteries originated from different origins in 705 (70.5%) patients. The majority of the right inferior phrenic artery (RIPA) and the left inferior phrenic artery (LIPA) originated independently from the celiac axis. Variation in the celiac axis were detected in 110 (11%) patients. The origin of IPA was found to be significantly different in the presence of celiac axis variation. The majority of IPA originated from the aorta in patients with a common IPA trunk, while the majority of RIPA and LIPA originating from the celiac axis in patients without a common IPA trunk. Thus, the origin of IPA may widely differ in the presence of celiac axis variation.

Are common names becoming less common? The rise in uniqueness and individualism in Japan.

Science.gov (United States)

Ogihara, Yuji; Fujita, Hiroyo; Tominaga, Hitoshi; Ishigaki, Sho; Kashimoto, Takuya; Takahashi, Ayano; Toyohara, Kyoko; Uchida, Yukiko

2015-01-01

We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates) suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual's psyche and behavior outside the head; e.g., advertising) can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by pairing common

Contribution of common non-synonymous variants in PCSK1 to body-mass index variation and risk of obesity

DEFF Research Database (Denmark)

Nead, Kevin T; Li, Aihua; Wehner, Mackenzie R

2015-01-01

data in up to 331,175 individuals from diverse ethnic groups. This process involved a systematic review of the literature in PubMed, Web of Science, Embase and the NIH GWAS catalog complemented by data extraction from pre-existing GWAS or custom-arrays in consortia and single studies. We employed......Polymorphisms rs6232 and rs6234/rs6235 in PCSK1 have been associated with extreme obesity (e.g. body mass index [BMI]≥40 kg/m(2)), but their contribution to common obesity (BMI≥30 kg/m(2)) and BMI variation in a multi-ethnic context is unclear. To fill this gap, we collected phenotypic and genetic...

Population structure analysis using rare and common functional variants

Directory of Open Access Journals (Sweden)

Ding Lili

2011-11-01

Full Text Available Abstract Next-generation sequencing technologies now make it possible to genotype and measure hundreds of thousands of rare genetic variations in individuals across the genome. Characterization of high-density genetic variation facilitates control of population genetic structure on a finer scale before large-scale genotyping in disease genetics studies. Population structure is a well-known, prevalent, and important factor in common variant genetic studies, but its relevance in rare variants is unclear. We perform an extensive population structure analysis using common and rare functional variants from the Genetic Analysis Workshop 17 mini-exome sequence. The analysis based on common functional variants required 388 principal components to account for 90% of the variation in population structure. However, an analysis based on rare variants required 532 significant principal components to account for similar levels of variation. Using rare variants, we detected fine-scale substructure beyond the population structure identified using common functional variants. Our results show that the level of population structure embedded in rare variant data is different from the level embedded in common variant data and that correcting for population structure is only as good as the level one wishes to correct.

An algorithm for finding a common solution for a system of mixed equilibrium problem, quasi-variational inclusion problem and fixed point problem of nonexpansive semigroup

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Liu Min

2010-01-01

Full Text Available In this paper, we introduce a hybrid iterative scheme for finding a common element of the set of solutions for a system of mixed equilibrium problems, the set of common fixed points for a nonexpansive semigroup and the set of solutions of the quasi-variational inclusion problem with multi-valued maximal monotone mappings and inverse-strongly monotone mappings in a Hilbert space. Under suitable conditions, some strong convergence theorems are proved. Our results extend some recent results in the literature.

Are common names becoming less common? The rise in uniqueness and individualism in Japan

Directory of Open Access Journals (Sweden)

Yuji eOgihara

2015-10-01

Full Text Available We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual’s psyche and behavior outside the head; e.g., advertising can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by

Are common names becoming less common? The rise in uniqueness and individualism in Japan

Science.gov (United States)

Ogihara, Yuji; Fujita, Hiroyo; Tominaga, Hitoshi; Ishigaki, Sho; Kashimoto, Takuya; Takahashi, Ayano; Toyohara, Kyoko; Uchida, Yukiko

2015-01-01

We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates) suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual’s psyche and behavior outside the head; e.g., advertising) can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by pairing common

Common genetic variations in the CYP2R1 and GC genes are determinants of vitamin D status in Danes

DEFF Research Database (Denmark)

Nissen, Ioanna

Vitamin D is considered a key fat-soluble vitamin critically important for good bone- and overall health throughout life. Vitamin D deficiency increases the risk of developing rickets, osteomalacia and osteoporosis, and moreover increases the risk of various non-skeletal adverse health outcomes......), after 6 months intake of vitamin D3-fortified bread and milk (paper II) and in 92 participants in the VitDgen study after artificial UVB irradiation during winter (paper III). Common genetic variations in the CYP2R1 and GC genes were found to be important determinants of vitamin D status in three out...

Genetic mechanisms and age-related macular degeneration: common variants, rare variants, copy number variations, epigenetics, and mitochondrial genetics

Directory of Open Access Journals (Sweden)

Liu Melissa M

2012-08-01

Full Text Available Abstract Age-related macular degeneration (AMD is a complex and multifaceted disease involving contributions from both genetic and environmental influences. Previous work exploring the genetic contributions of AMD has implicated numerous genomic regions and a variety of candidate genes as modulators of AMD susceptibility. Nevertheless, much of this work has revolved around single-nucleotide polymorphisms (SNPs, and it is apparent that a significant portion of the heritability of AMD cannot be explained through these mechanisms. In this review, we consider the role of common variants, rare variants, copy number variations, epigenetics, microRNAs, and mitochondrial genetics in AMD. Copy number variations in regulators of complement activation genes (CFHR1 and CFHR3 and glutathione S transferase genes (GSTM1 and GSTT1 have been associated with AMD, and several additional loci have been identified as regions of potential interest but require further evaluation. MicroRNA dysregulation has been linked to the retinal pigment epithelium degeneration in geographic atrophy, ocular neovascularization, and oxidative stress, all of which are hallmarks in the pathogenesis of AMD. Certain mitochondrial DNA haplogroups and SNPs in mitochondrially encoded NADH dehydrogenase genes have also been associated with AMD. The role of these additional mechanisms remains only partly understood, but the importance of their further investigation is clear to elucidate more completely the genetic basis of AMD.

Detection probability of cliff-nesting raptors during helicopter and fixed-wing aircraft surveys in western Alaska

Science.gov (United States)

Booms, T.L.; Schempf, P.F.; McCaffery, B.J.; Lindberg, M.S.; Fuller, M.R.

2010-01-01

We conducted repeated aerial surveys for breeding cliff-nesting raptors on the Yukon Delta National Wildlife Refuge (YDNWR) in western Alaska to estimate detection probabilities of Gyrfalcons (Falco rusticolus), Golden Eagles (Aquila chrysaetos), Rough-legged Hawks (Buteo lagopus), and also Common Ravens (Corvus corax). Using the program PRESENCE, we modeled detection histories of each species based on single species occupancy modeling. We used different observers during four helicopter replicate surveys in the Kilbuck Mountains and five fixed-wing replicate surveys in the Ingakslugwat Hills near Bethel, AK. During helicopter surveys, Gyrfalcons had the highest detection probability estimate (p^;p^ 0.79; SE 0.05), followed by Golden Eagles (p^=0.68; SE 0.05), Common Ravens (p^=0.45; SE 0.17), and Rough-legged Hawks (p^=0.10; SE 0.11). Detection probabilities from fixed-wing aircraft in the Ingakslugwat Hills were similar to those from the helicopter in the Kilbuck Mountains for Gyrfalcons and Golden Eagles, but were higher for Common Ravens (p^=0.85; SE 0.06) and Rough-legged Hawks (p^=0.42; SE 0.07). Fixed-wing aircraft provided detection probability estimates and SEs in the Ingakslugwat Hills similar to or better than those from helicopter surveys in the Kilbucks and should be considered for future cliff-nesting raptor surveys where safe, low-altitude flight is possible. Overall, detection probability varied by observer experience and in some cases, by study area/aircraft type.

Parkinson's disease and mitochondrial gene variations

DEFF Research Database (Denmark)

Andalib, Sasan; Vafaee, Manouchehr Seyedi; Gjedde, Albert

2014-01-01

Parkinson's disease (PD) is a common disorder of the central nervous system in the elderly. The pathogenesis of PD is a complex process, with genetics as an important contributing factor. This factor may stem from mitochondrial gene variations and mutations as well as from nuclear gene variations...

Genetic variation in Mediterranean Helichrysum italicum (Asteraceae; Gnaphalieae): do disjunct populations of subsp. microphyllum have a common origin?

Science.gov (United States)

Galbany-Casals, M; Blanco-Moreno, J M; Garcia-Jacas, N; Breitwieser, I; Smissen, R D

2011-07-01

The yellow-flowered everlasting daisy Helichrysum italicum (Asteraceae, Gnaphalieae) is widely distributed in the Mediterranean basin, where it grows in continuous and widespread populations in diverse open habitats. Helichrysum italicum subsp. microphyllum has a disjunct distribution in the Balearic Islands (Majorca and Dragonera), Corsica, Sardinia, Crete and Cyprus. Numerous morphological intermediates between subsp. italicum and subsp. microphyllum are known from Corsica, where the two subspecies co-occur. The aims of the study were to investigate if subsp. microphyllum has a common origin, constituting an independent gene pool from subsp. italicum, or if the morphological differences between subsp. microphyllum and subsp. italicum have arisen independently in different locations from a common wider gene pool. Our analyses of AFLP, cpDNA sequences and morphological characters show that there is geographic structure to the genetic variation within H. italicum, with eastern and western Mediterranean groups, which do not correspond with the division into subsp. microphyllum and subsp. italicum as currently circumscribed. Local selection on quantitative trait loci provides sufficient explanation for the morphological divergence observed and is consistent with genetic data. Within the western Mediterranean group of the species we found considerable polymorphism in chloroplast DNA sequences among and within some populations. Comparison with chloroplast DNA sequences from other Helichrysum species showed that some chloroplast haplotypes are shared across species. © 2010 German Botanical Society and The Royal Botanical Society of the Netherlands.

Greater sage-grouse nest predators in the Virginia Mountains of northwestern Nevada

Science.gov (United States)

Lockyer, Zachary B.; Coates, Peter S.; Casazza, Michael L.; Espinosa, Shawn; Delehanty, David J.

2013-01-01

Greater sage-grouse Centrocercus urophasianus, hereafter sage-grouse, populations have declined across their range due to the loss, degradation, and fragmentation of habitat. Habitat alterations can lead not only to vegetative changes but also to shifts in animal behavior and predator composition that may influence population vital rates, such as nest success. For example, common ravens Corvus corax are sage-grouse nest predators, and common raven abundance is positively associated with human-caused habitat alterations. Because nest success is a central component to sage-grouse population persistence, research that identifies factors influencing nest success will better inform conservation efforts. We used videography to unequivocally identify sage-grouse nest predators within the Virginia Mountains of northwestern Nevada, USA, from 2009 to 2011 and used maximum likelihood to calculate daily probability of nest survival. In the Virginia Mountains, fires, energy exploration, and other anthropogenic activities have altered historic sage-grouse habitat. We monitored 71 sage-grouse nests during the study, placing video cameras at 39 nests. Cumulative nest survival for all nests was 22.4% (95% CI, 13.0–33.4%), a survival rate that was significantly lower than other published results for sage-grouse in the Great Basin. Depredation was the primary cause for nest failure in our study (82.5%), and common ravens were the most frequent sage-grouse nest predator, accounting for 46.7% of nest depredations. We also successfully documented a suite of mammalian and reptilian species depredating sage-grouse nests, including some predators never previously confirmed in the literature to be sage-grouse nest predators (i.e., bobcats Lynx rufus and long-tailed weasels Mephitis frenata). Within the high elevation, disturbed habitat of the Virginia Mountains, low sage-grouse nest success may be limiting sage-grouse population growth. These results suggest that management actions that

Salix transect of Europe: variation in ploidy and genome size in willow-associated common nettle, Urtica dioica L. sens. lat., from Greece to arctic Norway

OpenAIRE

Quentin Cronk; Oriane Hidalgo; Jaume Pellicer; Diana Percy; Ilia Leitch

2016-01-01

Abstract Background The common stinging nettle, Urtica dioica L. sensu lato, is an invertebrate "superhost", its clonal patches maintaining large populations of insects and molluscs. It is extremely widespread in Europe and highly variable, and two ploidy levels (diploid and tetraploid) are known. However, geographical patterns in cytotype variation require further study. New information We assembled a collection of nettles in conjunction with a transect of Europe from the Aegean to Arctic No...

Multiple factors affect a population of Agassiz's desert tortoise (Gopherus agassizii) in the Northwestern Mojave Desert

Science.gov (United States)

Berry, Kristin H.; Yee, Julie L.; Coble, Ashley A.; Perry, William M.; Shields, Timothy A.

2013-01-01

Numerous factors have contributed to declines in populations of the federally threatened Agassiz's Desert Tortoise (Gopherus agassizii) and continue to limit recovery. In 2010, we surveyed a low-density population on a military test facility in the northwestern Mojave Desert of California, USA, to evaluate population status and identify potential factors contributing to distribution and low densities. Estimated densities of live tortoises ranged spatially from 1.2/km2 to 15.1/km2. Although only one death of a breeding-age tortoise was recorded for the 4-yr period prior to the survey, remains of 16 juvenile and immature tortoises were found, and most showed signs of predation by Common Ravens (Corvus corax) and mammals. Predation may have limited recruitment of young tortoises into the adult size classes. To evaluate the relative importance of different types of impacts to tortoises, we developed predictive models for spatially explicit densities of tortoise sign and live tortoises using topography (i.e., slope), predators (Common Raven, signs of mammalian predators), and anthropogenic impacts (distances from paved road and denuded areas, density of ordnance fragments) as covariates. Models suggest that densities of tortoise sign increased with slope and signs of mammalian predators and decreased with Common Ravens, while also varying based on interaction effects involving these predictors as well as distances from paved roads, denuded areas, and ordnance. Similarly, densities of live tortoises varied by interaction effects among distances to denuded areas and paved roads, density of ordnance fragments, and slope. Thus multiple factors predict the densities and distribution of this population.

Variation of energy absorption buildup factors with incident photon energy and penetration depth for some commonly used solvents

International Nuclear Information System (INIS)

Singh, Parjit S.; Singh, Tejbir; Kaur, Paramjeet

2008-01-01

G.P. fitting method has been used to compute energy absorption buildup factor of some commonly used solvents such as acetonitrile (C 4 H 3 N), butanol (C 4 H 9 OH), chlorobenzene (C 6 H 5 Cl), diethyl ether (C 4 H 10 O), ethanol (C 2 H 5 OH), methanol (CH 3 OH), propanol (C 3 H 7 OH) and water (H 2 O) for the wide energy range (0.015-15.0 MeV) up to the penetration depth of 10 mean free path. The variation of energy absorption buildup factor with chemical composition as well as incident photon energy for the selected solvents has been studied. It has been observed that the maximum value of energy absorption buildup factors shifts to the slightly higher incident photon energy with the increase in equivalent atomic number of the solvent and the solvent with least equivalent atomic number possesses the maximum value of energy absorption buildup factor

Exploring language variation across Europe

DEFF Research Database (Denmark)

Hovy, Dirk; Johannsen, Anders Trærup

2016-01-01

Language varies not only between countries, but also along regional and sociodemographic lines. This variation is one of the driving factors behind language change. However, investigating language variation is a complex undertaking: the more factors we want to consider, the more data we need. Tra...... use of large amounts of data and provides statistical analyses, maps, and interactive features that enable scholars to explore language variation in a data-driven way.......Language varies not only between countries, but also along regional and sociodemographic lines. This variation is one of the driving factors behind language change. However, investigating language variation is a complex undertaking: the more factors we want to consider, the more data we need...... training in both variational linguistics and computational methods, a combination that is still not common. We take a first step here to alleviate the problem by providing an interface to explore large-scale language variation along several socio-demographic factors without programming knowledge. It makes...

Arterial variations of upper limb: a case report

Directory of Open Access Journals (Sweden)

Vollala V

2005-01-01

Full Text Available Variations of upper limb arteries are common and there are many reports about this subject. We report multiple variations in arterial pattern of upper extremity, which were encountered in a single cadaver.

Portal vein branching order helps in the recognition of anomalous right-sided round ligament: common features and variations in portal vein anatomy.

Science.gov (United States)

Yamashita, Rikiya; Yamaoka, Toshihide; Nishitai, Ryuta; Isoda, Hiroyoshi; Taura, Kojiro; Arizono, Shigeki; Furuta, Akihiro; Ohno, Tsuyoshi; Ono, Ayako; Togashi, Kaori

2017-07-01

This study aimed to evaluate the common features and variations of portal vein anatomy in right-sided round ligament (RSRL), which can help propose a method to detect and diagnose this anomaly. In this retrospective study of 14 patients with RSRL, the branching order of the portal tree was analyzed, with special focus on the relationship between the dorsal branch of the right anterior segmental portal vein (P A-D ) and the lateral segmental portal vein (P LL ), to determine the common features. The configuration of the portal vein from the main portal trunk to the right umbilical portion (RUP), the inclination of the RUP, and the number and thickness of the ramifications branching from the right anterior segmental portal vein (P A ) were evaluated for variations. In all subjects, the diverging point of the P A-D was constantly distal to that of the P LL . The portal vein configuration was I- and Z-shaped in nine and five subjects, respectively. The RUP was tilted to the right in all subjects. In Z-shaped subjects, the portal trunk between the branching point of the right posterior segmental portal vein and that of the P LL was tilted to the left in one subject and was almost parallel to the vertical plane in four subjects. Multiple ramifications were radially distributed from the P A in eight subjects, whereas one predominant P A-D branched from the P A in six subjects. Based on the diverging points of the P A-D and P LL , we proposed a three-step method for the detection and diagnosis of RSRL.

Toward Meaningful Manufacturing Variation Data in Design - Feature Based Description of Variation in Manufacturing Processes

DEFF Research Database (Denmark)

Eifler, Tobias; Boorla, Srinivasa Murthy; Howard, Thomas J.

2016-01-01

The need to mitigate the effects of manufacturing variation already in design is nowadays commonly acknowledged and has led to a wide use of predictive modeling techniques, tolerancing approaches, etc. in industry. The trustworthiness of corresponding variation analyses is, however, not ensured...... by the availability of sophisticated methods and tools alone, but does evidently also depend on the accuracy of the input information used. As existing approaches for the description of manufacturing variation focus however, almost exclusively, on monitoring and controlling production processes, there is frequently...... a lack of objective variation data in design. As a result, variation analyses and tolerancing activities rely on numerous assumptions made to fill the gaps of missing or incomplete data. To overcome this hidden subjectivity, a schema for a consistent and standardised description of manufacturing...

Gastrointestinal parasites of the Common Eider (Somateria mollissima) – Seasonal, geographical and host related variations in the parasite burdens of two distinct Danish populations

DEFF Research Database (Denmark)

Jensen, Marie Stengaard; Chriél, Mariann; Al-Sabi, Mohammad Nafi Solaiman

Due to a recent decline in number of Common Eiders (Somateria mollissima) in Denmark, prevalence, intensity and composition of the gastrointestinal helminth fauna of Common Eiders from two distinct colonies were examined to establish reference data of the helminth fauna of apparently healthy birds....... Furthermore, seasonal, geographical and host related variations in helminth composition were studied. The birds were collected November 2010 to January 2012. Included were a total of 157 eiders from Jutland (N=103) and Zealand (N=54) respectively, comprising 54 males and 102 females of which 20 were gathered...... during the nesting period. The study is ongoing, and so far most parasites have only been identified to the family level. Eight trematode families, two nematode families, one acanthocephala and one cestode family were identified. Intensities of infections were primarily influenced by age of the birds...

The contribution of additive genetic variation to personality variation: heritability of personality.

Science.gov (United States)

Dochtermann, Ned A; Schwab, Tori; Sih, Andrew

2015-01-07

Individual animals frequently exhibit repeatable differences from other members of their population, differences now commonly referred to as 'animal personality'. Personality differences can arise, for example, from differences in permanent environmental effects--including parental and epigenetic contributors--and the effect of additive genetic variation. Although several studies have evaluated the heritability of behaviour, less is known about general patterns of heritability and additive genetic variation in animal personality. As overall variation in behaviour includes both the among-individual differences that reflect different personalities and temporary environmental effects, it is possible for personality to be largely genetically influenced even when heritability of behaviour per se is quite low. The relative contribution of additive genetic variation to personality variation can be estimated whenever both repeatability and heritability are estimated for the same data. Using published estimates to address this issue, we found that approximately 52% of animal personality variation was attributable to additive genetic variation. Thus, while the heritability of behaviour is often moderate or low, the heritability of personality is much higher. Our results therefore (i) demonstrate that genetic differences are likely to be a major contributor to variation in animal personality and (ii) support the phenotypic gambit: that evolutionary inferences drawn from repeatability estimates may often be justified. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Working memory capacity and fluid abilities: the more difficult the item, the more more is better.

Science.gov (United States)

Little, Daniel R; Lewandowsky, Stephan; Craig, Stewart

2014-01-01

The relationship between fluid intelligence and working memory is of fundamental importance to understanding how capacity-limited structures such as working memory interact with inference abilities to determine intelligent behavior. Recent evidence has suggested that the relationship between a fluid abilities test, Raven's Progressive Matrices, and working memory capacity (WMC) may be invariant across difficulty levels of the Raven's items. We show that this invariance can only be observed if the overall correlation between Raven's and WMC is low. Simulations of Raven's performance revealed that as the overall correlation between Raven's and WMC increases, the item-wise point bi-serial correlations involving WMC are no longer constant but increase considerably with item difficulty. The simulation results were confirmed by two studies that used a composite measure of WMC, which yielded a higher correlation between WMC and Raven's than reported in previous studies. As expected, with the higher overall correlation, there was a significant positive relationship between Raven's item difficulty and the extent of the item-wise correlation with WMC.

Working memory capacity and fluid abilities: The more difficult the item, the more more is better

Directory of Open Access Journals (Sweden)

Daniel R Little

2014-03-01

Full Text Available The relationship between fluid intelligence and working memory is of fundamental importance to understanding how capacity-limited structures such as working memory interact with inference abilities to determine intelligent behaviour. Recent evidence has suggested that the relationship between a fluid abilities test, Raven's Progressive Matrices, and working memory capacity (WMC may be invariant across difficulty levels of the Raven's items. We show that this invariance can only be observed if the overall correlation between Raven's and WMC is low. Simulations of Raven's performance revealed that as the overall correlation between Raven's and WMC increases, the item-wise point bi-serial correlations involving WMC are no longer constant but increase considerably with item difficulty. The simulation results were confirmed by two studies that used a composite measure of WMC, which yielded a higher correlation between WMC and Raven's than reported in previous studies. As expected, with the higher overall correlation, there was a signifi□cant positive relationship between Raven's item difficulty and the extent of the item-wise correlation with WMC.

the Size of the Common Bile Duct on Routine Radiography Variation

African Journals Online (AJOL)

... fatty meal stimulus showed reduction in the diameter of the common bile duct ... pancreatic pathology was noted. ... JOURNAL. 2149. Fig. 1. ... fatty meal stimulus is mediated through the endocrine action of ... 1O Histological studies have all ...

The SEMA5A gene is associated with hippocampal volume, and their interaction is associated with performance on Raven's Progressive Matrices.

Science.gov (United States)

Zhu, Bi; Chen, Chuansheng; Xue, Gui; Moyzis, Robert K; Dong, Qi; Chen, Chunhui; Li, Jin; He, Qinghua; Lei, Xuemei; Wang, Yunxin; Lin, Chongde

2014-03-01

The Allen Brain Atlas shows that the semaphorin 5A (SEMA5A) gene, which encodes an important protein for neurogenesis and neuronal apoptosis, is predominantly expressed in the human hippocampus. Structural and functional neuroimaging studies have further shown that the hippocampus plays an important role in the performance on Raven's Progressive Matrices (RPM), a measure of reasoning ability and general fluid intelligence. Thus far, however, no study has examined the relationships between the SEMA5A gene polymorphism, hippocampal volume, and RPM performance. The current study collected both structural MRI, genetic, and behavioral data in 329 healthy Chinese adults, and examined associations between SEMA5A variants, hippocampal volume, and performance on RAPM (the advanced form of RPM). After controlling for intracranial volume (ICV), sex, and age, SEMA5A genetic polymorphism at the SNP rs42352 had the strongest association with hippocampal volume (p=0.00000552 and 0.000103 for right and left hippocampal volumes, respectively), with TT homozygotes having higher hippocampal volume than the other genotypes. Furthermore, there was a high correlation between right hippocampal volume and RAPM performance (r=0.42, p=0.0000509) for SEMA5A rs42352 TT homozygotes. This study provides the first evidence for the involvement of the SEMA5A gene in hippocampal structure and their interaction on RAPM performance. Future studies of the hippocampus-RPM associations should consider genetic factors as potential moderators. Copyright © 2013 Elsevier Inc. All rights reserved.

Exploring subdomain variation in biomedical language

Directory of Open Access Journals (Sweden)

Séaghdha Diarmuid Ó

2011-05-01

Full Text Available Abstract Background Applications of Natural Language Processing (NLP technology to biomedical texts have generated significant interest in recent years. In this paper we identify and investigate the phenomenon of linguistic subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are characterised by different linguistic behaviour. While variation at a coarser domain level such as between newswire and biomedical text is well-studied and known to affect the portability of NLP systems, we are the first to conduct an extensive investigation into more fine-grained levels of variation. Results Using the large OpenPMC text corpus, which spans the many subdomains of biomedicine, we investigate variation across a number of lexical, syntactic, semantic and discourse-related dimensions. These dimensions are chosen for their relevance to the performance of NLP systems. We use clustering techniques to analyse commonalities and distinctions among the subdomains. Conclusions We find that while patterns of inter-subdomain variation differ somewhat from one feature set to another, robust clusters can be identified that correspond to intuitive distinctions such as that between clinical and laboratory subjects. In particular, subdomains relating to genetics and molecular biology, which are the most common sources of material for training and evaluating biomedical NLP tools, are not representative of all biomedical subdomains. We conclude that an awareness of subdomain variation is important when considering the practical use of language processing applications by biomedical researchers.

Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species.

Directory of Open Access Journals (Sweden)

Yoshihiro Matsuoka

Full Text Available The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome, namely Triticumturgidum L. (AABB genome and Aegilopstauschii Coss. (DD genome. An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL analysis showed that (1 production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2 first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3 six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated

Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

Directory of Open Access Journals (Sweden)

Steven R. Eichten

2013-07-01

Full Text Available Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize ( L.. We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.

Genetic divergence of common bean cultivars.

Science.gov (United States)

Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

2015-09-22

The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

Common genetic variation and the control of HIV-1 in humans

DEFF Research Database (Denmark)

Fellay, J.; Ge, D.; Shianna, K.V.

2009-01-01

provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies...

Variation of energy absorption buildup factors with incident photon energy and penetration depth for some commonly used solvents

Energy Technology Data Exchange (ETDEWEB)

Singh, Parjit S. [Department of Physics, Punjabi University, Patiala 147 002 (India)], E-mail: dr_parjit@hotmail.com; Singh, Tejbir [Department of Physics, Lovely Professional University, Phagwara 144 402 (India); Kaur, Paramjeet [IAS and Allied Services Training Centre, Punjabi University, Patiala 147 002 (India)

2008-06-15

G.P. fitting method has been used to compute energy absorption buildup factor of some commonly used solvents such as acetonitrile (C{sub 4}H{sub 3}N), butanol (C{sub 4}H{sub 9}OH), chlorobenzene (C{sub 6}H{sub 5}Cl), diethyl ether (C{sub 4}H{sub 10}O), ethanol (C{sub 2}H{sub 5}OH), methanol (CH{sub 3}OH), propanol (C{sub 3}H{sub 7}OH) and water (H{sub 2}O) for the wide energy range (0.015-15.0 MeV) up to the penetration depth of 10 mean free path. The variation of energy absorption buildup factor with chemical composition as well as incident photon energy for the selected solvents has been studied. It has been observed that the maximum value of energy absorption buildup factors shifts to the slightly higher incident photon energy with the increase in equivalent atomic number of the solvent and the solvent with least equivalent atomic number possesses the maximum value of energy absorption buildup factor.

Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval

DEFF Research Database (Denmark)

Lin, Honghuang; van Setten, Jessica; Smith, Albert V

2018-01-01

BACKGROUND: Electrical conduction from the cardiac sinoatrial node to the ventricles is critical for normal heart function. Genome-wide association studies have identified more than a dozen common genetic loci that are associated with PR interval. However, it is unclear whether rare and low-frequ...

Common variation in the vitamin D receptor gene and risk of inflammatory bowel disease in an Irish case-control study.

LENUS (Irish Health Repository)

Hughes, David J

2012-02-01

OBJECTIVE: Vitamin D may protect against the development of inflammatory bowel disease (IBD). Several preliminary studies in separate geographical locations suggest that these effects may be partly mediated by genetic variants of the vitamin D receptor (VDR). The data, however, are yet to be confirmed in large European cohorts. This study aimed to determine if common VDR polymorphisms affected IBD risk in an Irish population. MATERIALS AND METHODS: The study was based on a cohort of 1359 Irish participants. Frequencies of the common VDR gene polymorphisms rs2228570 (FokI), rs1544410 (BsmI), rs7975232 (ApaI), and rs731236 (TaqI) were determined using allele-specific PCR in a case-control analysis of 660 patients with IBD and 699 controls. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between these variants and risk of IBD. RESULTS: There was no statistically significant effect observed on IBD risk for any of the four VDR polymorphisms tested. Furthermore, no significant differences were observed in susceptibility when the population was stratified by sex or IBD subtype (Crohn\\'s disease or ulcerative colitis). Notably, however, there was an increased risk observed for both IBD and ulcerative colitis associated with heterozygote carriage of the FokI allele that approached significance (OR=1.21, 95% CI=0.95-1.53, P=0.12 and OR=1.36, 95% CI=0.98-1.89, P=0.06, respectively), this merits further investigation. CONCLUSION: This study indicates that there is no major effect for common variation in the VDR gene alone on predisposition to IBD in the Irish population.

Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs

DEFF Research Database (Denmark)

Lee, S Hong; DeCandia, Teresa R; Ripke, Stephan

2012-01-01

of schizophrenia is the same in males and females, and that a disproportionate proportion of variation is attributable to a set of 2,725 genes expressed in the central nervous system (CNS; P = 7.6 × 10(-8)). These results are consistent with a polygenic genetic architecture and imply more individual SNP...

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh.

Science.gov (United States)

Boocock, James; Chagné, David; Merriman, Tony R; Black, Michael A

2015-10-23

Copy number variation (CNV) is a common feature of eukaryotic genomes, and a growing body of evidence suggests that genes affected by CNV are enriched in processes that are associated with environmental responses. Here we use next generation sequence (NGS) data to detect copy-number variable regions (CNVRs) within the Malus x domestica genome, as well as to examine their distribution and impact. CNVRs were detected using NGS data derived from 30 accessions of M. x domestica analyzed using the read-depth method, as implemented in the CNVrd2 software. To improve the reliability of our results, we developed a quality control and analysis procedure that involved checking for organelle DNA, not repeat masking, and the determination of CNVR identity using a permutation testing procedure. Overall, we identified 876 CNVRs, which spanned 3.5 % of the apple genome. To verify that detected CNVRs were not artifacts, we analyzed the B- allele-frequencies (BAF) within a single nucleotide polymorphism (SNP) array dataset derived from a screening of 185 individual apple accessions and found the CNVRs were enriched for SNPs having aberrant BAFs (P apple scab. We present the first analysis and catalogue of CNVRs in the M. x domestica genome. The enrichment of the CNVRs with R gene models and their overlap with gene loci of agricultural significance draw attention to a form of unexplored genetic variation in apple. This research will underpin further investigation of the role that CNV plays within the apple genome.

Body composition variation following diaphragmatic breathing ...

African Journals Online (AJOL)

Body composition variation following diaphragmatic breathing. ... effect of commonly prescribed diaphragmatic breathing training on the body composition ... a non-exercising control (NE) group (n = 22) or diaphragmatic breathing (DB) group.

Faster on Easy Items, More Accurate on Difficult Ones: Cognitive Ability and Performance on a Task of Varying Difficulty

Science.gov (United States)

Dodonova, Yulia A.; Dodonov, Yury S.

2013-01-01

Using more complex items than those commonly employed within the information-processing approach, but still easier than those used in intelligence tests, this study analyzed how the association between processing speed and accuracy level changes as the difficulty of the items increases. The study involved measuring cognitive ability using Raven's…

Accommodating variation: dialects, idiolects, and speech processing.

Science.gov (United States)

Kraljic, Tanya; Brennan, Susan E; Samuel, Arthur G

2008-04-01

Listeners are faced with enormous variation in pronunciation, yet they rarely have difficulty understanding speech. Although much research has been devoted to figuring out how listeners deal with variability, virtually none (outside of sociolinguistics) has focused on the source of the variation itself. The current experiments explore whether different kinds of variation lead to different cognitive and behavioral adjustments. Specifically, we compare adjustments to the same acoustic consequence when it is due to context-independent variation (resulting from articulatory properties unique to a speaker) versus context-conditioned variation (resulting from common articulatory properties of speakers who share a dialect). The contrasting results for these two cases show that the source of a particular acoustic-phonetic variation affects how that variation is handled by the perceptual system. We also show that changes in perceptual representations do not necessarily lead to changes in production.

Common and separate origins of the left and right inferior phrenic artery with a review of the literature.

Science.gov (United States)

Terayama, H; Yi, S-Q; Tanaka, O; Kanazawa, T; Suyama, K; Kosemura, N; Tetsu, S; Yamazaki, H; Sakamoto, R; Kawakami, S; Suzuki, T; Sakabe, K

2017-01-01

In a 94-year-old male cadaver, upon which routine dissection was being conducted, a rare variation was found in the gastrophrenic trunk (GPT), the common trunk of the left gastric artery (LGA), right inferior phrenic artery (RIPA), and left inferior phrenic artery (LIPA); the GPT arises from the abdominal aorta. A hepatosplenic trunk accompanied the variation. In this variation, the RIPA first branched from the GPT and then to the LIPA and LGA. Variations in the common trunk of the LIPA and RIPA in the GPT are common, but to our knowledge, a variation (separate inferior phrenic artery in the GPT) similar to our findings has not been previously reported. We discuss the incidence and developmental and clinical significance of this variation with a detailed review of the literature. Knowledge of such a case has important clinical significance for invasive and non-invasive arterial procedures. Therefore, different variations concerning the LGA and inferior phrenic artery should be considered during surgical and non-surgical evaluations.

Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC)

DEFF Research Database (Denmark)

Jim, Heather S L; Lin, Hui-Yi; Tyrer, Jonathan P

2016-01-01

Disruption in circadian gene expression, whether due to genetic variation or environmental factors (e.g., light at night, shiftwork), is associated with increased incidence of breast, prostate, gastrointestinal and hematologic cancers and gliomas. Circadian genes are highly expressed in the ovari...

Hybrid Iterative Scheme for Triple Hierarchical Variational Inequalities with Mixed Equilibrium, Variational Inclusion, and Minimization Constraints

Directory of Open Access Journals (Sweden)

Lu-Chuan Ceng

2014-01-01

Full Text Available We introduce and analyze a hybrid iterative algorithm by combining Korpelevich's extragradient method, the hybrid steepest-descent method, and the averaged mapping approach to the gradient-projection algorithm. It is proven that, under appropriate assumptions, the proposed algorithm converges strongly to a common element of the fixed point set of finitely many nonexpansive mappings, the solution set of a generalized mixed equilibrium problem (GMEP, the solution set of finitely many variational inclusions, and the solution set of a convex minimization problem (CMP, which is also a unique solution of a triple hierarchical variational inequality (THVI in a real Hilbert space. In addition, we also consider the application of the proposed algorithm to solving a hierarchical variational inequality problem with constraints of the GMEP, the CMP, and finitely many variational inclusions.

Common Ion Effects In Zeoponic Substrates: Dissolution And Cation Exchange Variations Due to Additions of Calcite, Dolomite and Wollastonite

Science.gov (United States)

Beiersdorfer, R. E.; Ming, D. W.; Galindo, C., Jr.

2003-01-01

c1inoptilolite-rich tuff-hydroxyapatite mixture (zeoponic substrate) has the potential to serve as a synthetic soil-additive for plant growth. Essential plant macro-nutrients such as calcium, phosphorous, magnesium, ammonium and potassium are released into solution via dissolution of the hydroxyapatite and cation exchange on zeolite charged sites. Plant growth experiments resulting in low yield for wheat have been attributed to a Ca deficiency caused by a high degree of cation exchange by the zeolite. Batch-equilibration experiments were performed in order to determine if the Ca deficiency can be remedied by the addition of a second Ca-bearing, soluble, mineral such as calcite, dolomite or wollastonite. Variations in the amount of calcite, dolomite or wollastonite resulted in systematic changes in the concentrations of Ca and P. The addition of calcite, dolomite or wollastonite to the zeoponic substrate resulted in an exponential decrease in the phosphorous concentration in solution. The exponential rate of decay was greatest for calcite (5.60 wt. % -I), intermediate for wollastonite (2.85 wt.% -I) and least for dolomite (1.58 wt.% -I). Additions of the three minerals resulted in linear increases in the calcium concentration in solution. The rate of increase was greatest for calcite (3.64), intermediate for wollastonite (2.41) and least for dolomite (0.61). The observed changes in P and Ca concentration are consistent with the solubilities of calcite, dolomite and wollastonite and with changes expected from a common ion effect with Ca. Keywords: zeolite, zeoponics, common-ion effect, clinoptilolite, hydroxyapatite

COELIAC TRUNK BRANCHING PATTERN AND VARIATION

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Jude Jose Thomson

2017-01-01

Full Text Available BACKGROUND Anatomical variations involving the visceral arteries are common. However, variations in coeliac trunk are usually asymptomatic, they may become important in patients undergoing diagnostic angiography for gastrointestinal bleeding or prior to an operative procedure. This study was useful for knowing the possible morphological variations before an upper abdominal surgery. MATERIALS AND METHODS This was a descriptive study done by cadaveric dissection, conducted on thirty cadavers. The coeliac trunk being examined for its origin, branching pattern, distribution, and variations. Results were statistically analysed and compared with the previous studies. RESULTS In our study, 60% of the coeliac trunk shows variations and 40% have normal branching pattern. A complete absence of coeliac trunk was observed in one case. In the present study the Right inferior phrenic artery arising from coeliac trunk in 2 cases (6.6% and left inferior phrenic artery arising from coeliac trunk in 3 cases (9.9%. Both inferior phrenic arteries are arising from coeliac trunk in 2 cases (6.6%. The common hepatomesenteric trunk and gastro splenic trunk was found in 1 case (3.3%. Hepatosplenic trunk was found in 2 cases (6.6%. In another 2 cases (6.6% gastric and hepatic artery originate from coeliac trunk but splenic artery has a separate origin from abdominal aorta. An absent trunk was also found in 1 case (3.3%. In 5 cases (16.7% showed trifurcation with variation in the branching pattern. CONCLUSION The branching pattern and extreme degree variability in coeliac trunk as brought out in the observations of the present study make it obvious that the present study almost falls in description with previous studies.

Power in the role of the medical director: what it is and how to get more.

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Gabel, Stewart

2011-05-01

The formal leadership of mental health care organizations commonly resides in an executive director, who may or may not have had clinical training. The medical director is a psychiatrist who reports to the executive director. For some, this arrangement suggests that the medical director lacks or has lost power in the organization. This paper examines more specifically the types of power available to the medical director using French & Raven (1959) and Raven (2008) bases of power framework. The executive director/medical director relationship can be thought of as a relationship between individuals holding formal and informal power, respectively. Although medical directors lack formal or positional power, they potentially have and can gain more informal power based on their recognized clinical/medical expertise, their personal presence and an assertive involvement and focus on the organizational mission.

Common vole (Microtus arvalis) population sex ratio: biases and process variation

Czech Academy of Sciences Publication Activity Database

Bryja, Josef; Nesvadbová, Jiřina; Heroldová, Marta; Jánová, Eva; Losík, J.; Trebatická, L.; Tkadlec, Emil

2005-01-01

Roč. 83, č. 11 (2005), s. 1391-1399 ISSN 0008-4301 R&D Projects: GA ČR(CZ) GA524/01/1316; GA ČR(CZ) GP206/02/P068; GA ČR(CZ) GA206/04/2003 Institutional research plan: CEZ:AV0Z60930519 Keywords : common vole * population sex ratio Subject RIV: EH - Ecology, Behaviour Impact factor: 1.175, year: 2005

Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk

OpenAIRE

Chornokur, Ganna; Lin, Hui-Yi; Tyrer, Jonathan P.; Lawrenson, Kate; Dennis, Joe; Amankwah, Ernest K.; Qu, Xiaotao; Tsai, Ya-Yu; Jim, Heather S. L.; Chen, Zhihua; Chen, Ann Y.; Permuth-Wey, Jennifer; Aben, Katja KH.; Anton-Culver, Hoda; Antonenkova, Natalia

2015-01-01

Background\\ud \\ud Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contribu...

Common variation in the autism risk gene CNTNAP2, brain structural connectivity and multisensory speech integration.

Science.gov (United States)

Ross, Lars A; Del Bene, Victor A; Molholm, Sophie; Jae Woo, Young; Andrade, Gizely N; Abrahams, Brett S; Foxe, John J

2017-11-01

Three lines of evidence motivated this study. 1) CNTNAP2 variation is associated with autism risk and speech-language development. 2) CNTNAP2 variations are associated with differences in white matter (WM) tracts comprising the speech-language circuitry. 3) Children with autism show impairment in multisensory speech perception. Here, we asked whether an autism risk-associated CNTNAP2 single nucleotide polymorphism in neurotypical adults was associated with multisensory speech perception performance, and whether such a genotype-phenotype association was mediated through white matter tract integrity in speech-language circuitry. Risk genotype at rs7794745 was associated with decreased benefit from visual speech and lower fractional anisotropy (FA) in several WM tracts (right precentral gyrus, left anterior corona radiata, right retrolenticular internal capsule). These structural connectivity differences were found to mediate the effect of genotype on audiovisual speech perception, shedding light on possible pathogenic pathways in autism and biological sources of inter-individual variation in audiovisual speech processing in neurotypicals. Copyright © 2017 Elsevier Inc. All rights reserved.

A Brief Study of Variation Theory in Quality Management

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Mostafa Farah Bakhsh

2016-06-01

Full Text Available Variation is part of everyday life and exists all the time. Variation is the product of differences. Difference in nature of processes results in different products during the time. Proper diagnosis of variation patterns in minimizing the loss is necessary. Continuous quality improvement is regarded as successive reduction of performance variation for delivering high quality products to the customers. In Deming viewpoint, quality deviation is classified to two groups of common and special causes. Variation is not a new word, but understanding and concerns about it are modern. First step in performance variation management is acceptance and belief of variation. For proper management of variations, appropriate tools should be used for detection and display of them. Control are useful tools in recognition, analysis and removing process performance variations.

Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria.

Science.gov (United States)

Fry, Andrew E; Griffiths, Michael J; Auburn, Sarah; Diakite, Mahamadou; Forton, Julian T; Green, Angela; Richardson, Anna; Wilson, Jonathan; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Peshu, Norbert; Williams, Thomas N; Marsh, Kevin; Molyneux, Malcolm E; Taylor, Terrie E; Rockett, Kirk A; Kwiatkowski, Dominic P

2008-02-15

There is growing epidemiological and molecular evidence that ABO blood group affects host susceptibility to severe Plasmodium falciparum infection. The high frequency of common ABO alleles means that even modest differences in susceptibility could have a significant impact on the health of people living in malaria endemic regions. We performed an association study, the first to utilize key molecular genetic variation underlying the ABO system, genotyping >9000 individuals across three African populations. Using population- and family-based tests, we demonstrated that alleles producing functional ABO enzymes are associated with greater risk of severe malaria phenotypes (particularly malarial anemia) in comparison with the frameshift deletion underlying blood group O: case-control allelic odds ratio (OR), 1.2; 95% confidence interval (CI), 1.09-1.32; P = 0.0003; family-studies allelic OR, 1.19; 95% CI, 1.08-1.32; P = 0.001; pooled across all studies allelic OR, 1.18; 95% CI, 1.11-1.26; P = 2 x 10(-7). We found suggestive evidence of a parent-of-origin effect at the ABO locus by analyzing the family trios. Non-O haplotypes inherited from mothers, but not fathers, are significantly associated with severe malaria (likelihood ratio test of Weinberg, P = 0.046). Finally, we used HapMap data to demonstrate a region of low F(ST) (-0.001) between the three main HapMap population groups across the ABO locus, an outlier in the empirical distribution of F(ST) across chromosome 9 (approximately 99.5-99.9th centile). This low F(ST) region may be a signal of long-standing balancing selection at the ABO locus, caused by multiple infectious pathogens including P. falciparum.

Variation in clinical practice: forests and trees revisited.

Science.gov (United States)

Wallis, Christopher J D; Naylor, C David; Detsky, Allan S

2017-09-01

Variations in clinical practice are commonly viewed as a sign of uneven quality of care and attributed to provider self-interest. However, patient preferences, physician practice patterns, and diagnostic and therapeutic uncertainty also cause variations. Greater attention to both doctor-patient interactions and limits to the available evidence might enable more effective assessment and improvement of health-care quality.

Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC).

Science.gov (United States)

Jim, Heather S L; Lin, Hui-Yi; Tyrer, Jonathan P; Lawrenson, Kate; Dennis, Joe; Chornokur, Ganna; Chen, Zhihua; Chen, Ann Y; Permuth-Wey, Jennifer; Aben, Katja Kh; Anton-Culver, Hoda; Antonenkova, Natalia; Bruinsma, Fiona; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A; Brooks-Wilson, Angela; Bunker, Clareann H; Butzow, Ralf; Campbell, Ian G; Carty, Karen; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; du Bois, Andreas; Despierre, Evelyn; Sieh, Weiva; Doherty, Jennifer A; Dörk, Thilo; Dürst, Matthias; Easton, Douglas F; Eccles, Diana M; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goodman, Marc T; Gronwald, Jacek; Harter, Philipp; Hasmad, Hanis N; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Claus K; Hogdall, Estrid; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kellar, Melissa; Kiemeney, Lambertus A; Krakstad, Camilla; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Vierkant, Robert A; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lim, Boon Kiong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F A G; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Ian; Menon, Usha; Milne, Roger L; Modugno, Francesmary; Thomsen, Lotte; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Eilber, Ursula; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Palmieri Weber, Rachel; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Pelttari, Liisa M; Pike, Malcolm C; Poole, Elizabeth M; Schernhammer, Eva; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Song, Honglin; Southey, Melissa C; Spiewankiewicz, Beata; Sucheston-Campbell, Lara; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Tangen, Ingvild L; Tworoger, Shelley S; van Altena, Anne M; Vergote, Ignace; Walsh, Christine S; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Wu, Anna H; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Amankwah, Ernest; Berchuck, Andrew; Schildkraut, Joellen M; Kelemen, Linda E; Ramus, Susan J; Monteiro, Alvaro N A; Goode, Ellen L; Narod, Steven A; Gayther, Simon A; Pharoah, Paul D P; Sellers, Thomas A; Phelan, Catherine M

Disruption in circadian gene expression, whether due to genetic variation or environmental factors (e.g., light at night, shiftwork), is associated with increased incidence of breast, prostate, gastrointestinal and hematologic cancers and gliomas. Circadian genes are highly expressed in the ovaries where they regulate ovulation; circadian disruption is associated with several ovarian cancer risk factors (e.g., endometriosis). However, no studies have examined variation in germline circadian genes as predictors of ovarian cancer risk and invasiveness. The goal of the current study was to examine single nucleotide polymorphisms (SNPs) in circadian genes BMAL1, CRY2, CSNK1E, NPAS2, PER3, REV1 and TIMELESS and downstream transcription factors KLF10 and SENP3 as predictors of risk of epithelial ovarian cancer (EOC) and histopathologic subtypes. The study included a test set of 3,761 EOC cases and 2,722 controls and a validation set of 44,308 samples including 18,174 (10,316 serous) cases and 26,134 controls from 43 studies participating in the Ovarian Cancer Association Consortium (OCAC). Analysis of genotype data from 36 genotyped SNPs and 4600 imputed SNPs indicated that the most significant association was rs117104877 in BMAL1 (OR = 0.79, 95% CI = 0.68-0.90, p = 5.59 × 10 -4 ]. Functional analysis revealed a significant down regulation of BMAL1 expression following cMYC overexpression and increasing transformation in ovarian surface epithelial (OSE) cells as well as alternative splicing of BMAL1 exons in ovarian and granulosa cells. These results suggest that variation in circadian genes, and specifically BMAL1 , may be associated with risk of ovarian cancer, likely through disruption of hormonal pathways.

RAVEN AND THE CENTER OF MAFFEI 1: MULTI-OBJECT ADAPTIVE OPTICS OBSERVATIONS OF THE CENTER OF A NEARBY ELLIPTICAL GALAXY AND THE DETECTION OF AN INTERMEDIATE AGE POPULATION

Energy Technology Data Exchange (ETDEWEB)

Davidge, T. J.; Andersen, D. R. [Dominion Astrophysical Observatory, National Research Council of Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Lardière, O.; Bradley, C.; Blain, C. [Department of Mechanical Engineering, University of Victoria, Victoria, BC V8W 3P2 (Canada); Oya, S. [Subaru Telescope, National Optical Observatory of Japan Hilo, HI 96720 (United States); Akiyama, M.; Ono, Y. H., E-mail: tim.davidge@nrc.ca, E-mail: david.andersen@nrc.ca, E-mail: lardiere@uvic.ca, E-mail: cbr@uvic.ca, E-mail: celia.blain@gmail.com, E-mail: oya@subaru.naoj.org, E-mail: akiyama@astr.tohoku.ac.jp, E-mail: yo-2007@astr.tohoku.ac.jp [Astronomical Institute, Tohoku University 6–3 Aramaki, Aoba-ku, Sedai, 980-8578 Japan (Japan)

2015-10-01

Near-infrared (NIR) spectra that have an angular resolution of ∼0.15 arcsec are used to examine the stellar content of the central regions of the nearby elliptical galaxy Maffei 1. The spectra were recorded at the Subaru Telescope, with wavefront distortions corrected by the RAVEN Multi-object Adaptive Optics science demonstrator. The Ballick–Ramsey C{sub 2} absorption bandhead near 1.76 μm is detected, and models in which ∼10%–20% of the light near 1.8 μm originates from stars of spectral type C5 reproduce the depth of this feature. Archival NIR and mid-infrared images are also used to probe the structural and photometric properties of the galaxy. Comparisons with models suggest that an intermediate age population dominates the spectral energy distribution between 1 and 5 μm near the galaxy center. This is consistent not only with the presence of C stars, but also with the large Hβ index that has been measured previously for Maffei 1. The J − K color is more or less constant within 15 arcsec of the galaxy center, suggesting that the brightest red stars are well-mixed in this area.

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

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Yanliang Jiang

Full Text Available The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

Science.gov (United States)

Jiang, Yanliang; Zhang, Songhao; Xu, Jian; Feng, Jianxin; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

2014-01-01

The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

NARCIS (Netherlands)

Armour, J.A.; Palla, R.; Zeeuwen, P.L.J.M.; Heijer, M. den; Schalkwijk, J.; Hollox, E.J.

2007-01-01

Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and

Anatomic variations of the branches of the aortic arch in a Peruvian population.

Science.gov (United States)

Huapaya, Julio Arturo; Chávez-Trujillo, Kristhy; Trelles, Miguel; Dueñas Carbajal, Roy; Ferrandiz Espadin, Renato

2015-07-31

Previous publications from two countries in South America found one anatomical variation not previously reported in the rest of the world, which in turn give some clues with regard to a racial difference. The objective of the present study is to describe variations in the anatomical distribution of the branches of the aortic arch in a Peruvian population. To describe variations in the anatomical distribution of the branches of the aortic arch in a Peruvian population. A descriptive study of patients who underwent a tomography angiography of the aorta was performed. We analyzed the reports that showed the description of the variations of the branches of the aortic arch based on the eight types currently described in the literature. From 361 analyzed reports, 282 patients (78.12%) had a normal aortic arch configuration (type I; aortic arch gives rise to the brachiocephalic trunk, left common carotid and left subclavian arteries); followed by type II (left common carotid artery as a branch of the aorta) with 41 patients (11.36%); and type IX (common ostium for the brachiocephalic trunk and the left common carotid artery) with 25 patients (6.93%). The latter and two other types are new variations. Aortic Arch Type I, Type II and Type IX were the most frequent variations in this Peruvian study. Additionally, we also found two more new types that have not been previously described in the literature. Further investigation regarding these variations is needed in order to assess a racial factor in South America and possible relationships with clinical or surgical events.

Common scab and its control in seed-potato crops

NARCIS (Netherlands)

Labruyere, R.E.

1971-01-01

In the Netherlands common scab of the potato is usually caused by Streptomyces scabies (Thaxter) Waksman et Henrici, following Corbaz's description, and rarely by other Streptomyces species. Variation in morphological and other characteristics

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages.

Directory of Open Access Journals (Sweden)

Shelly C Wu

Full Text Available Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.. Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups-the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas than on northern turtles (where mean abundance/state was > 10%. L. cf. mutica was the most abundant species (40% on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts.

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages

Science.gov (United States)

Wu, Shelly C.; Bergey, Elizabeth A.

2017-01-01

Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina) across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.). Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups–the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas) than on northern turtles (where mean abundance/state was > 10%). L. cf. mutica was the most abundant species (40%) on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts. PMID:28192469

Acromioclavicular joint: Normal variation and the diagnosis of dislocation

Energy Technology Data Exchange (ETDEWEB)

Keats, T.E.; Pope, T.L. Jr.

1988-04-01

Acromioclavicular separation is a common traumatic injury. Diagnosis rests on clinical and radiographic findings. However, normal variation in the alignment of the acromioclavicular joint may make the roentgen diagnosis more difficult. We stress the variations of normal alignment at the acromioclavicular joint and offer suggestions for avoiding pitfalls in this clinical situation.

(Ln-bar, g)-spaces. Variation operator

International Nuclear Information System (INIS)

Manoff, S.; Dimitrov, B.

1998-01-01

A variation operator is determined over (L n bar, g)-spaces as a linear differential operator, acting on tensor fields in a given basis. Its commutation relations with the Lie differential operator, with the covariant differential operator and with the contraction operator are imposed. The corollaries from using the different commutation relations in a Lagrangian formalism are found and two types of variation methods are distinguished: the common (canonical) method of Lagrangians with partial derivatives (MLPD) and the method of Lagrangians with covariant derivatives (MLCD)

Variation in behaviour and growth of common sole : genetic and environmental influences

NARCIS (Netherlands)

Mas Muñoz, J.

2013-01-01

Common sole (Solea solea) has a high potential for commercial aquaculture because of its consumer popularity and high market values in Europe. However, a major economic constraint for the culture of sole is its slow and variable growth. The aim of this thesis was to investigate: 1) the

Common mental disorders and the built environment in Santiago, Chile.

Science.gov (United States)

Araya, Ricardo; Montgomery, Alan; Rojas, Graciela; Fritsch, Rosemarie; Solis, Jaime; Signorelli, Andres; Lewis, Glyn

2007-05-01

There is growing research interest in the influence of the built environment on mental disorders. To estimate the variation in the prevalence of common mental disorders attributable to individuals and the built environment of geographical sectors where they live. A sample of 3870 adults (response rate 90%) clustered in 248 geographical sectors participated in a household cross-sectional survey in Santiago, Chile. Independently rated contextual measures of the built environment were obtained. The Clinical Interview Schedule was used to estimate the prevalence of common mental disorders. There was a significant association between the quality of the built environment of small geographical sectors and the presence of common mental disorders among its residents. The better the quality of the built environment, the lower the scores for psychiatric symptoms; however, only a small proportion of the variation in common mental disorder existed at sector level, after adjusting for individual factors. Findings from our study, using a contextual assessment of the quality of the built environment and multilevel modelling in the analysis, suggest these associations may be more marked in non-Western settings with more homogeneous geographical sectors.

Procyanidin content and variation in some commonly consumed foods.

Science.gov (United States)

Hammerstone, J F; Lazarus, S A; Schmitz, H H

2000-08-01

Procyanidins are a subclass of flavonoids found in commonly consumed foods that have attracted increasing attention due to their potential health benefits. However, little is known regarding their dietary intake levels because detailed quantitative information on the procyanidin profiles present in many food products is lacking. Therefore, the procyanidin content of red wine, chocolate, cranberry juice and four varieties of apples has been determined. On average, chocolate and apples contained the largest procyanidin content per serving (164.7 and 147.1 mg, respectively) compared with red wine and cranberry juice (22.0 and 31.9 mg, respectively). However, the procyanidin content varied greatly between apple samples (12.3-252.4 mg/serving) with the highest amounts on average observed for the Red Delicious (207.7 mg/serving) and Granny Smith (183.3 mg/serving) varieties and the lowest amounts in the Golden Delicious (92.5 mg/serving) and McIntosh (105.0 mg/serving) varieties. The compositional data reported herein are important for the initial understanding of which foods contribute most to the dietary intake of procyanidins and may be used to compile a database necessary to infer epidemiological relationships to health and disease.

Automated quantification of pulmonary emphysema from computed tomography scans: comparison of variation and correlation of common measures in a large cohort

Science.gov (United States)

Keller, Brad M.; Reeves, Anthony P.; Yankelevitz, David F.; Henschke, Claudia I.

2010-03-01

The purpose of this work was to retrospectively investigate the variation of standard indices of pulmonary emphysema from helical computed tomographic (CT) scans as related to inspiration differences over a 1 year interval and determine the strength of the relationship between these measures in a large cohort. 626 patients that had 2 scans taken at an interval of 9 months to 15 months (μ: 381 days, σ: 31 days) were selected for this work. All scans were acquired at a 1.25mm slice thickness using a low dose protocol. For each scan, the emphysema index (EI), fractal dimension (FD), mean lung density (MLD), and 15th percentile of the histogram (HIST) were computed. The absolute and relative changes for each measure were computed and the empirical 95% confidence interval was reported both in non-normalized and normalized scales. Spearman correlation coefficients are computed between the relative change in each measure and relative change in inspiration between each scan-pair, as well as between each pair-wise combination of the four measures. EI varied on a range of -10.5 to 10.5 on a non-normalized scale and -15 to 15 on a normalized scale, with FD and MLD showing slightly larger but comparable spreads, and HIST having a much larger variation. MLD was found to show the strongest correlation to inspiration change (r=0.85, pemphysema index and fractal dimension have the least variability overall of the commonly used measures of emphysema and that they offer the most unique quantification of emphysema relative to each other.

Status on the Development of a Modeling and Simulation Framework for the Economic Assessment of Nuclear Hybrid Energy

International Nuclear Information System (INIS)

Epiney, Aaron Simon; Chen, Jun; Rabiti, Cristian

2016-01-01

Continued effort to design and build a modeling and simulation framework to assess the economic viability of Nuclear Hybrid Energy Systems (NHES) was undertaken in fiscal year (FY) 2016. The purpose of this report is to document the various tasks associated with the development of such a framework and to provide a status of their progress. Several tasks have been accomplished. First, a synthetic time history generator has been developed in RAVEN, which consists of Fourier series and autoregressive moving average model. The former is used to capture the seasonal trend in historical data, while the latter is to characterize the autocorrelation in residue time series (e.g., measurements with seasonal trends subtracted). As demonstration, both synthetic wind speed and grid demand are generated, showing matching statistics with database. In order to build a design and operations optimizer in RAVEN, a new type of sampler has been developed with highly object-oriented design. In particular, simultaneous perturbation stochastic approximation algorithm is implemented. The optimizer is capable to drive the model to optimize a scalar objective function without constraint in the input space, while the constraints handling is a work in progress and will be implemented to improve the optimization capability. Furthermore, a simplified cash flow model of the performance of an NHES in the electric market has been developed in Python and used as external model in RAVEN to confirm expectations on the analysis capability of RAVEN to provide insight into system economics and to test the capability of RAVEN to identify limit surfaces. Finally, an example calculation is performed that shows the integration and proper data passing in RAVEN of the synthetic time history generator, the cash flow model and the optimizer. It has been shown that the developed Python models external to RAVEN are able to communicate with RAVEN and each other through the newly developed RAVEN capability called “EnsembleModel”.

Status on the Development of a Modeling and Simulation Framework for the Economic Assessment of Nuclear Hybrid Energy

Energy Technology Data Exchange (ETDEWEB)

Epiney, Aaron Simon [Idaho National Lab. (INL), Idaho Falls, ID (United States); Chen, Jun [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-09-01

Continued effort to design and build a modeling and simulation framework to assess the economic viability of Nuclear Hybrid Energy Systems (NHES) was undertaken in fiscal year (FY) 2016. The purpose of this report is to document the various tasks associated with the development of such a framework and to provide a status of their progress. Several tasks have been accomplished. First, a synthetic time history generator has been developed in RAVEN, which consists of Fourier series and autoregressive moving average model. The former is used to capture the seasonal trend in historical data, while the latter is to characterize the autocorrelation in residue time series (e.g., measurements with seasonal trends subtracted). As demonstration, both synthetic wind speed and grid demand are generated, showing matching statistics with database. In order to build a design and operations optimizer in RAVEN, a new type of sampler has been developed with highly object-oriented design. In particular, simultaneous perturbation stochastic approximation algorithm is implemented. The optimizer is capable to drive the model to optimize a scalar objective function without constraint in the input space, while the constraints handling is a work in progress and will be implemented to improve the optimization capability. Furthermore, a simplified cash flow model of the performance of an NHES in the electric market has been developed in Python and used as external model in RAVEN to confirm expectations on the analysis capability of RAVEN to provide insight into system economics and to test the capability of RAVEN to identify limit surfaces. Finally, an example calculation is performed that shows the integration and proper data passing in RAVEN of the synthetic time history generator, the cash flow model and the optimizer. It has been shown that the developed Python models external to RAVEN are able to communicate with RAVEN and each other through the newly developed RAVEN capability called “EnsembleModel”.

Child Development and Structural Variation in the Human Genome

Science.gov (United States)

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Status on the Development of a Modeling and Simulation Framework for the Economic Assessment of Nuclear Hybrid Energy Systems

Energy Technology Data Exchange (ETDEWEB)

Bragg-Sitton, Shannon Michelle [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert Arthur [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kim, Jong Suk [Idaho National Lab. (INL), Idaho Falls, ID (United States); Deason, Wesley Ray [Idaho National Lab. (INL), Idaho Falls, ID (United States); Boardman, Richard Doin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Garcia, Humberto E. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2015-09-01

An effort to design and build a modeling and simulation framework to assess the economic viability of Nuclear Hybrid Energy Systems (NHES) was undertaken in fiscal year 2015 (FY15). The purpose of this report is to document the various tasks associated with the development of such a framework and to provide a status on its progress. Several tasks have been accomplished. First, starting from a simulation strategy, a rigorous mathematical formulation has been achieved in which the economic optimization of a Nuclear Hybrid Energy System is presented as a constrained robust (under uncertainty) optimization problem. Some possible algorithms for the solution of the optimization problem are presented. A variation of the Simultaneous Perturbation Stochastic Approximation algorithm has been implemented in RAVEN and preliminary tests have been performed. The development of the software infrastructure to support the simulation of the whole NHES has also moved forward. The coupling between RAVEN and an implementation of the Modelica language (OpenModelica) has been implemented, migrated under several operating systems and tested using an adapted model of a desalination plant. In particular, this exercise was focused on testing the coupling of the different code systems; testing parallel, computationally expensive simulations on the INL cluster; and providing a proof of concept for the possibility of using surrogate models to represent the different NHES subsystems. Another important step was the porting of the RAVEN code under the Windows™ operating system. This accomplishment makes RAVEN compatible with the development environment that is being used for dynamic simulation of NHES components. A very simplified model of a NHES on the electric market has been built in RAVEN to confirm expectations on the analysis capability of RAVEN to provide insight into system economics and to test the capability of RAVEN to identify limit surfaces even for stochastic constraints. This

Mini-review: Strategies for Variation and Evolution of Bacterial Antigens

Science.gov (United States)

Foley, Janet

2015-01-01

Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evolution and numerous commonalities reflecting considerations of natural selection and biochemical restraints. Unlike in viruses, mechanisms of antigenic variation in most bacteria involve larger DNA movement such as gene conversion or DNA rearrangement, although some antigens vary due to point mutations or modified transcriptional regulation. The convergent evolution that promotes antigenic variation integrates various evolutionary forces: these include mutations underlying variant production; drift which could remove alleles especially early in infection or during life history phases in arthropod vectors (when the bacterial population size goes through a bottleneck); selection not only for any particular variant but also for the mechanism for the production of variants (i.e., selection for mutability); and overcoming negative selection against variant production. This review highlights the complexities of drivers of antigenic variation, in particular extending evaluation beyond the commonly cited theory of immune evasion. A deeper understanding of the diversity of purpose and mechanisms of antigenic variation in bacteria will contribute to greater insight into bacterial pathogenesis, ecology and coevolution with hosts. PMID:26288700

Association of common genetic variants with human skin color variation in Indian populations.

Science.gov (United States)

Sarkar, Anujit; Nandineni, Madhusudan R

2018-01-01

Human skin color is one of the most conspicuously variable physical traits that has attracted the attention of physical anthropologists, social scientists and human geneticists. Although several studies have established the underlying genes and their variants affecting human skin color, they were mostly confined to Europeans and Africans and similar studies in Indian populations have been scanty. Studying the association between candidate genetic variants and skin color will help to validate previous findings and to better understand the molecular mechanism of skin color variation. In this study, 22 candidate SNPs from 12 genes were tested for association with skin color in 299 unrelated samples sourced from nine geographical locations in India. Our study establishes the association of 9 SNPs with the phenotype in Indian populations and could explain ∼31% of the variance in skin color. Haplotype analysis of chromosome 15 revealed a significant association of alleles G, A and C of SNPs rs1426654, rs11070627, and rs12913316, respectively, to the phenotype, and accounted for 17% of the variance. Latitude of the sampling location was also a significant factor, contributing to ∼19% of the variation observed in the samples. These observations support the findings that rs1426654 and rs4775730 located in SLC24A5, and rs11070627 and rs12913316 located in MYEF2 and CTXN2 genes respectively, are major contributors toward skin pigmentation and would aid in further unraveling the genotype-phenotype association in Indian populations. These findings can be utilized in forensic DNA applications for criminal investigations. © 2017 Wiley Periodicals, Inc.

Sex reduces genetic variation: a multidisciplinary review.

Science.gov (United States)

Gorelick, Root; Heng, Henry H Q

2011-04-01

For over a century, the paradigm has been that sex invariably increases genetic variation, despite many renowned biologists asserting that sex decreases most genetic variation. Sex is usually perceived as the source of additive genetic variance that drives eukaryotic evolution vis-à-vis adaptation and Fisher's fundamental theorem. However, evidence for sex decreasing genetic variation appears in ecology, paleontology, population genetics, and cancer biology. The common thread among many of these disciplines is that sex acts like a coarse filter, weeding out major changes, such as chromosomal rearrangements (that are almost always deleterious), but letting minor variation, such as changes at the nucleotide or gene level (that are often neutral), flow through the sexual sieve. Sex acts as a constraint on genomic and epigenetic variation, thereby limiting adaptive evolution. The diverse reasons for sex reducing genetic variation (especially at the genome level) and slowing down evolution may provide a sufficient benefit to offset the famed costs of sex. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Reavistamientos de Corvus corax en las tierras altas de Nicaragua

Science.gov (United States)

Francisco J. Muñoz; Wayne J. Arendt; Marvin A. Tórrez; Liliana Chavarría; Arlen Pinell.

2009-01-01

The common raven (Corvus corax) is one of the most widespread naturally occurring birds in the world. Thus, from a conservation and management perspective, it is of minimum concern. Yet, in Nicaragua, observations of this species are few and not well documented. After a lapse of almost 40 years since the last written report, we describe recent sightings from the...

Improved determination of hadron matrix elements using the variational method

International Nuclear Information System (INIS)

Dragos, J.; Kamleh, W.; Leinweber, D.B.; Zanotti, J.M.; Rakow, P.E.L.; Young, R.D.; Adelaide Univ.

2015-11-01

The extraction of hadron form factors in lattice QCD using the standard two- and three-point correlator functions has its limitations. One of the most commonly studied sources of systematic error is excited state contamination, which occurs when correlators are contaminated with results from higher energy excitations. We apply the variational method to calculate the axial vector current g A and compare the results to the more commonly used summation and two-exponential fit methods. The results demonstrate that the variational approach offers a more efficient and robust method for the determination of nucleon matrix elements.

State Variation in Medicaid Reimbursements for Orthopaedic Surgery.

Science.gov (United States)

Lalezari, Ramin M; Pozen, Alexis; Dy, Christopher J

2018-02-07

Medicaid reimbursements are determined by each state and are subject to variability. We sought to quantify this variation for commonly performed inpatient orthopaedic procedures. The 10 most commonly performed inpatient orthopaedic procedures, as ranked by the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample, were identified for study. Medicaid reimbursement amounts for those procedures were benchmarked to state Medicare reimbursement amounts in 3 ways: (1) ratio, (2) dollar difference, and (3) dollar difference divided by the relative value unit (RVU) amount. Variability was quantified by determining the range and coefficient of variation for those reimbursement amounts. The range of variability of Medicaid reimbursements among states exceeded $1,500 for all 10 procedures. The coefficients of variation ranged from 0.32 (hip hemiarthroplasty) to 0.57 (posterior or posterolateral lumbar interbody arthrodesis) (a higher coefficient indicates greater variability), compared with 0.07 for Medicare reimbursements for all 10 procedures. Adjusted as a dollar difference between Medicaid and Medicare per RVU, the median values ranged from -$8/RVU (total knee arthroplasty) to -$17/RVU (open reduction and internal fixation of the femur). Variability of Medicaid reimbursement for inpatient orthopaedic procedures among states is substantial. This variation becomes especially remarkable given recent policy shifts toward focusing reimbursements on value.

The acromioclavicular joint: Normal variation and the diagnosis of dislocation

International Nuclear Information System (INIS)

Keats, T.E.; Pope, T.L. Jr.

1988-01-01

Acromioclavicular separation is a common traumatic injury. Diagnosis rests on clinical and radiographic findings. However, normal variation in the alignment of the acromioclavicular joint may make the roentgen diagnosis more difficult. We stress the variations of normal alignment at the acromioclavicular joint and offer suggestions for avoiding pitfalls in this clinical situation. (orig.)

A New Approximation Method for Solving Variational Inequalities and Fixed Points of Nonexpansive Mappings

Directory of Open Access Journals (Sweden)

Klin-eam Chakkrid

2009-01-01

Full Text Available Abstract A new approximation method for solving variational inequalities and fixed points of nonexpansive mappings is introduced and studied. We prove strong convergence theorem of the new iterative scheme to a common element of the set of fixed points of nonexpansive mapping and the set of solutions of the variational inequality for the inverse-strongly monotone mapping which solves some variational inequalities. Moreover, we apply our main result to obtain strong convergence to a common fixed point of nonexpansive mapping and strictly pseudocontractive mapping in a Hilbert space.

Genetic Variation in Cardiomyopathy and Cardiovascular Disorders.

Science.gov (United States)

McNally, Elizabeth M; Puckelwartz, Megan J

2015-01-01

With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.

Coarse Grained Exponential Variational Autoencoders

KAUST Repository

Sun, Ke

2017-02-25

Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually much more sophisticated. To break this limitation and apply arbitrary parametric distribution during inference, this paper derives a \\\\emph{semi-continuous} latent representation, which approximates a continuous density up to a prescribed precision, and is much easier to analyze than its continuous counterpart because it is fundamentally discrete. We showcase the proposition by applying polynomial exponential family distributions as the posterior, which are universal probability density function generators. Our experimental results show consistent improvements over commonly used VAE models.

Genetic Parameters of Common Wheat in Nepal

OpenAIRE

Bal Krishna Joshi; Dhruba Bahadur Thapa; Madan Raj Bhatta

2015-01-01

Knowledge on variation within traits and their genetics are prerequisites in crop improvement program. Thus, in present paper we aimed to estimate genetic and environmental indices of common wheat genotypes. For the purpose, eight quantitative traits were measured from 30 wheat genotypes, which were in randomized complete block design with 3 replicates. Components of variance and covariance were estimated along with heritability, genetic gain, realized heritability, coheritability and correla...

Only 7% of the variation in feed efficiency in veal calves can be predicted from variation in feeding motivation, digestion, metabolism, immunology, and behavioral traits in early life

NARCIS (Netherlands)

Gilbert, M.S.; Borne, van den J.J.G.C.; Reenen, van C.G.; Gerrits, W.J.J.

2017-01-01

High interindividual variation in growth performance is commonly observed in veal calf production and appears to depend on milk replacer (MR) composition. Our first objective was to examine whether variation in growth performance in healthy veal calves can be predicted from early life

Nucleon matrix elements using the variational method in lattice QCD

International Nuclear Information System (INIS)

Dragos, J.; Kamleh, W.; Leinweber, D.B.; Zanotti, J.M.; Rakow, P.E.L.; Young, R.D.; Adelaide Univ., SA

2016-06-01

The extraction of hadron matrix elements in lattice QCD using the standard two- and threepoint correlator functions demands careful attention to systematic uncertainties. One of the most commonly studied sources of systematic error is contamination from excited states. We apply the variational method to calculate the axial vector current g_A, the scalar current g_S and the quark momentum fraction left angle x right angle of the nucleon and we compare the results to the more commonly used summation and two-exponential fit methods. The results demonstrate that the variational approach offers a more efficient and robust method for the determination of nucleon matrix elements.

Uptake of recommended common reference intervals for chemical pathology in Australia.

Science.gov (United States)

Jones, Graham Rd; Koetsier, Sabrina

2017-05-01

Background Reference intervals are a vital part of reporting numerical pathology results. It is known, however, that variation in reference intervals between laboratories is common, even when analytical methods support common reference intervals. In response to this, in Australia, the Australasian Association of Clinical Biochemists together with the Royal College of Pathologists of Australasia published in 2014 a set of recommended common reference intervals for 11 common serum analytes (sodium, potassium, chloride, bicarbonate, creatinine male, creatinine female, calcium, calcium adjusted for albumin, phosphate, magnesium, lactate dehydrogenase, alkaline phosphatase and total protein). Methods Uptake of recommended common reference intervals in Australian laboratories was assessed using data from four annual cycles of the RCPAQAP reference intervals external quality assurance programme. Results Over three years, from 2013 to 2016, the use of the recommended upper and lower reference limits has increased from 40% to 83%. Nearly half of the intervals in use by enrolled laboratories in 2016 have been changed in this time period, indicating an active response to the guidelines. Conclusions These data support the activities of the Australasian Association of Clinical Biochemists and Royal College of Pathologists of Australasia in demonstrating a change in laboratory behaviour to reduce unnecessary variation in reference intervals and thus provide a consistent message to doctor and patients irrespective of the laboratory used.

A global reference for human genetic variation

DEFF Research Database (Denmark)

Auton, Adam; Abecasis, Goncalo R.; M. Altshuler, David

2015-01-01

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals ...

Common-image gathers in the offset domain from reverse-time migration

KAUST Repository

Zhan, Ge; Zhang, Minyu

2014-01-01

Kirchhoff migration is flexible to output common-image gathers (CIGs) in the offset domain by imaging data with different offsets separately. These CIGs supply important information for velocity model updates and amplitude-variation-with-offset (AVO

Common cause failure rate estimates for diesel generators in nuclear power plants

International Nuclear Information System (INIS)

Steverson, J.A.; Atwood, C.L.

1982-01-01

Common cause fault rates for diesel generators in nuclear power plants are estimated, using Licensee Event Reports for the years 1976 through 1978. The binomial failure rate method, used for obtaining the estimates, is briefly explained. Issues discussed include correct classification of common cause events, grouping of the events into homogeneous data subsets, and dealing with plant-to-plant variation

Antidepressant prescribing in five European countries: application of common methods to assess the variation in prevalence.

NARCIS (Netherlands)

Abbing-Karahagopian, V.; Huerta, C.; Souverein, P.C.; Abajo, F. de; Leufkens, H.G.M.; Slattery, J.; Alvarez, Y.; Montserrat, M.; Gill, M.; Hesse, U.; Requena, G.; Vries, F. de; Rottenkolber, M.; Schmiedl, S.; Reynolds, R.; Schlinger, R.; Groot, M. de; Klungel, O.H.; Staa, T.P. van; Dijk, L. van; Egberts, A.C.G.; Gardarsdottir, H.; Bruin, M.L. de

2013-01-01

Background: Drug utilization studies have applied different methods on various data types to describe medication use which may hamper comparisons across populations. Objectives: The aim of this study was to describe the variation in the prevalence of antidepressant prescribing, applying standard

Epigenetic variation during the adult lifespan

DEFF Research Database (Denmark)

Talens, Rudolf P; Christensen, Kaare; Putter, Hein

2012-01-01

The accumulation of epigenetic changes was proposed to contribute to the age-related increase in the risk of most common diseases. In this study on 230 monozygotic twin pairs (MZ pairs), aged 18-89 years, we investigated the occurrence of epigenetic changes over the adult lifespan. Using mass...... individuals, ranging from 1.2-fold larger at ABCA1 (P = 0.010) to 1.6-fold larger at INS (P = 3.7 × 10(-07) ). Similarly, there was more within-MZ-pair discordance in old as compared with young MZ pairs, except for GNASAS, ranging from an 8% increase in discordance each decade at CRH (P = 8.9 × 10...... spectrometry, we investigated variation in global (LINE1) DNA methylation and in DNA methylation at INS, KCNQ1OT1, IGF2, GNASAS, ABCA1, LEP, and CRH, candidate loci for common diseases. Except for KCNQ1OT1, interindividual variation in locus-specific DNA methylation was larger in old individuals than in young...

Annual variation in the composition of major nutrients of the common starfish (Asterias Rubens)

DEFF Research Database (Denmark)

van der Heide, Marleen Elise; Møller, Lene Friis; Petersen, Jens Kjerulf

2018-01-01

To study the annual variation in the composition of nutrients relevant to pig and poultry feeding, monthly samples of starfish (Asterias Rubens) were taken in Denmark. The effect of different locations and starfish sizes was also assessed. Crude protein (CP) and phosphorus were high from February...... and calcium levels. The most profound differences between locations were observed in May. The seasonal pattern in chemical composition seemed related to spawning and gonadal developments. Large and medium sized starfish caught between February and May will be most suitable for pig and poultry feed....

Pulse-to-pulse variations in accreting X-ray pulsars

Directory of Open Access Journals (Sweden)

Kretschmar Peter

2014-01-01

Full Text Available In most accreting X-ray pulsars, the periodic signal is very clear and easily shows up as soon as data covering sufficient pulse periods (a few ten are available. The mean pulse profile is often quite typical for a given source and with minor variations repeated and recognisable across observations done years or even decades apart. At the time scale of individual pulses, significant pulse-to-pulse variations are commonly observed. While at low energies some of these variations might be explained by absorption, in the hard X-rays they will reflect changes in the accretion and subsequent emission. The amount of these variations appears to be quite different between sources and contains information about the surrounding material as well ass possibly interactions at the magnetosphere. We investigate such variations for a sample of well-known sources.

Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa

Science.gov (United States)

Huckins, L M; Hatzikotoulas, K; Southam, L; Thornton, L M; Steinberg, J; Aguilera-McKay, F; Treasure, J; Schmidt, U; Gunasinghe, C; Romero, A; Curtis, C; Rhodes, D; Moens, J; Kalsi, G; Dempster, D; Leung, R; Keohane, A; Burghardt, R; Ehrlich, S; Hebebrand, J; Hinney, A; Ludolph, A; Walton, E; Deloukas, P; Hofman, A; Palotie, A; Palta, P; van Rooij, F J A; Stirrups, K; Adan, R; Boni, C; Cone, R; Dedoussis, G; van Furth, E; Gonidakis, F; Gorwood, P; Hudson, J; Kaprio, J; Kas, M; Keski-Rahonen, A; Kiezebrink, K; Knudsen, G-P; Slof-Op 't Landt, M C T; Maj, M; Monteleone, A M; Monteleone, P; Raevuori, A H; Reichborn-Kjennerud, T; Tozzi, F; Tsitsika, A; van Elburg, A; Adan, R A H; Alfredsson, L; Ando, T; Andreassen, O A; Aschauer, H; Baker, J H; Barrett, J C; Bencko, V; Bergen, A W; Berrettini, W H; Birgegard, A; Boni, C; Boraska Perica, V; Brandt, H; Breen, G; Bulik, C M; Carlberg, L; Cassina, M; Cichon, S; Clementi, M; Cohen-Woods, S; Coleman, J; Cone, R D; Courtet, P; Crawford, S; Crow, S; Crowley, J; Danner, U N; Davis, O S P; de Zwaan, M; Dedoussis, G; Degortes, D; DeSocio, J E; Dick, D M; Dikeos, D; Dina, C; Ding, B; Dmitrzak-Weglarz, M; Docampo, E; Duncan, L; Egberts, K; Ehrlich, S; Escaramís, G; Esko, T; Espeseth, T; Estivill, X; Favaro, A; Fernández-Aranda, F; Fichter, M M; Finan, C; Fischer, K; Floyd, J A B; Foretova, L; Forzan, M; Franklin, C S; Gallinger, S; Gambaro, G; Gaspar, H A; Giegling, I; Gonidakis, F; Gorwood, P; Gratacos, M; Guillaume, S; Guo, Y; Hakonarson, H; Halmi, K A; Hatzikotoulas, K; Hauser, J; Hebebrand, J; Helder, S; Herms, S; Herpertz-Dahlmann, B; Herzog, W; Hilliard, C E; Hinney, A; Hübel, C; Huckins, L M; Hudson, J I; Huemer, J; Inoko, H; Janout, V; Jiménez-Murcia, S; Johnson, C; Julià, A; Juréus, A; Kalsi, G; Kaminska, D; Kaplan, A S; Kaprio, J; Karhunen, L; Karwautz, A; Kas, M J H; Kaye, W; Kennedy, J L; Keski-Rahkonen, A; Kiezebrink, K; Klareskog, L; Klump, K L; Knudsen, G P S; Koeleman, B P C; Koubek, D; La Via, M C; Landén, M; Le Hellard, S; Levitan, R D; Li, D; Lichtenstein, P; Lilenfeld, L; Lissowska, J; Lundervold, A; Magistretti, P; Maj, M; Mannik, K; Marsal, S; Martin, N; Mattingsdal, M; McDevitt, S; McGuffin, P; Merl, E; Metspalu, A; Meulenbelt, I; Micali, N; Mitchell, J; Mitchell, K; Monteleone, P; Monteleone, A M; Mortensen, P; Munn-Chernoff, M A; Navratilova, M; Nilsson, I; Norring, C; Ntalla, I; Ophoff, R A; O'Toole, J K; Palotie, A; Pante, J; Papezova, H; Pinto, D; Rabionet, R; Raevuori, A; Rajewski, A; Ramoz, N; Rayner, N W; Reichborn-Kjennerud, T; Ripatti, S; Roberts, M; Rotondo, A; Rujescu, D; Rybakowski, F; Santonastaso, P; Scherag, A; Scherer, S W; Schmidt, U; Schork, N J; Schosser, A; Slachtova, L; Sladek, R; Slagboom, P E; Slof-Op 't Landt, M C T; Slopien, A; Soranzo, N; Southam, L; Steen, V M; Strengman, E; Strober, M; Sullivan, P F; Szatkiewicz, J P; Szeszenia-Dabrowska, N; Tachmazidou, I; Tenconi, E; Thornton, L M; Tortorella, A; Tozzi, F; Treasure, J; Tsitsika, A; Tziouvas, K; van Elburg, A A; van Furth, E F; Wagner, G; Walton, E; Watson, H; Wichmann, H-E; Widen, E; Woodside, D B; Yanovski, J; Yao, S; Yilmaz, Z; Zeggini, E; Zerwas, S; Zipfel, S; Collier, D A; Sullivan, P F; Breen, G; Bulik, C M; Zeggini, E

2018-01-01

Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. To date, only one genome-wide significant locus associated with AN has been identified. We performed an exome-chip based genome-wide association studies (GWAS) in 2158 cases from nine populations of European origin and 15 485 ancestrally matched controls. Unlike previous studies, this GWAS also probed association in low-frequency and rare variants. Sixteen independent variants were taken forward for in silico and de novo replication (11 common and 5 rare). No findings reached genome-wide significance. Two notable common variants were identified: rs10791286, an intronic variant in OPCML (P=9.89 × 10−6), and rs7700147, an intergenic variant (P=2.93 × 10−5). No low-frequency variant associations were identified at genome-wide significance, although the study was well-powered to detect low-frequency variants with large effect sizes, suggesting that there may be no AN loci in this genomic search space with large effect sizes. PMID:29155802

Epigenetic Variation May Compensate for Decreased Genetic Variation with Introductions: A Case Study Using House Sparrows (Passer domesticus on Two Continents

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Aaron W. Schrey

2012-01-01

Full Text Available Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion <50 years old, Florida invasion ~150 years old, and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.

Common variation at 1q24.1 (ALDH9A1 is a potential risk factor for renal cancer.

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Marc Y R Henrion

Full Text Available So far six susceptibility loci for renal cell carcinoma (RCC have been discovered by genome-wide association studies (GWAS. To identify additional RCC common risk loci, we performed a meta-analysis of published GWAS (totalling 2,215 cases and 8,566 controls of Western-European background with imputation using 1000 Genomes Project and UK10K Project data as reference panels and followed up the most significant association signals [22 single nucleotide polymorphisms (SNPs and 3 indels in eight genomic regions] in 383 cases and 2,189 controls from The Cancer Genome Atlas (TCGA. A combined analysis identified a promising susceptibility locus mapping to 1q24.1 marked by the imputed SNP rs3845536 (Pcombined =2.30x10-8. Specifically, the signal maps to intron 4 of the ALDH9A1 gene (aldehyde dehydrogenase 9 family, member A1. We further evaluated this potential signal in 2,461 cases and 5,081 controls from the International Agency for Research on Cancer (IARC GWAS of RCC cases and controls from multiple European regions. In contrast to earlier findings no association was shown in the IARC series (P=0.94; Pcombined =2.73x10-5. While variation at 1q24.1 represents a potential risk locus for RCC, future replication analyses are required to substantiate our observation.

Seizure-related factors and non-verbal intelligence in children with epilepsy. A population-based study from Western Norway.

Science.gov (United States)

Høie, B; Mykletun, A; Sommerfelt, K; Bjørnaes, H; Skeidsvoll, H; Waaler, P E

2005-06-01

To study the relationship between seizure-related factors, non-verbal intelligence, and socio-economic status (SES) in a population-based sample of children with epilepsy. The latest ILAE International classifications of epileptic seizures and syndromes were used to classify seizure types and epileptic syndromes in all 6-12 year old children (N=198) with epilepsy in Hordaland County, Norway. The children had neuropediatric and EEG examinations. Of the 198 patients, demographic characteristics were collected on 183 who participated in psychological studies including Raven matrices. 126 healthy controls underwent the same testing. Severe non-verbal problems (SNVP) were defined as a Raven score at or Raven percentile group, whereas controls were highly over-represented in the higher percentile groups. SNVP were present in 43% of children with epilepsy and 3% of controls. These problems were especially common in children with remote symptomatic epilepsy aetiology, undetermined epilepsy syndromes, myoclonic seizures, early seizure debut, high seizure frequency and in children with polytherapy. Seizure-related characteristics that were not usually associated with SNVP were idiopathic epilepsies, localization related (LR) cryptogenic epilepsies, absence and simple partial seizures, and a late debut of epilepsy. Adjusting for socio-economic status factors did not significantly change results. In childhood epilepsy various seizure-related factors, but not SES factors, were associated with the presence or absence of SNVP. Such deficits may be especially common in children with remote symptomatic epilepsy aetiology and in complex and therapy resistant epilepsies. Low frequencies of SNVP may be found in children with idiopathic and LR cryptogenic epilepsy syndromes, simple partial or absence seizures and a late epilepsy debut. Our study contributes to an overall picture of cognitive function and its relation to central seizure characteristics in a childhood epilepsy population

Asymmetric ramification of deep femoral artery: Incidental detection of an anatomic variation

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Hamit Serdar Başbuğ

2017-09-01

Full Text Available The origin of the deep femoral artery (DFA is most commonly located posterolaterally constituting the 40% of all studied specimens. Second most common course is the posterior origin (37%, that is followed by the lateral (12%, posteromedial (12% and medial (2% origins respectively. In this case report, we presented a case with a lateral originated DFA which is the third common anatomic variation. This case is especially important that it demonstrates the branching behaviors of vascular structures may differ between the right and the left limbs creating an asymmetry between the both sides of the same patient. Clinicians should be aware of anatomic variation during the cardiac catheterization, trans-arterial interventions, arteriography and the surgical dissections of the groin region.

Sociodemographic, psychosocial and physical health correlates of common mental disorder symptoms among mothers in Trinidad and Tobago: Examining ethnic variations.

Science.gov (United States)

Krishnakumar, Ambika; Narine, Lutchmie; Roopnarine, Jaipaul L; Logie, Carol

2016-08-22

Historical and cultural experiences have shaped the life experiences of cultural communities in Trinidad and Tobago. Using a cultural focus, the goal of this investigation was to examine ethnic variations both in the prevalence of common mental disorder (CMD) symptoms as well as in the associations between sociodemographic, psychosocial, physical health correlates and CMDs among mothers in Trinidad and Tobago. Participants included 1002 mothers (359 African-, 353 Indo- and 290 Mixed-Ethnic Trinidadian). Mean comparisons indicated similarities in the levels of depression, somatisation and anxiety across ethnic groups. The associations between physical ill health, experiences of pain and depression and between physical ill health and somatisation were stronger for Mixed-Ethnic Trinidadian than Indo-Trinidadian mothers. The relationship between early experiences of domestic violence and depression was stronger for Indo-Trinidadian than Mixed-Ethnic Trinidadian mothers. The associations between early experiences of domestic violence and depression and between experiences of pain and somatisation were stronger for African Trinidadian than Mixed-Ethnic Trinidadian mothers. Thus beyond the direct effects, mothers belonging to specific ethnic groups indicated greater or lesser vulnerabilities to CMDs depending on their exposure to specific correlates. Results have applicability for the development of culturally sensitive interventions for mothers experiencing CMDs. © 2016 International Union of Psychological Science.

Interactions of raptors and Lesser Prairie-Chickens at leks in the Texas Southern High Plains

Science.gov (United States)

Behney, Adam C.; Boal, Clint W.; Whitlaw, Heather A.; Lucia, Duane R.

2011-01-01

We examined behavioral interactions of raptors, Chihuahuan Ravens (Corvus cryptoleucus), and Lesser Prairie-Chickens (Tympanuchus pallidicinctus) at leks in the Texas Southern High Plains. Northern Harriers (Circus cyaneus) and Swainson's Hawks (Buteo swainsoni) were the most common raptors observed at leks. Only 15 of 61 (25%) raptor encounters at leks (0.09/hr) resulted in a capture attempt (0.02/hr). Mean (± SD) time for Lesser Prairie-Chickens to return to lekking behavior following a raptor encounter was 4.2 ± 5.5 min suggesting the disturbance had little influence on lekking behaviors. Lesser Prairie-Chickens engaged in different escape behaviors depending on raptor species and, generally, did not respond to ravens suggesting they are able to assess different predation risks. The raptors in our study area posed little predation risk to lekking prairie-chickens. Behavioral disturbance at leks appears minimal due to the lack of successful predation events, low raptor encounter rates, and short time to return to lekking behavior.

Influence of Design Variations on Systems Performance

Science.gov (United States)

Tumer, Irem Y.; Stone, Robert B.; Huff, Edward M.; Norvig, Peter (Technical Monitor)

2000-01-01

High-risk aerospace components have to meet very stringent quality, performance, and safety requirements. Any source of variation is a concern, as it may result in scrap or rework. poor performance, and potentially unsafe flying conditions. The sources of variation during product development, including design, manufacturing, and assembly, and during operation are shown. Sources of static and dynamic variation during development need to be detected accurately in order to prevent failure when the components are placed in operation. The Systems' Health and Safety (SHAS) research at the NASA Ames Research Center addresses the problem of detecting and evaluating the statistical variation in helicopter transmissions. In this work, we focus on the variations caused by design, manufacturing, and assembly of these components, prior to being placed in operation (DMV). In particular, we aim to understand and represent the failure and variation information, and their correlation to performance and safety and feed this information back into the development cycle at an early stage. The feedback of such critical information will assure the development of more reliable components with less rework and scrap. Variations during design and manufacturing are a common source of concern in the development and production of such components. Accounting for these variations, especially those that have the potential to affect performance, is accomplished in a variety ways, including Taguchi methods, FMEA, quality control, statistical process control, and variation risk management. In this work, we start with the assumption that any of these variations can be represented mathematically, and accounted for by using analytical tools incorporating these mathematical representations. In this paper, we concentrate on variations that are introduced during design. Variations introduced during manufacturing are investigated in parallel work.

Hybrid Steepest-Descent Methods for Triple Hierarchical Variational Inequalities

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L. C. Ceng

2015-01-01

Full Text Available We introduce and analyze a relaxed iterative algorithm by combining Korpelevich’s extragradient method, hybrid steepest-descent method, and Mann’s iteration method. We prove that, under appropriate assumptions, the proposed algorithm converges strongly to a common element of the fixed point set of infinitely many nonexpansive mappings, the solution set of finitely many generalized mixed equilibrium problems (GMEPs, the solution set of finitely many variational inclusions, and the solution set of general system of variational inequalities (GSVI, which is just a unique solution of a triple hierarchical variational inequality (THVI in a real Hilbert space. In addition, we also consider the application of the proposed algorithm for solving a hierarchical variational inequality problem with constraints of finitely many GMEPs, finitely many variational inclusions, and the GSVI. The results obtained in this paper improve and extend the corresponding results announced by many others.

Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk

DEFF Research Database (Denmark)

Chornokur, Ganna; Lin, Hui-Yi; Tyrer, Jonathan P

2015-01-01

. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contributes to EOC risk. METHODS: In total, DNA samples were obtained from 14,525 case subjects with invasive EOC......BACKGROUND: Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes...... and from 23,447 controls from 43 sites in the Ovarian Cancer Association Consortium (OCAC). Two hundred seventy nine SNPs, representing 131 genes, were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). SNP analyses were conducted...

Liquidity in the foreign exchange market : Measurement, commonality, and risk premiums

NARCIS (Netherlands)

Mancini, Loriano; Ranaldo, Angelo; Wrampelmeyer, Jan

2013-01-01

We provide the first systematic study of liquidity in the foreign exchange market. We find significant variation in liquidity across exchange rates, substantial illiquidity costs, and strong commonality in liquidity across currencies and with equity and bond markets. Analyzing the impact of

MetaRanker 2.0: a web server for prioritization of genetic variation data

DEFF Research Database (Denmark)

Pers, Tune Hannes; Dworzynski, Piotr; Thomas, Cecilia Engel

2013-01-01

MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein–protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, Meta...

Personality matters: individual variation in reactions of naive bird predators to aposematic prey

NARCIS (Netherlands)

Exnerová, A.; Hotova Svadova, K.; Fucikova, E.; Drent, P.; Stys, P.

2010-01-01

Variation in reactions to aposematic prey is common among conspecific individuals of bird predators. It may result from different individual experience but it also exists among naive birds. This variation may possibly be explained by the effect of personality—a complex of correlated, heritable

Appendicitis: Trends in incidence, age, sex, and seasonal variations ...

African Journals Online (AJOL)

Background:Appendicitis is a common clinical condition worldwide. Differences in ... Aim:To assess the trends in incidence and pattern of variation with age, sex, and seasons of the year. .... population of 465000 (an annual population growth.

Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation.

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Stephanie E Hesselson

2009-09-01

Full Text Available Membrane transporters play crucial roles in the cellular uptake and efflux of an array of small molecules including nutrients, environmental toxins, and many clinically used drugs. We hypothesized that common genetic variation in the proximal promoter regions of transporter genes contribute to observed variation in drug response. A total of 579 polymorphisms were identified in the proximal promoters (-250 to +50 bp and flanking 5' sequence of 107 transporters in the ATP Binding Cassette (ABC and Solute Carrier (SLC superfamilies in 272 DNA samples from ethnically diverse populations. Many transporter promoters contained multiple common polymorphisms. Using a sliding window analysis, we observed that, on average, nucleotide diversity (pi was lowest at approximately 300 bp upstream of the transcription start site, suggesting that this region may harbor important functional elements. The proximal promoters of transporters that were highly expressed in the liver had greater nucleotide diversity than those that were highly expressed in the kidney consistent with greater negative selective pressure on the promoters of kidney transporters. Twenty-one promoters were evaluated for activity using reporter assays. Greater nucleotide diversity was observed in promoters with strong activity compared to promoters with weak activity, suggesting that weak promoters are under more negative selective pressure than promoters with high activity. Collectively, these results suggest that the proximal promoter region of membrane transporters is rich in variation and that variants in these regions may play a role in interindividual variation in drug disposition and response.

Behavioural Effects of Tourism on Oceanic Common Dolphins, Delphinus sp., in New Zealand: The Effects of Markov Analysis Variations and Current Tour Operator Compliance with Regulations

Science.gov (United States)

Meissner, Anna M.; Christiansen, Fredrik; Martinez, Emmanuelle; Pawley, Matthew D. M.; Orams, Mark B.; Stockin, Karen A.

2015-01-01

Common dolphins, Delphinus sp., are one of the marine mammal species tourism operations in New Zealand focus on. While effects of cetacean-watching activities have previously been examined in coastal regions in New Zealand, this study is the first to investigate effects of commercial tourism and recreational vessels on common dolphins in an open oceanic habitat. Observations from both an independent research vessel and aboard commercial tour vessels operating off the central and east coast Bay of Plenty, North Island, New Zealand were used to assess dolphin behaviour and record the level of compliance by permitted commercial tour operators and private recreational vessels with New Zealand regulations. Dolphin behaviour was assessed using two different approaches to Markov chain analysis in order to examine variation of responses of dolphins to vessels. Results showed that, regardless of the variance in Markov methods, dolphin foraging behaviour was significantly altered by boat interactions. Dolphins spent less time foraging during interactions and took significantly longer to return to foraging once disrupted by vessel presence. This research raises concerns about the potential disruption to feeding, a biologically critical behaviour. This may be particularly important in an open oceanic habitat, where prey resources are typically widely dispersed and unpredictable in abundance. Furthermore, because tourism in this region focuses on common dolphins transiting between adjacent coastal locations, the potential for cumulative effects could exacerbate the local effects demonstrated in this study. While the overall level of compliance by commercial operators was relatively high, non-compliance to the regulations was observed with time restriction, number or speed of vessels interacting with dolphins not being respected. Additionally, prohibited swimming with calves did occur. The effects shown in this study should be carefully considered within conservation management

Behavioural effects of tourism on oceanic common dolphins, Delphinus sp., in New Zealand: the effects of Markov analysis variations and current tour operator compliance with regulations.

Science.gov (United States)

Meissner, Anna M; Christiansen, Fredrik; Martinez, Emmanuelle; Pawley, Matthew D M; Orams, Mark B; Stockin, Karen A

2015-01-01

Common dolphins, Delphinus sp., are one of the marine mammal species tourism operations in New Zealand focus on. While effects of cetacean-watching activities have previously been examined in coastal regions in New Zealand, this study is the first to investigate effects of commercial tourism and recreational vessels on common dolphins in an open oceanic habitat. Observations from both an independent research vessel and aboard commercial tour vessels operating off the central and east coast Bay of Plenty, North Island, New Zealand were used to assess dolphin behaviour and record the level of compliance by permitted commercial tour operators and private recreational vessels with New Zealand regulations. Dolphin behaviour was assessed using two different approaches to Markov chain analysis in order to examine variation of responses of dolphins to vessels. Results showed that, regardless of the variance in Markov methods, dolphin foraging behaviour was significantly altered by boat interactions. Dolphins spent less time foraging during interactions and took significantly longer to return to foraging once disrupted by vessel presence. This research raises concerns about the potential disruption to feeding, a biologically critical behaviour. This may be particularly important in an open oceanic habitat, where prey resources are typically widely dispersed and unpredictable in abundance. Furthermore, because tourism in this region focuses on common dolphins transiting between adjacent coastal locations, the potential for cumulative effects could exacerbate the local effects demonstrated in this study. While the overall level of compliance by commercial operators was relatively high, non-compliance to the regulations was observed with time restriction, number or speed of vessels interacting with dolphins not being respected. Additionally, prohibited swimming with calves did occur. The effects shown in this study should be carefully considered within conservation management

Behavioural effects of tourism on oceanic common dolphins, Delphinus sp., in New Zealand: the effects of Markov analysis variations and current tour operator compliance with regulations.

Directory of Open Access Journals (Sweden)

Anna M Meissner

Full Text Available Common dolphins, Delphinus sp., are one of the marine mammal species tourism operations in New Zealand focus on. While effects of cetacean-watching activities have previously been examined in coastal regions in New Zealand, this study is the first to investigate effects of commercial tourism and recreational vessels on common dolphins in an open oceanic habitat. Observations from both an independent research vessel and aboard commercial tour vessels operating off the central and east coast Bay of Plenty, North Island, New Zealand were used to assess dolphin behaviour and record the level of compliance by permitted commercial tour operators and private recreational vessels with New Zealand regulations. Dolphin behaviour was assessed using two different approaches to Markov chain analysis in order to examine variation of responses of dolphins to vessels. Results showed that, regardless of the variance in Markov methods, dolphin foraging behaviour was significantly altered by boat interactions. Dolphins spent less time foraging during interactions and took significantly longer to return to foraging once disrupted by vessel presence. This research raises concerns about the potential disruption to feeding, a biologically critical behaviour. This may be particularly important in an open oceanic habitat, where prey resources are typically widely dispersed and unpredictable in abundance. Furthermore, because tourism in this region focuses on common dolphins transiting between adjacent coastal locations, the potential for cumulative effects could exacerbate the local effects demonstrated in this study. While the overall level of compliance by commercial operators was relatively high, non-compliance to the regulations was observed with time restriction, number or speed of vessels interacting with dolphins not being respected. Additionally, prohibited swimming with calves did occur. The effects shown in this study should be carefully considered within

Bonobos fall within the genomic variation of chimpanzees.

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Anne Fischer

Full Text Available To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.

Ravens at Play

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Deborah Bird Rose

2011-09-01

Full Text Available  ‘We were driving through Death Valley, an American-Australian and two Aussies, taking the scenic route from Las Vegas to Santa Cruz.’ This multi-voiced account of multispecies encounters along a highway takes up the challenge of playful and humorous writing that is as well deeply serious and theoretically provocative. Our travels brought us into what Donna Haraway calls the contact zone: a region of recognition and response. The contact zone is a place of significant questions: ‘Who are you, and so who are we? Here we are, and so what are we to become?’ Events were everything in this ecology of play, in which the movements of all the actors involved the material field in its entirety. We were brought into dances of approach and withdrawal, dances emerging directly, to paraphrase Brian Massumi, from the dynamic relation between a myriad of charged particles.

Identification and treatment of variation of extrahepatic bile duct in laparoscopic cholecystectomy

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PENG Lei

2015-10-01

Full Text Available ObjectiveTo investigate the identification and treatment of variation of extrahepatic bile duct in laparoscopic cholecystectomy (LC, and to reduce the occurrence of bile duct injury. MethodsThis study included 60 patients who received LC in the People′s Hospital of Caidian District in Wuhan and had structural variation of extrahepatic bile duct found during the operation from January 2012 to January 2014. The clinical data were retrospectively analyzed, and the intraoperative and postoperative conditions were summarized. ResultsDuring operation, cystic duct variation was found in 32 cases, abnormal position of the point where the cystic duct joins the extrahepatic bile duct in 20 cases, the cystic duct and the common hepatic duct having the common wall before joining the common bile duct in 2 cases, aberrant bile duct in the gallbladder bed in 2 cases, and accessory hepatic duct in 4 cases. Fifty-one patients (85% successfully underwent LC; 9 patients (15% were converted to open surgery. All patients finished surgery successfully. There were 2 cases of postoperative complications; one patient developed residual stones in the bile duct, and bile leakage occurred in the other patient at one week after LC, who recovered after reoperation. All patients were cured and discharged, without severe complications such as intraperitoneal hemorrhage, infection, and intestinal injury. ConclusionIdentifying the structural variation of extrahepatic bile duct, dissecting the Calot′s triangle meticulously, and determining the type of variation of extrahepatic bile duct play important roles in LC and significantly reduce the incidence of bile duct injury.

Variant Branching of the Common Femoral Artery in a Black Kenyan ...

African Journals Online (AJOL)

Branching pattern of common femoral artery is important during artery catheterization, orthopaedic, plastic and general surgery in the proximal thigh. Frequency of variant branching shows ethnic variation but there are no data for black African populations. Since atherosclerotic diseases are increasing and femoral artery ...

Recommendations for designing and conducting veterinary clinical pathology biologic variation studies.

Science.gov (United States)

Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K; Nielsen, Søren Saxmose; Jensen, Asger L

2017-06-01

The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review and selection of publications as standard references. The following recommendations are provided in the format and order commonly found in veterinary publications. A checklist is provided to aid in planning, implementing, and evaluating veterinary studies on biologic variation (Appendix S1). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing. © 2017 American Society for Veterinary Clinical Pathology.

Variation of nuclear radii in the drip line regions

CERN Document Server

Beiner, M; Mas, D

1976-01-01

The authors are concerned with predictions of the energy density method with respect to the nuclear sizes (RMS radii). It is known that the commonly accepted A/sup 1/3/-type laws are only approximative and deviations are expected to grow significantly as one goes away from the beta -stability region. Particular attention is paid to the variation of nuclear radii in the drip line regions. Implications of the resulting large total Coulomb energy variations between neighbouring nuclei will be emphasized.

Variations in Transverse Foramina of Cervical Vertebrae: Morphology & Clinical Importance

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Vaishakhi Gonsai

2015-12-01

Full Text Available Background: The purpose of this study is to investigate variations in transverse foramina in the cervical vertebrae and its morphological and clinical importance. Materials and Method : The variations in the number and size of transverse foramina was studied in total 200 human dried cervical vertebrae, which were taken from the Department of Anatomy, B.J.Medical College, Ahmedabad. All the vertebrae were observed for variation in number and size of transverse foramina. Results: Out of 200 cervical vertebrae, complete double transverse foramina were observed in 40 vertebrae (20%, among them unilateral double foramina were found in 31 vertebrae (15.5% and the bilateral double foramina were found in 9 vertebrae (4.5%. Incomplete double transverse foramina were observed in 22 vertebrae (11%, among them unilateral double foramina were found in 16 vertebrae (8% and bilateral double foramina were observed in 6 vertebrae (3%. Conclusion: Complete unilateral double transverse foramina of cervical vertebrae were more common than bilateral. Also unilateral small size transverse foramina of cervical vertebrae were also common. This variation is important for the neurosurgeon during cervical surgery. Under such condition the course of the vertebral artery may be distorted. It is also useful for Radiologist during CT and MRI scan.

The incidence of congenital malformations and variations in Göttingen minipigs.

Science.gov (United States)

Ellemann-Laursen, S; Marsden, E; Peter, B; Downes, N; Coulby, D; Grossi, A B

2016-09-01

Knowledge of the incidence of spontaneous congenital abnormalities is critical for the accurate interpretation of findings in teratogenicity studies in any species. In this paper, results of the examination of 1739 neonatal Göttingen Minipigs are presented. Over the 2-year period under consideration, the incidence of external and visceral malformations was less than 0.2 and 0.1%, respectively. The most common external malformations were syndactyly, limb hyperflexion, domed head and scoliosis. The most common internal malformations were undescended testes, ventricular septal defect, diaphragmatic hernia and atrial septal defects. Pentadactyly and variation in the aortic arch's bifurcation (absent truncus bicaroticus) were the most common variations. These data will help support the use of the Göttingen Minipig as a non-rodent species in embryofetal development studies where concerns persist about the availability of background data. Copyright © 2016 Elsevier Inc. All rights reserved.

Fiber and nonstarch polysaccharide content and variation in common crops used in broiler diets.

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Knudsen, Knud Erik Bach

2014-09-01

The current paper reviews content and variation in fiber and nonstarch polysaccharides (NSP) of common crops used in broiler diets. The cereal grain is a complex structure, and its cell walls (CW) differ in their composition and hence properties. Arabinoxylan (AX), mixed linkage (1→3; 1→4)-β-glucan (β-glucan), cellulose, and the noncarbohydrate component lignin are the predominant polymers in cereals. They occur in different proportions depending on the species and tissue type. Rye, triticale, wheat, corn, and sorghum are all rich in AX, whereas barley and oats contain a high level of β-glucan. The AX from rye, wheat, and triticale and β-glucan from barley and oats are to a large extent soluble, whereas the solubility of AX found in corn and sorghum is lower than the other cereals. The ratio of arabinose to xylose gives a crude indication of the AX structure, which varies between the endosperm, the aleurone and the outer grain layers as well as between the same tissues from different grains. Varietal differences in AX structure of the endosperm are also identified. From the analysis of the released oligomers after hydrolysis with a specific (1→3,1→4)-β-d-glucan hydrolase, it is found that the ratio of trisaccharides (degree of polymerization 3) and tetrasaccharides (degree of polymerization 4) varies depending on the source, being higher in barley than in oats but lower than in wheat. The molecular weight of β-glucan is higher than that of AX, and both polymers contribute to the viscosity of the extract. However, because AX molecules are more resistant to degradation than β-glucan, the use of AX rich grains in broiler diets is usually more problematic than those containing high concentrations of β-glucan. The cereal coproducts (brans and hulls) are concentrated sources of cellulose, lignin, and insoluble AX, but β-glucan can also be present mainly in rye and wheat brans. The CW composition of seeds and grains of protein crops and feedstuffs are

Genome-wide association analysis of symbiotic nitrogen fixation in common bean

Science.gov (United States)

A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean diversity panel (ADP) comprised of 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in...

Voltage variation due to solar photovoltaic in distribution network

International Nuclear Information System (INIS)

Azad, H I; Ramachandaramurthy, V K; Maleki, Hesamaldin

2013-01-01

Grid integration of solar photovoltaic (PV) plant offers reduction in greenhouse emissions and independence from fossil fuels for power generation. The integration of such forms of power generation also brings with it a variety of policy and technical issues. One of the technical issues is the variation in grid voltages in the presence of solar photovoltaic (PV) plant, resulting in degradation of power quality. In this paper, the application of a dq current controller to limit the voltage variation at the point of common coupling (PCC) due to a 2 MW solar photovoltaic (PV) plant will be discussed. The controller's goal is to ensure that the voltage variation meets the momentary voltage change limits specified in TNB's Technical Guidebook for the connection of distributed generation. The proposed dq current controller is shown to be able to limit the voltage variation.

Morphological variation and habitat modification are strongly correlated for the autogenic ecosystem engineer Spartina anglica (common cordgrass)

NARCIS (Netherlands)

van Hulzen, J.B.; Van Soelen, J.; Bouma, T.J.

2007-01-01

We explored to what extent morphological variation and habitat modification are correlated for an autogenic ecosystem engineer, which is an organism that modifies its habitat via its own physical structures. The intertidal salt marsh species Spartina anglica is well known for its capacity to enhance

Triple Hierarchical Variational Inequalities with Constraints of Mixed Equilibria, Variational Inequalities, Convex Minimization, and Hierarchical Fixed Point Problems

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Lu-Chuan Ceng

2014-01-01

Full Text Available We introduce and analyze a hybrid iterative algorithm by virtue of Korpelevich's extragradient method, viscosity approximation method, hybrid steepest-descent method, and averaged mapping approach to the gradient-projection algorithm. It is proven that under appropriate assumptions, the proposed algorithm converges strongly to a common element of the fixed point set of infinitely many nonexpansive mappings, the solution set of finitely many generalized mixed equilibrium problems (GMEPs, the solution set of finitely many variational inequality problems (VIPs, the solution set of general system of variational inequalities (GSVI, and the set of minimizers of convex minimization problem (CMP, which is just a unique solution of a triple hierarchical variational inequality (THVI in a real Hilbert space. In addition, we also consider the application of the proposed algorithm to solve a hierarchical fixed point problem with constraints of finitely many GMEPs, finitely many VIPs, GSVI, and CMP. The results obtained in this paper improve and extend the corresponding results announced by many others.

The clinical importance of the anatomic variations in the paranasal sinuses

International Nuclear Information System (INIS)

Teixeira Junior, Francisco Ribeiro; Bretas, Elisa Almeida Sathler; Madeira, Ivana Andrade; Diniz, Renata Furletti; Ribeiro, Marcelo Almeida; Motta, Emilia Guerra Pinto Coelho; Moreira, Wanderval

2008-01-01

The anatomic variations of the paranasal sinuses are common findings. The importance of such variations predisposing disease through the obstruction of the drainage pathway has been discussed by several authors, although it is not yet a matter of agreement. The literature was reviewed and a iconographic assay was prepared aiming the discussion of the importance of the main anatomic variations of the paranasal sinuses. The prevalence of anatomic variations of the paranasal sinuses varies largely amongst studies and its role in sinus disease is controversial. In this article, it is described the different variations associated to paranasal disease and how they relate to pathologic conditions. Most studies confirm the concept that anatomic variations of the paranasal sinuses are related to disease when they obstruct the drainage pathways. The knowledge of such alterations and its relations to pathologic conditions is expected from the general radiologist. (author)

Stress associated with group living in a long-lived bird

OpenAIRE

Selva, Nuria; Cortés-Avizanda, Ainara; Lemus, Jesús A.; Blanco, Guillermo; Mueller, Thomas; Heinrich, Bernd; Donázar, José A.

2011-01-01

Many long-lived avian species adopt life strategies that involve a gregarious way of life at juvenile and sub-adult stages and territoriality during adulthood. However, the potential associated costs of these life styles, such as stress, are poorly understood. We examined the effects of group living, sex and parasite load on the baseline concentration of faecal stress hormone (corticosterone) metabolites in a wild population of common ravens (Corvus corax). Corticosterone concentrations were ...

Survival of breeding Pacific common eiders on the Yukon-Kuskokwim Delta, Alaska

Science.gov (United States)

Wilson, H.M.; Flint, Paul L.; Moran, Christine L.; Powell, A.N.

2007-01-01

Populations of Pacific common eiders (Somateria mollissima v-nigrum) breeding in Alaska, USA, have declined markedly over the past 40 years. We studied survival of adult female Pacific common eiders using capture—recapture of nesting hens at 3 sites on the Yukon-Kuskokwim Delta (YKD), Alaska from 1994 to 2004. We used data consisting of 268 recapture events from 361 uniquely marked individuals to investigate temporal, geographic, and environmental variation in adult female survival. Our results suggest apparent annual survival of adult eiders from the YKD was high (0.892, SE = 0.022) and spatially and temporally invariant (σ2 = 0.005), a pattern consistent with other long-lived marine birds. Moreover, our results suggest adult survival may be functionally fixed for Pacific common eiders, and at the present, adult survival may be relatively unresponsive to environmental or management perturbations. Our data did not support hypothesized variation in survival relative to mortality factors such as predation on breeding grounds, physiologic costs of reproduction, and wintering conditions. Although changes in adult survival likely have a large potential effect on prospective population growth, our results suggest viable management actions aimed at increasing survival may be extremely limited.

Variation of hepatic artery on arteriogram and its clinical significance in interventional therapy for hepatic cancer

International Nuclear Information System (INIS)

Wang Xiaodong; Yang Renjie

2009-01-01

Objective: To investigate the variations of hepatic artery and its extrahepatic arteries on hepatic arteriogram and to provide benefit for transhepatic arterical chemoemblization. Methods: The hepatic arteriograms of 200 cases with unresectable hepatic malignant tumor before interventional therapy were analysed. Two interventional radiologists in common reviewed the incidences of various types according to Michels' classification, the absence of proper hepatic artery, and the variations of extrahepatic arteries originating from hepatic artery. Results: The most common hepatic artery variation was Michels type III(n=17,8.5%), followed by type II(n=10,5.0%) and V(n=9,4.5%). Proper hepatic absence was found in 25 cases and appeared as 5 subtypes. 5 kinds of extrahepatic arteries were found. The most common extrahepatic artery was the right gastric artery (n=156,78.0%), followed by cystic artery (n=126,63.0%), accessory left gastric artery (n=19,9.5%), the hepatic falciform artery (n=5,2.5%), and accessory left inferior phrenic artery (n=4,2.0%). Conclusion: There are some other variations of hepatic artery beside Michels' classification,and there are many variations of extrahepatic arteries originating from hepatic artery, it is important to assure interventional therapy effect for hepatic cancer and prevent complication. (authors)

Joint Kinetics and Kinematics During Common Lower Limb Rehabilitation Exercises.

Science.gov (United States)

Comfort, Paul; Jones, Paul Anthony; Smith, Laura Constance; Herrington, Lee

2015-10-01

Unilateral body-weight exercises are commonly used to strengthen the lower limbs during rehabilitation after injury, but data comparing the loading of the limbs during these tasks are limited. To compare joint kinetics and kinematics during 3 commonly used rehabilitation exercises. Descriptive laboratory study. Laboratory. A total of 9 men (age = 22.1 ± 1.3 years, height = 1.76 ± 0.08 m, mass = 80.1 ± 12.2 kg) participated. Participants performed the single-legged squat, forward lunge, and reverse lunge with kinetic data captured via 2 force plates and 3-dimensional kinematic data collected using a motion-capture system. Peak ground reaction forces, maximum joint angles, and peak sagittal-joint moments. We observed greater eccentric and concentric peak vertical ground reaction forces during the single-legged squat than during both lunge variations (P ≤ .001). Both lunge variations demonstrated greater knee and hip angles than did the single-legged squat (P .05). Greater dorsiflexion occurred during the single-legged squat than during both lunge variations (P reverse lunge (P = .003) and the single-legged squat (P = .011). Knee-joint moments were greater in the single-legged squat than in the reverse lunge (P reverse lunge (P reverse lunge and then the forward lunge. In contrast, loading progressions for the knee and ankle should begin with the reverse lunge and progress to the forward lunge and then the single-legged squat.

Structural genomic variations and Parkinson's disease.

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Bandrés-Ciga, Sara; Ruz, Clara; Barrero, Francisco J; Escamilla-Sevilla, Francisco; Pelegrina, Javier; Vives, Francisco; Duran, Raquel

2017-10-01

Parkinson's disease (PD) is the second most common neurodegenerative disease, whose prevalence is projected to be between 8.7 and 9.3 million by 2030. Until about 20 years ago, PD was considered to be the textbook example of a "non-genetic" disorder. Nowadays, PD is generally considered a multifactorial disorder that arises from the combination and complex interaction of genes and environmental factors. To date, a total of 7 genes including SNCA, LRRK2, PARK2, DJ-1, PINK 1, VPS35 and ATP13A2 have been seen to cause unequivocally Mendelian PD. Also, variants with incomplete penetrance in the genes LRRK2 and GBA are considered to be strong risk factors for PD worldwide. Although genetic studies have provided valuable insights into the pathogenic mechanisms underlying PD, the role of structural variation in PD has been understudied in comparison with other genomic variations. Structural genomic variations might substantially account for such genetic substrates yet to be discovered. The present review aims to provide an overview of the structural genomic variants implicated in the pathogenesis of PD.

Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

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Cremer Thomas

2005-12-01

Full Text Available Abstract Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.

Raven’s test performance of sub-Saharan Africans: average performance, psychometric properties, and the Flynn Effect

NARCIS (Netherlands)

Wicherts, J.M.; Dolan, C.V.; Carlson, J.S.; van der Maas, H.L.J.

2010-01-01

This paper presents a systematic review of published data on the performance of sub-Saharan Africans on Raven's Progressive Matrices. The specific goals were to estimate the average level of performance, to study the Flynn Effect in African samples, and to examine the psychometric meaning of Raven's

Personality may confound common measures of mate-choice.

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Morgan David

Full Text Available The measurement of female mating preferences is central to the study of the evolution of male ornaments. Although several different methods have been developed to assess sexual preference in some standardized way, the most commonly used procedure consists of recording female spatial association with different males presented simultaneously. Sexual preference is then inferred from time spent in front of each male. However, the extent to which the measurement of female mate-choice is related to exploration tendencies has not been addressed so far. In the present study we assessed the influence of variation in exploration tendencies, a trait closely associated to global personality, on the measurement of female mating preference in the zebra finch (Taeniopygia guttata using the widely used four-chamber choice-apparatus. The number of movements performed within both exploration and mate-choice apparatus was consistent within and across the two contexts. In addition, personality explained variation in selectivity, preference strength and consistency. High-exploratory females showed lower selectivity, lower preference scores and displayed more consistent preference scores. Our results suggest that variation in personality may affect the measurement of female mating preference and may contribute to explain existing inconsistencies across studies.

Variational principles for locally variational forms

International Nuclear Information System (INIS)

Brajercik, J.; Krupka, D.

2005-01-01

We present the theory of higher order local variational principles in fibered manifolds, in which the fundamental global concept is a locally variational dynamical form. Any two Lepage forms, defining a local variational principle for this form, differ on intersection of their domains, by a variationally trivial form. In this sense, but in a different geometric setting, the local variational principles satisfy analogous properties as the variational functionals of the Chern-Simons type. The resulting theory of extremals and symmetries extends the first order theories of the Lagrange-Souriau form, presented by Grigore and Popp, and closed equivalents of the first order Euler-Lagrange forms of Hakova and Krupkova. Conceptually, our approach differs from Prieto, who uses the Poincare-Cartan forms, which do not have higher order global analogues

Seasonal variations in the biochemical composition of some common seaweed species from the coast of Abu Qir Bay, Alexandria, Egypt

OpenAIRE

Khairy, Hanan M.; El-Shafay, Shimaa M.

2013-01-01

Variations in protein, carbohydrate, lipid, ash, moisture, fatty acid and aminoacid contents of the seaweeds Ulva lactuca Linnaeus (Chlorophyta),Jania rubens (Linnaeus) J.V. Lamouroux and Pterocladia capillacea (S.G. Gmelin) Bornet(Rhodophyta) were studied seasonally from spring to autumn 2010. The seaweeds were collected from a rocky site near Boughaz El-Maadya on the coast of Abu Qir Bay east of Alexandria, Egypt. Remarkable seasonal variations were recorded in the levels of the studied pa...

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

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Jamie A. O'Rourke

2013-06-01

Full Text Available A small fast neutron mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five Phaseolus vulgaris cv. Red Hawk fast neutron mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation; between cultivar variation, natural variation within the fast neutron mutant population, and fast neutron induced mutagenesis. Our analyses focused on the latter two classes. We identified 23 large deletions (>40 bp common to multiple individuals, illustrating residual heterogeneity and regions of structural variation within the common bean cv. Red Hawk. An additional 18 large deletions were identified in individual mutant plants. These deletions, ranging in size from 40 bp to 43,000 bp, are potentially the result of fast neutron mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype.

Variation in commercial smoking mixtures containing third-generation synthetic cannabinoids.

Science.gov (United States)

Frinculescu, Anca; Lyall, Catherine L; Ramsey, John; Miserez, Bram

2017-02-01

Variation in ingredients (qualitative variation) and in quantity of active compounds (quantitative variation) in herbal smoking mixtures containing synthetic cannabinoids has been shown for older products. This can be dangerous to the user, as accurate and reproducible dosing is impossible. In this study, 69 packages containing third-generation cannabinoids of seven brands on the UK market in 2014 were analyzed both qualitatively and quantitatively for variation. When comparing the labels to actual active ingredients identified in the sample, only one brand was shown to be correctly labelled. The other six brands contained less, more, or ingredients other than those listed on the label. Only two brands were inconsistent, containing different active ingredients in different samples. Quantitative variation was assessed both within one package and between several packages. Within-package variation was within a 10% range for five of the seven brands, but two brands showed larger variation, up to 25% (Relative Standard Deviation). Variation between packages was significantly higher, with variation up to 38% and maximum concentration up to 2.7 times higher than the minimum concentration. Both qualitative and quantitative variation are common in smoking mixtures and endanger the user, as it is impossible to estimate the dose or to know the compound consumed when smoking commercial mixtures. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility

DEFF Research Database (Denmark)

Fahmideh, Maral Adel; Lavebratt, Catharina; Schüz, Joachim

2016-01-01

Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk. The study is...... cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways....

Commonness of Amazonian palm (Arecaceae) species: Cross-scale links and potential determinants

DEFF Research Database (Denmark)

Kristiansen, Thea; Svenning, J.-C.; Grández, César

2009-01-01

was positively related to topographic niche breadth. Stem height correlated with continental range size and was the only species life-history trait related to any commonness measure. Distance from the study area to a species' range centre did not influence any of the commonness measures. The factors determining......The mechanisms that cause variation in commonness (abundances and range sizes) of species remain debated in ecology, and a repeatedly observed pattern is the positive relation between local abundances and larger scale range sizes. We used the Amazonian palm species (Arecaceae) to investigate...... the dependence between and potential determinants of commonness across three (local, landscape, continental) spatial scales. Commonness at the smaller scales (local abundance, landscape frequency) was estimated using data from 57 transects (5 × 500 m) in primary, non-inundated (terra firme) rainforest...

Anatomic variations in intrahepatic bile ducts in a north Indian population.

Science.gov (United States)

Sharma, Vijay; Saraswat, Vivek Anand; Baijal, Sanjay Saran; Choudhuri, Gourdas

2008-07-01

In the present study, we described the anatomical variations in the branching patterns of intrahepatic bile ducts (IHD) and determined the frequency of each variation in north Indian patients. There are no data from India. The study group consisted of 253 consecutive patients (131 women) undergoing endoscopic retrograde cholangiograms for different indications. Anatomical variations in IHD were classified according to the branching pattern of the right anterior segmental duct (RASD) and the right posterior segmental duct (RPSD), presence or absence of first-order branch of left hepatic duct (LHD) and of an accessory hepatic duct. Anatomy of the IHD was typical in 52.9% of cases (n = 134), showing triple confluence in 11.46% (n = 29), anomalous drainage of the RPSD into the LHD in 18.2% (n = 46), anomalous drainage of the RPSD into the common hepatic duct (CHD) in 7.1% (n = 18), drainage of the right hepatic duct (RHD) into the cystic duct 0.4% (n = 1), presence of an accessory duct leading to the CHD or RHD in 4.7% (n = 12), individual drainage of the LHD into the RHD or CHD in 2.4% (n = 6), and unclassified or complex variations in 2.7% (n = 7). None had anomalous drainage of RPSD into the cystic duct. The branching pattern of IHD was atypical in 47% patients. The two most common variations were drainage of the RPSD into the LHD (18.2%) and triple confluence of the RASD, RPSD, and LHD (11.5%).

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

Science.gov (United States)

Groza, Tudor; Köhler, Sebastian; Moldenhauer, Dawid; Vasilevsky, Nicole; Baynam, Gareth; Zemojtel, Tomasz; Schriml, Lynn Marie; Kibbe, Warren Alden; Schofield, Paul N.; Beck, Tim; Vasant, Drashtti; Brookes, Anthony J.; Zankl, Andreas; Washington, Nicole L.; Mungall, Christopher J.; Lewis, Suzanna E.; Haendel, Melissa A.; Parkinson, Helen; Robinson, Peter N.

2015-01-01

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available. PMID:26119816

Variations in government contract in Malaysia

Directory of Open Access Journals (Sweden)

Jaspal Singh Nachatar

2010-12-01

Full Text Available The complexity of construction works means that it is hardly possible to complete a project without changes to the plans or the construction process itself. There can only be a minority of contracts of any size in which the subject matter when completed is identical in every respect with what was contemplated at the outset. As such, variations are inevitable in even the best-planned contracts. This study is attempted to examine the ways a variation was formed in law and project, in finding out whether the Standard Form of Contract used in Malaysia particularly the government Public Works Department (PWD form has been utilized to the best level in variation cases. Additionally, this study examined the benefits of variations to parties in contract and also provides suggestions and assumptions in an effort to contribute solutions to issues and problem detected. The research methodology used in this study was an extensive review of relevant literature, case study, empirical questionnaires and structured interviews and general observations based on experience and surroundings. The academic study approach incorporated stages such as initial understanding, data and information gathering, analysis of data, findings and conclusion and general suggestions in the study. The major findings of this study, among others, revealed that the existences of variations are common in projects. The main cause of variations was due to client request because of inadequate project objectives for the designer to develop comprehensive design. Besides, the analysis pointed out that the government form of contract the Public Works Department (PWD 203/203A can help in overcoming projects with variation because of the clear defined procedure. This study also found that proper planning and coordination at tender stage can minimize the risk of ‘unwanted’ variations. In conclusion, this study recommended that future research should be done in design and build based contract

Common genetic variation in the indoleamine-2,3-dioxygenase genes and antidepressant treatment outcome in major depressive disorder.

Science.gov (United States)

Cutler, Jessica A; Rush, A John; McMahon, Francis J; Laje, Gonzalo

2012-03-01

The essential amino acid tryptophan is the precursor to serotonin, but it can also be metabolized into kynurenine through indoleamine-2,3-dioxygenase (IDO). Increased immune activation has long been associated with symptoms of depression and has been shown to upregulate the expression of IDO. The presence of additional IDO directs more tryptophan down the kynurenine pathway, leaving less available for synthesis of serotonin and its metabolites. Kynurenine can be metabolized through a series of enzymes to quinolinic acid, a potent N-methyl-D-aspartate receptor agonist with demonstrated neurotoxic effects. We tested the hypothesis that IDO plays a role in outcome of treatment with the selective serotonin reuptake inhibitor, citalopram. Patients consisted of 1953 participants enrolled in the Sequenced Treatment Alternatives to Relieve Depression study (STAR*D). Genotypes corresponding to 94 single nucleotide polymorphisms (SNPs) in the genes IDO1 and IDO2, which encode IDO and IDO2, were extracted from a larger genome-wide set and analyzed using single marker tests to look for association with previously defined response, remission and QIDS-C score change phenotypes, with adequate correction for racial stratification and multiple testing. One SNP, rs2929115, showed evidence of association with citalopram response (OR = 0.64, p = 0.0005) after experiment-wide correction for multiple testing. Another closely associated marker, rs2929116 (OR = 0.64, p = 0.0006) had an experiment-wide significant result. Both implicated SNPs are located between 26 kb and 28 kb downstream of IDO2. We conclude that common genetic variation in IDO1 and IDO2 may play a role in antidepressant treatment outcome. These results are modest in a genome-wide context and need to be replicated in an independent sample.

Investigating the Conceptual Variation of Major Physics Textbooks

Science.gov (United States)

Stewart, John; Campbell, Richard; Clanton, Jessica

2008-04-01

The conceptual problem content of the electricity and magnetism chapters of seven major physics textbooks was investigated. The textbooks presented a total of 1600 conceptual electricity and magnetism problems. The solution to each problem was decomposed into its fundamental reasoning steps. These fundamental steps are, then, used to quantify the distribution of conceptual content among the set of topics common to the texts. The variation of the distribution of conceptual coverage within each text is studied. The variation between the major groupings of the textbooks (conceptual, algebra-based, and calculus-based) is also studied. A measure of the conceptual complexity of the problems in each text is presented.

Variational lower bound on the scattering length

International Nuclear Information System (INIS)

Rosenberg, L.; Spruch, L.

1975-01-01

The scattering length A characterizes the zero-energy scattering of one system by another. It was shown some time ago that a variational upper bound on A could be obtained using methods, of the Rayleigh-Ritz type, which are commonly employed to obtain upper bounds on energy eigenvalues. Here we formulate a method for obtaining a variational lower bound on A. Once again the essential idea is to express the scattering length as a variational estimate plus an error term and then to reduce the problem of bounding the error term to one involving bounds on energy eigenvalues. In particular, the variational lower bound on A is rigorously established provided a certin modified Hamiltonian can be shown to have no discrete states lying below the level of the continuum threshold. It is unfortunately true that necessary conditions for the existence of bound states are not available for multiparticle systems in general. However, in the case of positron-atom scattering the adiabatic approximation can be introduced as an (essentially) solvable comparison problem to rigorously establish the nonexistence of bound states of the modified Hamiltonian. It has recently been shown how the validity of the variational upper bound on A can be maintained when the target ground-state wave function is imprecisely known. Similar methods can be used to maintain the variational lower bound on A. Since the bound is variational, the error in the calculated scattering length will be of second order in the error in the wave function. The use of the adiabatic approximation in the present context places no limitation in principle on the accuracy achievable

Reply to Colom and Abad (2006)

Science.gov (United States)

Mackintosh, N. J.

2007-01-01

Mackintosh and Bennett [Mackintosh, N. J., Bennett, E. S. (2005). What do Raven's Matrices measure? An analysis in terms of sex differences. "Intelligence, 33," 663-674] reported that male students obtained higher scores than females on Raven's items that required for their solution addition/subtraction or distribution of two rules, but…

Stress associated with group living in a long-lived bird.

Science.gov (United States)

Selva, Nuria; Cortés-Avizanda, Ainara; Lemus, Jesús A; Blanco, Guillermo; Mueller, Thomas; Heinrich, Bernd; Donázar, José A

2011-08-23

Many long-lived avian species adopt life strategies that involve a gregarious way of life at juvenile and sub-adult stages and territoriality during adulthood. However, the potential associated costs of these life styles, such as stress, are poorly understood. We examined the effects of group living, sex and parasite load on the baseline concentration of faecal stress hormone (corticosterone) metabolites in a wild population of common ravens (Corvus corax). Corticosterone concentrations were significantly higher in non-breeding gregarious ravens than in territorial adults. Among territorial birds, males showed higher stress levels than their mates. Parasite burdens did not affect hormone levels. Our results suggest a key role of the social context in the stress profiles of the two population fractions, and that group living may be more energetically demanding than maintaining a territory. These findings have implications for understanding hormonal mechanisms under different life styles and may inspire further research on the link between hormone levels and selective pressures modulating gregarious and territorial strategies in long-lived birds. This journal is © 2011 The Royal Society

Aberrant ovarian artery arising from the common Iliac artery: Case report

Energy Technology Data Exchange (ETDEWEB)

Kim, Won Kyung [Dept. of Radiology, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon (Korea, Republic of); Yang, Seung Boo; Lee, Jae Myeong [Dept. of Radiology, Soonchunhyang University Gumi Hospital, Soonchunhyang University College of Medicine, Gumi (Korea, Republic of); Goo, Dong Erk; Kim, Yong Jae; Chang, Yun Woo [Dept. of Radiology, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul (Korea, Republic of)

2013-01-15

A 46-year-old Vietnamese woman received embolization therapy in order to control postpartum hemorrhage. Angiography revealed an aberrant ovarian artery arising from the right common iliac artery. Superselective catheterization and subsequent embolization of the aberrant ovarian artery and bilateral uterine arteries were performed. Precise knowledge of the anatomic variations of the ovarian artery is important for successful embolization.

Aberrant ovarian artery arising from the common Iliac artery: Case report

International Nuclear Information System (INIS)

Kim, Won Kyung; Yang, Seung Boo; Lee, Jae Myeong; Goo, Dong Erk; Kim, Yong Jae; Chang, Yun Woo

2013-01-01

A 46-year-old Vietnamese woman received embolization therapy in order to control postpartum hemorrhage. Angiography revealed an aberrant ovarian artery arising from the right common iliac artery. Superselective catheterization and subsequent embolization of the aberrant ovarian artery and bilateral uterine arteries were performed. Precise knowledge of the anatomic variations of the ovarian artery is important for successful embolization.

Data analysis using the Binomial Failure Rate common cause model

International Nuclear Information System (INIS)

Atwood, C.L.

1983-09-01

This report explains how to use the Binomial Failure Rate (BFR) method to estimate common cause failure rates. The entire method is described, beginning with the conceptual model, and covering practical issues of data preparation, treatment of variation in the failure rates, Bayesian estimation of the quantities of interest, checking the model assumptions for lack of fit to the data, and the ultimate application of the answers

Examination of Association to Autism of Common Genetic Variation in Genes Related to Dopamine

OpenAIRE

Anderson, B.M.; Schnetz-Boutaud, N.; Bartlett, J.; Wright, H.H.; Abramson, R.K.; Cuccaro, M.L.; Gilbert, J.R.; Pericak-Vance, M.A.; Haines, J.L.

2008-01-01

Autism is a severe neurodevelopmental disorder characterized by a triad of complications. Autistic individuals display significant disturbances in language and reciprocal social interactions, combined with repetitive and stereotypic behaviors. Prevalence studies suggest that autism is more common than originally believed, with recent estimates citing a rate of one in 150. Although this genomic approach has yielded multiple suggestive regions, a specific risk locus has yet to be identified and...

Sensitivity of euphotic zone properties to CDOM variations in marine ecosystem models

OpenAIRE

Urtizberea, Agurtzane; Dupont, Nicolas; Rosland, Rune; Aksnes, Dag L.

2013-01-01

In marine ecosystem models, the underwater light intensity is commonly characterized by the shading of phytoplankton in addition to a background light attenuation coefficient. Colour dissolved organic matter (CDOM) is an important component of the background light attenuation, and we investigate how variation in CDOM attenuation affects euphotic zone properties in a general marine ecosystem model. Our results suggest that euphotic zone properties are highly sensitive to CDOM variations occurr...

A common variation in EDAR is a genetic determinant of shovel-shaped incisors.

Science.gov (United States)

Kimura, Ryosuke; Yamaguchi, Tetsutaro; Takeda, Mayako; Kondo, Osamu; Toma, Takashi; Haneji, Kuniaki; Hanihara, Tsunehiko; Matsukusa, Hirotaka; Kawamura, Shoji; Maki, Koutaro; Osawa, Motoki; Ishida, Hajime; Oota, Hiroki

2009-10-01

Shovel shape of upper incisors is a common characteristic in Asian and Native American populations but is rare or absent in African and European populations. Like other common dental traits, genetic polymorphisms involved in the tooth shoveling have not yet been clarified. In ectodysplasin A receptor (EDAR), where dysfunctional mutations cause hypohidrotic ectodermal dysplasia, there is a nonsynonymous-derived variant, 1540C (rs3827760), that has a geographic distribution similar to that of the tooth shoveling. This allele has been recently reported to be associated with Asian-specific hair thickness. We aimed to clarify whether EDAR 1540C is also associated with dental morphology. For this purpose, we measured crown diameters and tooth-shoveling grades and analyzed the correlations between the dental traits and EDAR genotypes in two Japanese populations, inhabitants around Tokyo and in Sakishima Islands. The number of EDAR 1540C alleles in an individual was strongly correlated with the tooth-shoveling grade (p = 7.7 x 10(-10)). The effect of the allele was additive and explained 18.9% of the total variance in the shoveling grade, which corresponds to about one-fourth of the heritability of the trait reported previously. For data reduction of individual-level metric data, we applied a principal-component analysis, which yielded PC1-4, corresponding to four patterns of tooth size; this result implies that multiple factors are involved in dental morphology. The 1540C allele also significantly affected PC1 (p = 4.9 x 10(-3)), which denotes overall tooth size, and PC2 (p = 2.6 x 10(-3)), which denotes the ratio of mesiodistal diameter to buccolingual diameter.

MONTHLY VARIATION IN SPERM MOTILITY IN COMMON CARP ASSESSED USING COMPUTER-ASSISTED SPERM ANALYSIS (CASA)

Science.gov (United States)

Sperm motility variables from the milt of the common carp Cyprinus carpio were assessed using a computer-assisted sperm analysis (CASA) system across several months (March-August 1992) known to encompass the natural spawning period. Two-year-old pond-raised males obtained each mo...

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

NARCIS (Netherlands)

Astle, William J.; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L.; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A.; Lambourne, John J.; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R.; Daugherty, Louise C.; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F.; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M.; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H. A.; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M.; Staley, James R.; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P.; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G.; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W.; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S.; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J.; Ouwehand, Willem H.; Butterworth, Adam S.; Soranzo, Nicole

2016-01-01

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell,

Phenotypic variation in a core collection of common bean (Phaseolus vulgaris L.) in the Netherlands

NARCIS (Netherlands)

Zeven, A.C.; Waninge, J.; Hintum, van Th.J.L.; Singh, S.P.

1999-01-01

Forty accessions, forming a core collection of mainly bush type of the common bean (Phaseolus vulgaris L.) germplasm in the Netherlands, were evaluated for 14 qualitative and quantitative traits at the Agricultural University, Wageningen (WAU), the Netherlands in 1992. These and an additional 117

Comprehensive mapping of common immunodominant epitopes in the West Nile virus nonstructural protein 1 recognized by avian antibody responses.

Directory of Open Access Journals (Sweden)

Encheng Sun

Full Text Available West Nile virus (WNV is a mosquito-borne flavivirus that primarily infects birds but occasionally infects humans and horses. Certain species of birds, including crows, house sparrows, geese, blue jays and ravens, are considered highly susceptible hosts to WNV. The nonstructural protein 1 (NS1 of WNV can elicit protective immune responses, including NS1-reactive antibodies, during infection of animals. The antigenicity of NS1 suggests that NS1-reactive antibodies could provide a basis for serological diagnostic reagents. To further define serological reagents for diagnostic use, the antigenic sites in NS1 that are targeted by host immune responses need to be identified and the potential diagnostic value of individual antigenic sites also needs to be defined. The present study describes comprehensive mapping of common immunodominant linear B-cell epitopes in the WNV NS1 using avian WNV NS1 antisera. We screened antisera from chickens, ducks and geese immunized with purified NS1 for reactivity against 35 partially overlapping peptides covering the entire WNV NS1. This study identified twelve, nine and six peptide epitopes recognized by chicken, duck and goose antibody responses, respectively. Three epitopes (NS1-3, 14 and 24 were recognized by antibodies elicited by immunization in all three avian species tested. We also found that NS1-3 and 24 were WNV-specific epitopes, whereas the NS1-14 epitope was conserved among the Japanese encephalitis virus (JEV serocomplex viruses based on the reactivity of avian WNV NS1 antisera against polypeptides derived from the NS1 sequences of viruses of the JEV serocomplex. Further analysis showed that the three common polypeptide epitopes were not recognized by antibodies in Avian Influenza Virus (AIV, Newcastle Disease Virus (NDV, Duck Plague Virus (DPV and Goose Parvovirus (GPV antisera. The knowledge and reagents generated in this study have potential applications in differential diagnostic approaches and

Personality and Information Processing Speed: Independent Influences on Intelligent Performance

Science.gov (United States)

Bates, Timothy C.; Rock, Andrew

2004-01-01

Raven's matrices and inspection time (IT) were recorded from 56 subjects under five arousal levels. Raven's and IT correlated strongly (r = -0.7) as predicted by processing-speed theories of "g." In line with Eysenck's [Eysenck, H. J. (1967). "The biological basis of personality". Springfield, IL: Thomas] arousal theory of extraversion, there was…

The Influence of Gender on the Likelihood of Using Soft Social Power Strategies in School Consultation

Science.gov (United States)

Getty, Kimberly C.; Erchul, William P.

2009-01-01

The social power typology developed originally by French and Raven in 1959 and revised by Raven in 1965 and 1992 was applied to study school consultation. Specifically, we investigated how the gender of school psychologist consultants and teacher consultees influence how likely consultants are to use soft power strategies, identified as those…

Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin.

Directory of Open Access Journals (Sweden)

Jennifer L Bolton

2014-07-01

Full Text Available Variation in plasma levels of cortisol, an essential hormone in the stress response, is associated in population-based studies with cardio-metabolic, inflammatory and neuro-cognitive traits and diseases. Heritability of plasma cortisol is estimated at 30-60% but no common genetic contribution has been identified. The CORtisol NETwork (CORNET consortium undertook genome wide association meta-analysis for plasma cortisol in 12,597 Caucasian participants, replicated in 2,795 participants. The results indicate that <1% of variance in plasma cortisol is accounted for by genetic variation in a single region of chromosome 14. This locus spans SERPINA6, encoding corticosteroid binding globulin (CBG, the major cortisol-binding protein in plasma, and SERPINA1, encoding α1-antitrypsin (which inhibits cleavage of the reactive centre loop that releases cortisol from CBG. Three partially independent signals were identified within the region, represented by common SNPs; detailed biochemical investigation in a nested sub-cohort showed all these SNPs were associated with variation in total cortisol binding activity in plasma, but some variants influenced total CBG concentrations while the top hit (rs12589136 influenced the immunoreactivity of the reactive centre loop of CBG. Exome chip and 1000 Genomes imputation analysis of this locus in the CROATIA-Korcula cohort identified missense mutations in SERPINA6 and SERPINA1 that did not account for the effects of common variants. These findings reveal a novel common genetic source of variation in binding of cortisol by CBG, and reinforce the key role of CBG in determining plasma cortisol levels. In turn this genetic variation may contribute to cortisol-associated degenerative diseases.

Low-frequency and common genetic variation in ischemic stroke: The METASTROKE collaboration.

Science.gov (United States)

Malik, Rainer; Traylor, Matthew; Pulit, Sara L; Bevan, Steve; Hopewell, Jemma C; Holliday, Elizabeth G; Zhao, Wei; Abrantes, Patricia; Amouyel, Philippe; Attia, John R; Battey, Thomas W K; Berger, Klaus; Boncoraglio, Giorgio B; Chauhan, Ganesh; Cheng, Yu-Ching; Chen, Wei-Min; Clarke, Robert; Cotlarciuc, Ioana; Debette, Stephanie; Falcone, Guido J; Ferro, Jose M; Gamble, Dale M; Ilinca, Andreea; Kittner, Steven J; Kourkoulis, Christina E; Lemmens, Robin; Levi, Christopher R; Lichtner, Peter; Lindgren, Arne; Liu, Jingmin; Meschia, James F; Mitchell, Braxton D; Oliveira, Sofia A; Pera, Joana; Reiner, Alex P; Rothwell, Peter M; Sharma, Pankaj; Slowik, Agnieszka; Sudlow, Cathie L M; Tatlisumak, Turgut; Thijs, Vincent; Vicente, Astrid M; Woo, Daniel; Seshadri, Sudha; Saleheen, Danish; Rosand, Jonathan; Markus, Hugh S; Worrall, Bradford B; Dichgans, Martin

2016-03-29

To investigate the influence of common and low-frequency genetic variants on the risk of ischemic stroke (all IS) and etiologic stroke subtypes. We meta-analyzed 12 individual genome-wide association studies comprising 10,307 cases and 19,326 controls imputed to the 1000 Genomes (1 KG) phase I reference panel. We selected variants showing the highest degree of association (p frequencies for all IS and stroke subtypes. We showed genome-wide significance for 4 loci: ABO for all IS, HDAC9 for large vessel disease (LVD), and both PITX2 and ZFHX3 for cardioembolic stroke (CE). We further refined the association peaks for ABO and PITX2. Analyzing different allele frequency bins, we showed significant enrichment in low-frequency variants (allele frequency frequency variants (allele frequency 10% and 30%) for CE (all p low-frequency and rare variants. Larger sample sizes are needed to identify the variants associated with all IS and stroke subtypes. © 2016 American Academy of Neurology.

Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC)

DEFF Research Database (Denmark)

Jim, Heather S L; Lin, Hui-Yi; Tyrer, Jonathan P

2015-01-01

where they regulate ovulation; circadian disruption is associated with several ovarian cancer risk factors (e.g., endometriosis). However, no studies have examined variation in germline circadian genes as predictors of ovarian cancer risk and invasiveness. The goal of the current study was to examine...... single nucleotide polymorphisms (SNPs) in circadian genes BMAL1, CRY2, CSNK1E, NPAS2, PER3, REV1 and TIMELESS and downstream transcription factors KLF10 and SENP3 as predictors of risk of epithelial ovarian cancer (EOC) and histopathologic subtypes. The study included a test set of 3,761 EOC cases and 2......,722 controls and a validation set of 44,308 samples including 18,174 (10,316 serous) cases and 26,134 controls from 43 studies participating in the Ovarian Cancer Association Consortium (OCAC). Analysis of genotype data from 36 genotyped SNPs and 4600 imputed SNPs indicated that the most significant...

On the notion of Jacobi fields in constrained calculus of variations

Directory of Open Access Journals (Sweden)

Massa Enrico

2016-12-01

Full Text Available In variational calculus, the minimality of a given functional under arbitrary deformations with fixed end-points is established through an analysis of the so called second variation. In this paper, the argument is examined in the context of constrained variational calculus, assuming piecewise differentiable extremals, commonly referred to as extremaloids. The approach relies on the existence of a fully covariant representation of the second variation of the action functional, based on a family of local gauge transformations of the original Lagrangian and on a set of scalar attributes of the extremaloid, called the corners' strengths [16]. In dis- cussing the positivity of the second variation, a relevant role is played by the Jacobi fields, defined as infinitesimal generators of 1-parameter groups of diffeomorphisms preserving the extremaloids. Along a piecewise differentiable extremal, these fields are generally discontinuous across the corners. A thorough analysis of this point is presented. An alternative characterization of the Jacobi fields as solutions of a suitable accessory variational problem is established.

Sounds scary? Lack of habituation following the presentation of novel sounds.

Directory of Open Access Journals (Sweden)

Tine A Biedenweg

Full Text Available BACKGROUND: Animals typically show less habituation to biologically meaningful sounds than to novel signals. We might therefore expect that acoustic deterrents should be based on natural sounds. METHODOLOGY: We investigated responses by western grey kangaroos (Macropus fulignosus towards playback of natural sounds (alarm foot stomps and Australian raven (Corvus coronoides calls and artificial sounds (faux snake hiss and bull whip crack. We then increased rate of presentation to examine whether animals would habituate. Finally, we varied frequency of playback to investigate optimal rates of delivery. PRINCIPAL FINDINGS: Nine behaviors clustered into five Principal Components. PC factors 1 and 2 (animals alert or looking, or hopping and moving out of area accounted for 36% of variance. PC factor 3 (eating cessation, taking flight, movement out of area accounted for 13% of variance. Factors 4 and 5 (relaxing, grooming and walking; 12 and 11% of variation, respectively discontinued upon playback. The whip crack was most evocative; eating was reduced from 75% of time spent prior to playback to 6% following playback (post alarm stomp: 32%, raven call: 49%, hiss: 75%. Additionally, 24% of individuals took flight and moved out of area (50 m radius in response to the whip crack (foot stomp: 0%, raven call: 8% and 4%, hiss: 6%. Increasing rate of presentation (12x/min ×2 min caused 71% of animals to move out of the area. CONCLUSIONS/SIGNIFICANCE: The bull whip crack, an artificial sound, was as effective as the alarm stomp at eliciting aversive behaviors. Kangaroos did not fully habituate despite hearing the signal up to 20x/min. Highest rates of playback did not elicit the greatest responses, suggesting that 'more is not always better'. Ultimately, by utilizing both artificial and biological sounds, predictability may be masked or offset, so that habituation is delayed and more effective deterrents may be produced.

[Loss of intelligence in aphasic disorders].

Science.gov (United States)

Blazková-Ctrnáctá, D; Kalvach, P; Preissová, I; Müllerová, B

2004-01-01

Certain level of aphasia is considered to be an integral component of dementia. More controversial is the question whether every--e.g. also strictly focal--aphasia must be accompanied with dementia. 41 persons hospitalized after the cerebral stroke (17 men, 24 women, average age 64.6, 47 to 89 years old) were tested to correlate the level of aphasia with mental and intelligence scores. 35 patients had an ischaemic stroke, 6 had a hemorrhagic one; according to CT/MRI there were 37 patients with left sided impairment, one patient with a right sided one and 3 patients with bilateral lesions. As an aphasiologic test the Western Aphasia Battery (WAB) was used, to determine the general mental performance as an equivalent of IQ test the non-verbal Raven's and verbal Euro-ADAS test were used. Correlation analysis using non-parametric Spearman's coefficient showed a significant relation between results in phatic functions and the score in intelligence tests. Phatic performance had in all elementary tests closer relation to verbal IQ in Euro-ADAS than with non-verbal IQ in Raven's test. The highest correlation was found in the relation between "apprehension vs. Euro-ADAS" (-0.842) and "apprehension vs. Raven" (0.782), while the lowest correlation was found for "repetition vs. Euro-ADAS" (-0.769), and "repetition vs. Raven" (0.646). The correlation was in all cases significant (p intelligence tests. Sensory aphasia was associated most closely with both relations, with Euro-ADAS (-0.800), and Raven's test (0.800), while global aphasia had the lowest correlation with Euro-ADAS (-0.451) and with Raven's test (0.517). Speech is not only a product of thinking but also represents a source and structural tool for thinking.

Steady-state entanglement and thermalization of coupled qubits in two common heat baths

Science.gov (United States)

Hu, Li-Zhen; Man, Zhong-Xiao; Xia, Yun-Jie

2018-03-01

In this work, we study the steady-state entanglement and thermalization of two coupled qubits embedded in two common baths with different temperatures. The common bath is relevant when the two qubits are difficult to be isolated to only contact with their local baths. With the quantum master equation constructed in the eigenstate representation of the coupled qubits, we have demonstrated the variations of steady-state entanglement with respect to various parameters of the qubits' system in both equilibrium and nonequilibrium cases of the baths. The coupling strength and energy detuning of the qubits as well as the temperature gradient of the baths are found to be beneficial to the enhancement of the entanglement. We note a dark state of the qubits that is free from time-evolution and its initial population can greatly influence the steady-state entanglement. By virtues of effective temperatures, we also study the thermalization of the coupled qubits and their variations with energy detuning.

Incidence Rate and Distribution of Common Cancers among Iranian Children

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Salman Khazaei

2017-01-01

Full Text Available Background: Geographic differences in the incidence of cancers may suggest unique genetic or environmental exposures that impact the risk of acquiring cancer. This research aims to determine the incidence rate and geographical distribution of common cancers among Iranian children. Methods: In this ecological study, we extracted data that pertained to the incidence rate of common cancers among children from reports by the National Registry of Cancer and Disease Control and Prevention in 2008. A map of the cancer incidence rates was designed by using geographic information system. Results:The most common cancer sites among children were the hematology system, brain and central nervous system, and lymph nodes. The central provinces had the lowest cancer incidences. Conclusion: The considerable variation in incidence of childhood cancers in Iran suggests a possible potential environmental risk factor or genetic background related to this increased risk among children.

Dopa decarboxylase (Ddc) affects variation in Drosophila longevity.

Science.gov (United States)

De Luca, Maria; Roshina, Nataliya V; Geiger-Thornsberry, Gretchen L; Lyman, Richard F; Pasyukova, Elena G; Mackay, Trudy F C

2003-08-01

Mutational analyses in model organisms have shown that genes affecting metabolism and stress resistance regulate life span, but the genes responsible for variation in longevity in natural populations are largely unidentified. Previously, we mapped quantitative trait loci (QTLs) affecting variation in longevity between two Drosophila melanogaster strains. Here, we show that the longevity QTL in the 36E;38B cytogenetic interval on chromosome 2 contains multiple closely linked QTLs, including the Dopa decarboxylase (Ddc) locus. Complementation tests to mutations show that Ddc is a positional candidate gene for life span in these strains. Linkage disequilibrium (LD) mapping in a sample of 173 alleles from a single population shows that three common molecular polymorphisms in Ddc account for 15.5% of the genetic contribution to variance in life span from chromosome 2. The polymorphisms are in strong LD, and the effects of the haplotypes on longevity suggest that the polymorphisms are maintained by balancing selection. DDC catalyzes the final step in the synthesis of the neurotransmitters, dopamine and serotonin. Thus, these data implicate variation in the synthesis of bioamines as a factor contributing to natural variation in individual life span.

Anatomical variation of celiac axis, superior mesenteric artery, and hepatic artery: Evaluation with multidetector computed tomography angiography

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Maryam Farghadani

2016-01-01

Full Text Available Background: The celiac axis, superior mesenteric artery (SMA, and hepatic artery are the most important branches of abdominal aorta due to their vascularization field. The aim of our study was to evaluate the prevalence of different anatomical variation of celiac axis, SMA, hepatic artery, and its branches with multidetector computed tomography (MDCT angiography of upper abdomen arteries. Materials and Methods: MDCT of 607 kidney donor and traumatic patients that referred to MDCT unit at Al Zahra Hospital in Isfahan from 2012 to 2015 were retrospectively evaluated. We excluded patients with history of abdominal vascular surgery and hepatic or pancreatic surgery. Computed tomography images of the patient were obtained with 64-row MDCT scanner and anatomical variations were analyzed. Results: Three hundred and eighty-eight (63.9% of the 607 patients had classic arterial anatomy and 219 (36.1% patients had variant types. The most common type of variation was the origin of the right hepatic artery (RHA from SMA (9.6%, and the next common variation was the origin of the left hepatic artery (LHA from the left gastric artery (6.9%. Variations in the origin of the common hepatic artery (CHA were seen in 16 (2.6% patients. Buhler arc was identified in two patients. The RHA originated from the celiac axis in 11 (1.8% patients and from the aorta in 8 (1.3% patients. Trifurcation of CHA into gastroduodenal artery, RHA, and LHA was detected in 11 (1.8% patients. Conclusion: The results of the present study showed that anatomical variation occurs in a high percentage of patients. Detection of these variations can guide surgical and radiological interventional planning.

Huntingtin gene repeat size variations affect risk of lifetime depression

DEFF Research Database (Denmark)

Gardiner, Sarah L.; van Belzen, Martine J.; Boogaard, Merel W.

2017-01-01

Huntington disease (HD) is a severe neuropsychiatric disorder caused by a cytosine-adenine-guanine (CAG) repeat expansion in the HTT gene. Although HD is frequently complicated by depression, it is still unknown to what extent common HTT CAG repeat size variations in the normal range could affect...

Dynamic assessment of intelligence is a better reply to adaptive behavior and cognitive plasticity.

Science.gov (United States)

Fabio, Rosa Angela

2005-01-01

In the present study, the author conducted 3 experiments to examine the dynamic testing of potential intelligence. She investigated the relationship between dynamic measures and other factors such as (a) static measures of intelligence (Raven's Colored Progressive Matrices Test [J. C. Raven, J. H. Court, & J. Raven, 1979] and the D48 [J. D. Black, 1961]) and (b) codifying speed, codifying accuracy, and school performance. The participants were kindergarten children (n = 150), primary school children (n = 287), and teenaged students (n = 198) who were all trained to master problem solving tests with dynamic measures of intelligence. The results showed that dynamic measures predict more accurately the relationships of codifying speed, codifying accuracy, and school performance.

Modeling response variation for radiometric calorimeters

International Nuclear Information System (INIS)

Mayer, R.L. II.

1986-01-01

Radiometric calorimeters are widely used in the DOE complex for accountability measurements of plutonium and tritium. Proper characterization of response variation for these instruments is, therefore, vital for accurate assessment of measurement control as well as for propagation of error calculations. This is not difficult for instruments used to measure items within a narrow range of power values; however, when a single instrument is used to measure items over a wide range of power values, improper estimates of uncertainty can result since traditional error models for radiometric calorimeters assume that uncertainty is not a function of sample power. This paper describes methods which can be used to accurately estimate random response variation for calorimeters used to measure items over a wide range of sample powers. The model is applicable to the two most common modes of calorimeter operation: heater replacement and servo control. 5 refs., 4 figs., 1 tab

Common Variation in the NOS1AP Gene Is Associated With Drug-Induced QT Prolongation and Ventricular Arrhythmia

NARCIS (Netherlands)

Jamshidi, Yalda; Nolte, Ilja M.; Dalageorgou, Chrysoula; Zheng, Dongling; Johnson, Toby; Bastiaenen, Rachel; Ruddy, Suzanne; Talbott, Daniel; Norris, Kris J.; Snieder, Harold; George, Alfred L.; Marshall, Vanessa; Shakir, Saad; Kannankeril, Prince J.; Munroe, Patricia B.; Camm, A. John; Jeffery, Steve; Roden, Dan M.; Behr, Elijah R.

2012-01-01

Objectives This study sought to determine whether variations in NOS1AP affect drug-induced long QT syndrome (LQTS). Background Use of antiarrhythmic drugs is limited by the high incidence of serious adverse events including QT prolongation and torsades de pointes. NOS1AP gene variants play a role in

Variations in brain DNA

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Jesus eAvila

2014-11-01

Full Text Available It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.

Slope instability caused by small variations in hydraulic conductivity

Science.gov (United States)

Reid, M.E.

1997-01-01

Variations in hydraulic conductivity can greatly modify hillslope ground-water flow fields, effective-stress fields, and slope stability. In materials with uniform texture, hydraulic conductivities can vary over one to two orders of magnitude, yet small variations can be difficult to determine. The destabilizing effects caused by small (one order of magnitude or less) hydraulic conductivity variations using ground-water flow modeling, finite-element deformation analysis, and limit-equilibrium analysis are examined here. Low hydraulic conductivity materials that impede downslope ground-water flow can create unstable areas with locally elevated pore-water pressures. The destabilizing effects of small hydraulic heterogeneities can be as great as those induced by typical variations in the frictional strength (approximately 4??-8??) of texturally similar materials. Common "worst-case" assumptions about ground-water flow, such as a completely saturated "hydrostatic" pore-pressure distribution, do not account for locally elevated pore-water pressures and may not provide a conservative slope stability analysis. In site characterization, special attention should be paid to any materials that might impede downslope ground-water flow and create unstable regions.

A Rare Variation of the Human Median Nerve Direction

Directory of Open Access Journals (Sweden)

Barfi

2016-04-01

Full Text Available Introduction The brachial plexus, a complex network of nerves, innervates to the upper limbs. Variation in the course of the nerves in the upper limb is common. Case Presentation This paper describes two cases of upper limb variations in a cadaver dissected at Lorestan University of Medical Sciences. In the first variation, the median nerve in the arm has a different route, so that the median moves deep into the brachialis muscle. In the latter case, after piercing the coracobrachialis muscle a musculocutaneous nerve exists between the brachialis and biceps and goes to the lateral region of the forearm. This is known as the lateral cutaneous nerve of the forearm nerve, and innervates the skin of the lateral part of the forearm and the dorsal part of the hand. Conclusions Because of the possibility of damage to the brachial plexus branches is high in upper limb injuries and surgeries, full knowledge of normal anatomy and variations of these branches is essential for orthopedic specialists, neurosurgeons, radiologists, and anatomists.

Variation in Quality of Urgent Health Care Provided During Commercial Virtual Visits.

Science.gov (United States)

Schoenfeld, Adam J; Davies, Jason M; Marafino, Ben J; Dean, Mitzi; DeJong, Colette; Bardach, Naomi S; Kazi, Dhruv S; Boscardin, W John; Lin, Grace A; Duseja, Reena; Mei, Y John; Mehrotra, Ateev; Dudley, R Adams

2016-05-01

Commercial virtual visits are an increasingly popular model of health care for the management of common acute illnesses. In commercial virtual visits, patients access a website to be connected synchronously-via videoconference, telephone, or webchat-to a physician with whom they have no prior relationship. To date, whether the care delivered through those websites is similar or quality varies among the sites has not been assessed. To assess the variation in the quality of urgent health care among virtual visit companies. This audit study used 67 trained standardized patients who presented to commercial virtual visit companies with the following 6 common acute illnesses: ankle pain, streptococcal pharyngitis, viral pharyngitis, acute rhinosinusitis, low back pain, and recurrent female urinary tract infection. The 8 commercial virtual visit websites with the highest web traffic were selected for audit, for a total of 599 visits. Data were collected from May 1, 2013, to July 30, 2014, and analyzed from July 1, 2014, to September 1, 2015. Completeness of histories and physical examinations, the correct diagnosis (vs an incorrect or no diagnosis), and adherence to guidelines of key management decisions. Sixty-seven standardized patients completed 599 commercial virtual visits during the study period. Histories and physical examinations were complete in 417 visits (69.6%; 95% CI, 67.7%-71.6%); diagnoses were correctly named in 458 visits (76.5%; 95% CI, 72.9%-79.9%), and key management decisions were adherent to guidelines in 325 visits (54.3%; 95% CI, 50.2%-58.3%). Rates of guideline-adherent care ranged from 206 visits (34.4%) to 396 visits (66.1%) across the 8 websites. Variation across websites was significantly greater for viral pharyngitis and acute rhinosinusitis (adjusted rates, 12.8% to 82.1%) than for streptococcal pharyngitis and low back pain (adjusted rates, 74.6% to 96.5%) or ankle pain and recurrent urinary tract infection (adjusted rates, 3.4% to 40

Experimental infection of nontarget species of rodents and birds with Brucella abortus strain RB51 vaccine

Science.gov (United States)

Januszewski, M.C.; Olsen, S.C.; McLean, R.G.; Clark, L.; Rhyan, Jack C.

2001-01-01

The Brucella abortus vaccine strain RB51 (SRB51) is being considered for use in the management of bnucellosis in wild bison (Bison bison) and elk (Cervus elaphus) populations in the Greater Yellowstone Area (USA). Evaluation of the vaccines safety in non-target species was considered necessary prior to field use. Between June 1998 and December 1999, ground squirrels (Spermophilus richardsonii, n = 21), deer mice (Peromyscus maniculatus, n = 14), prairie voles (Microtus ochrogaster, n = 21), and ravens (Corvus corax, n = 13) were orally inoculated with SRB51 or physiologic saline. Oral and rectal swabs and blood samples were collected for bacteriologic evaluation. Rodents were necropsied at 8 to 10 wk and 12 to 21 wk post inoculation (PI), and ravens at 7 and 11 wk PI. Spleen, liver and reproductive tissues were collected for bacteriologic and histopathologic evaluation. No differences in clinical signs, appetite, weight loss or gain, or activity were observed between saline- and SRB51-inoculated animals in all four species. Oral and rectal swabs from all species were negative throughout the study. In tissues obtained from SRB51-inoculated animals, the organism was isolated from six of seven (86%) ground squirrels, one of six (17%) deer mice, none of seven voles, and one of five (20%) ravens necropsied at 8, 8, 10, and 7 wk PI, respectively. Tissues from four of seven (57%) SRB51-inoculated ground squirrels were culture positive for the organism 12 wk PI; SRB51 was not recovered from deer mice, voles. or ravens necropsied 12, 21, or 11 wk, respectively, PI. SRB51 was not recovered from saline-inoculated ground squirrels, deer mice, or voles at any time but was recovered from one saline-inoculated raven at necropsy, 7 wk PI, likely attributable to contact with SRB51-inoculated ravens in an adjacent aviary room. Spleen was time primary tissue site of colonization in ground squirrels, followed by the liver and reproductive organs. The results indicate oral exposure to

Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

Science.gov (United States)

Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

2013-01-01

Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

Anatomical variations of paranasal sinuses: what to inform the otolaryngologist?

International Nuclear Information System (INIS)

Villela, Caroline Laurita Batista Couto; Gomes, Natalia Delage; Gaiotti, Juliana Oggioni; Costa, Ana Maria Doffemond; Ribeiro, Marcelo Almeida; Motta, Emilia Guerra Pinto Coelho; Moreira, Wanderval; Ramos, Laura Filgueiras Mourao; Diniz, Renata Lopes Furletti Caldeira

2012-01-01

Anatomic variations of paranasal sinuses are common findings in daily practice. For a radiologist, to know these variations is necessary because of the pathological conditions related to them, and also because they are import for planning a functional endoscopic endonasal surgery, the procedure of choice for diagnosis, biopsy and treatment of various sinonasal diseases. To assure that this surgery is done safely, preventing iatrogenic injuries, it is essential that the surgeon has the mapping of these structures. Thus, a CT is indispensable for preoperative evaluation of paranasal sinuses. Since a general radiologist is expected to know these changes and their relationship to pathological conditions, a literature review and a iconographic essay were conducted with the aim of discussing the importance of major anatomic variations of paranasal sinuses. (author)

Variation in Postsepsis Readmission Patterns: A Cohort Study of Veterans Affairs Beneficiaries

Science.gov (United States)

2017-01-01

Rationale: Rehospitalization is common after sepsis, but little is known about the variation in readmission patterns across patient groups and care locations. Objectives: To examine the variation in postsepsis readmission rates and diagnoses by patient age, nursing facility use, admission year, and hospital among U.S. Veterans Affairs (VA) beneficiaries. Methods: Observational cohort study of VA beneficiaries who survived a sepsis hospitalization (2009–2011) at 114 VA hospitals, stratified by age (readmission after sepsis hospitalization and proportion of readmissions resulting from specific diagnoses, including the proportion of “potentially preventable” readmissions. Readmission diagnoses were similar from 2009 to 2011, with little variation in readmission rates across hospitals. The top six readmission diagnoses (heart failure, pneumonia, sepsis, urinary tract infection, acute renal failure, and chronic obstructive pulmonary disease) accounted for 30% of all readmissions. Although about one in five readmissions had a principal diagnosis for infection, 58% of all readmissions received early systemic antibiotics. Infection accounted for a greater proportion of readmissions among patients discharged to nursing facilities compared with patients discharged to home (25.0–27.1% vs. 16.8%) and among older vs. younger patients (22.2% vs. 15.8%). Potentially preventable readmissions accounted for a quarter of readmissions overall and were more common among older patients and patients discharged to nursing facilities. Conclusions: Hospital readmission rates after sepsis were similar by site and admission year. Heart failure, pneumonia, sepsis, and urinary tract infection were common readmission diagnoses across all patient groups. Readmission for infection and potentially preventable diagnoses were more common in older patients and patients discharged to nursing facilities. PMID:27854510

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

Directory of Open Access Journals (Sweden)

Juliana Morini Küpper Cardoso Perseguini

2011-01-01

Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

Institute of Scientific and Technical Information of China (English)

Jifeng Zhu; Jing Wu; Lanfen Wang; Matthew W. Blair; Zhendong Zhu; Shumin Wang

2016-01-01

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans (Xff), is a worldwide disease of common bean (Phaseolus vulgaris L.). Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance, we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 plants. Plant resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1. A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previously-identified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19%to 12.15%and 7.72%to 8.80%at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China

Institute of Scientific and Technical Information of China (English)

Jifeng; Zhu; Jing; Wu; Lanfen; Wang; Matthew; W.Blair; Zhendong; Zhu; Shumin; Wang

2016-01-01

Common bacterial blight(CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans(Xff), is a worldwide disease of common bean(Phaseolus vulgaris L.).Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance,we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 plants.Plant resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1.A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previouslyidentified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19% to 12.15% and 7.72% to 8.80% at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

Theories of Population Variation in Genes and Genomes

DEFF Research Database (Denmark)

Christiansen, Freddy

This textbook provides an authoritative introduction to both classical and coalescent approaches to population genetics. Written for graduate students and advanced undergraduates by one of the world’s leading authorities in the field, the book focuses on the theoretical background of population...... genetics, while emphasizing the close interplay between theory and empiricism. Traditional topics such as genetic and phenotypic variation, mutation, migration, and linkage are covered and advanced by contemporary coalescent theory, which describes the genealogy of genes in a population, ultimately...... connecting them to a single common ancestor. Effects of selection, particularly genomic effects, are discussed with reference to molecular genetic variation. The book is designed for students of population genetics, bioinformatics, evolutionary biology, molecular evolution, and theoretical biology—as well...

Association between common germline genetic variation in 94 candidate genes or regions and risks of invasive epithelial ovarian cancer

DEFF Research Database (Denmark)

Quaye, Lydia; Tyrer, Jonathan; Ramus, Susan J

2009-01-01

BACKGROUND: Recent studies have identified several single nucleotide polymorphisms (SNPs) in the population that are associated with variations in the risks of many different diseases including cancers such as breast, prostate and colorectal. For ovarian cancer, the known highly penetrant suscept...

Sequence variation in TgROP7 gene among Toxoplasma gondii ...

African Journals Online (AJOL)

Yomi

2012-03-27

Mar 27, 2012 ... Toxoplasma gondii can infect a wide range of hosts including mammals and birds, causing toxoplasmosis which is one of the most common parasitic zoonoses worldwide. The present study examined sequence variation in rhoptry 7 (ROP7) gene among different T. gondii isolates from different hosts and ...

Nest survival is influenced by parental behaviour and heterospecifics in a mixed-species colony

Science.gov (United States)

Brussee, Brianne E.; Coates, Peter S.; Hothem, Roger L.; Howe, Kristy; Casazza, Michael L.; Eadie, John M.

2016-01-01

Studies of avian nest success often focus on examining influences of variation in environmental and seasonal factors. However, in-depth evaluations can also incorporate variation in individual incubation behaviour to further advance our understanding of avian reproductive ecology. We examined these relationships in colonially nesting Black-crowned Night-Herons Nycticorax nycticorax using intensive video-monitoring methods to quantify incubation behaviours. We modelled nest survival as a function of both extrinsic factors and incubation behaviours over a 3-year period (2010–12) on Alcatraz Island, USA. Model-averaged parameter estimates indicated that nest survival increased as a function of greater incubation constancy (% of time spent incubating eggs within a 24-h period), and average daily precipitation throughout the nesting stage. Common Ravens Corvus corax are the only known nest predator of Night-Herons on Alcatraz Island, as on many other coastal Pacific islands. We also investigated the effects of heterospecific nesting of California Gulls Larus californicus and Western Gulls Larus occidentalis in a mixed-species colony with Night-Herons, based on nesting proximity data collected over a 2-year period (2011–12). This second analysis indicated that, in addition to incubation behaviours, nesting heterospecifics are an important factor for explaining variation in Night-Heron nest survival. However, contrary to our original expectation, we found that Night-Herons experienced increased nest survival with increasing distance from gull colony boundaries. These results may apply to other areas with multiple colonial nesting species and similar predator communities and climatic patterns.

Mitochondrial DNA T4216C and A4917G variations in multiple sclerosis

DEFF Research Database (Denmark)

Andalib, Sasan; Talebi, Mahnaz; Sakhinia, Ebrahim

2015-01-01

DNA gene and A4917G variation in the mtDNA NADH Dehydrogenase 2 (ND2) gene are associated with MS in an Iranian population. MATERIAL AND METHODS: Blood samples were collected from 100 patients with MS and 100 unrelated healthy controls, and DNA extraction was performed by salting-out. By means.......637). Logistic regression analysis revealed an odds ratio (OR) of 1.2 with 95% CI of 0.4-3.5. CONCLUSION: The present study revealed no association between MS and T4216C variation in the ND1 mtDNA gene and A4917G variation in the mtDNA ND2 gene in the Iranian population....... focuses on the neurogenetics of the complex pathogenesis of MS in relation to factors such as mitochondrial DNA (mtDNA) variations. T4216C and A4917G are common mitochondrial gene variations associated with MS. The present study tested whether mtDNA T4216C variation in the NADH Dehydrogenase 1 (ND1) mt...

Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake

NARCIS (Netherlands)

T. Tanaka (Toshiko); J.S. Ngwa; F.J.A. van Rooij (Frank); M.C. Zillikens (Carola); M.K. Wojczynski (Mary ); A.C. Frazier-Wood (Alexis); D.K. Houston (Denise); S. Kanoni (Stavroula); R.N. Lemaitre (Rozenn ); J. Luan; V. Mikkilä (Vera); F. Renström (Frida); E. Sonestedt (Emily); J.H. Zhao (Jing Hua); A.Y. Chu (Audrey); L. Qi (Lu); D.I. Chasman (Daniel); M.C. De Oliveira Otto (Marcia); E.J. Dhurandhar (Emily); M.F. Feitosa (Mary Furlan); I. Johansson (Ingegerd); K-T. Khaw (Kay-Tee); K. Lohman (Kurt); A. Manichaikul (Ani); N.M. McKeown (Nicola ); D. Mozaffarian (Dariush); A.B. Singleton (Andrew); K. Stirrups (Kathy); J. Viikari (Jorma); Z. Ye (Zheng); S. Bandinelli (Stefania); I.E. Barroso (Inês); P. Deloukas (Panagiotis); N.G. Forouhi (Nita); A. Hofman (Albert); Y. Liu (YongMei); L.-P. Lyytikäinen (Leo-Pekka); K.E. North (Kari); M. Dimitriou (Maria); G. Hallmans (Göran); M. Kähönen (Mika); C. Langenberg (Claudia); J.M. Ordovas (Jose); A.G. Uitterlinden (André); F.B. Hu (Frank); I.-P. Kalafati (Ioanna-Panagiota); O. Raitakari (Olli); O.H. Franco (Oscar); A. Johnson (Anthony); V. Emilsson (Valur); J.A. Schrack (Jennifer); R.D. Semba; D.S. Siscovick (David); D.K. Arnett (Donna); I.B. Borecki (Ingrid); P.W. Franks (Paul); S.B. Kritchevsky (Stephen); R.J.F. Loos (Ruth); M. Orho-Melander (Marju); J.I. Rotter (Jerome); N.J. Wareham (Nick); J.C.M. Witteman (Jacqueline); L. Ferrucci (Luigi); G.V. Dedoussis (George); L.A. Cupples (Adrienne); J.A. Nettleton (Jennifer )

2013-01-01

textabstractBackground: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake.

Common approach to common interests

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-06-01

In referring to issues confronting the energy field in this region and options to be exercised in the future, I would like to mention the fundamental condition of the utmost importance. That can be summed up as follows: any subject in energy area can never be solved by one country alone, given the geographical and geopolitical characteristics intrinsically possessed by energy. So, a regional approach is needed and it is especially necessary for the main players in the region to jointly address problems common to them. Though it may be a matter to be pursued in the distant future, I am personally dreaming a 'Common Energy Market for Northeast Asia,' in which member countries' interests are adjusted so that the market can be integrated and the region can become a most economically efficient market, thus formulating an effective power to encounter the outside. It should be noted that Europe needed forty years to integrate its market as the unified common market. It is necessary for us to follow a number of steps over the period to eventually materialize our common market concept, too. Now is the time for us to take a first step to lay the foundation for our descendants to enjoy prosperity from such a common market.

Genetic Parameters of Common Wheat in Nepal

Directory of Open Access Journals (Sweden)

Bal Krishna Joshi

2015-12-01

Full Text Available Knowledge on variation within traits and their genetics are prerequisites in crop improvement program. Thus, in present paper we aimed to estimate genetic and environmental indices of common wheat genotypes. For the purpose, eight quantitative traits were measured from 30 wheat genotypes, which were in randomized complete block design with 3 replicates. Components of variance and covariance were estimated along with heritability, genetic gain, realized heritability, coheritability and correlated response. Differences between phenotypic and genotypic variances in heading days, maturity days and plant height were not large. Grain yield and plant height showed the highest phenotypic (18.189% and genotypic (12.06% coefficient of variances, respectively. Phenotypic covariance was higher than genotypic and environmental covariance in most of the traits. The highest heritability and realized heritability were of heading days followed by maturity days. Genetic gain for plant height was the highest. Co-heritability of 1000-grain weight with tillers number was the highest. The highest correlated response was expressed by grain yield with tillers number. This study indicates the possibility of improving wheat genotypes through selection utilizing existing variation in these traits.

Cone-Beam Computed Tomography Evaluation of Mental Foramen Variations: A Preliminary Study

International Nuclear Information System (INIS)

Sheikhi, Mahnaz; Karbasi Kheir, Mitra; Hekmatian, Ehsan

2015-01-01

Background. Mental foramen is important in surgical operations of premolars because it transfers the mental nerves and vessels. This study evaluated the variations of mental foramen by cone-beam computed tomography among a selected Iranian population. Materials and Methods. A total number of 180 cone-beam computed tomography projections were analyzed in terms of shape, size, direction, and horizontal and vertical positions of mental foramen in the right and left sides. Results. The most common shape was oval, opening direction was posterior-superior, horizontal position was in line with second premolar, and vertical position was apical to the adjacent dental root. The mean of foremen diameter was 3.59 mm. Conclusion. In addition to the most common types of mental foramen, other variations exist, too. Hence, it reflects the significance of preoperative radiographic examinations, especially 3-dimensional images to prevent nerve damage

High risk of lead contamination for scavengers in an area with high moose hunting success.

Science.gov (United States)

Legagneux, Pierre; Suffice, Pauline; Messier, Jean-Sébastien; Lelievre, Frédérick; Tremblay, Junior A; Maisonneuve, Charles; Saint-Louis, Richard; Bêty, Joël

2014-01-01

Top predators and scavengers are vulnerable to pollutants, particularly those accumulated along the food chain. Lead accumulation can induce severe disorders and alter survival both in mammals (including humans) and in birds. A potential source of lead poisoning in wild animals, and especially in scavengers, results from the consumption of ammunition residues in the tissues of big game killed by hunters. For two consecutive years we quantified the level lead exposure in individuals of a sentinel scavenger species, the common raven (Corvus corax), captured during the moose (Alces alces) hunting season in eastern Quebec, Canada. The source of the lead contamination was also determined using stable isotope analyses. Finally, we identified the different scavenger species that could potentially be exposed to lead by installing automatic cameras targeting moose gut piles. Blood lead concentration in ravens increased over time, indicating lead accumulation over the moose-hunting season. Using a contamination threshold of 100 µg x L(-1), more than 50% of individuals were lead-contaminated during the moose hunting period. Lead concentration was twice as high in one year compared to the other, matching the number of rifle-shot moose in the area. Non-contaminated birds exhibited no ammunition isotope signatures. The isotope signature of the lead detected in contaminated ravens tended towards the signature from lead ammunition. We also found that black bears (Ursus americanus), golden eagles and bald eagles (Aquila chrysaetos and Haliaeetus leucocephalus, two species of conservation concern) scavenged heavily on moose viscera left by hunters. Our unequivocal results agree with other studies and further motivate the use of non-toxic ammunition for big game hunting.

High risk of lead contamination for scavengers in an area with high moose hunting success.

Directory of Open Access Journals (Sweden)

Pierre Legagneux

Full Text Available Top predators and scavengers are vulnerable to pollutants, particularly those accumulated along the food chain. Lead accumulation can induce severe disorders and alter survival both in mammals (including humans and in birds. A potential source of lead poisoning in wild animals, and especially in scavengers, results from the consumption of ammunition residues in the tissues of big game killed by hunters. For two consecutive years we quantified the level lead exposure in individuals of a sentinel scavenger species, the common raven (Corvus corax, captured during the moose (Alces alces hunting season in eastern Quebec, Canada. The source of the lead contamination was also determined using stable isotope analyses. Finally, we identified the different scavenger species that could potentially be exposed to lead by installing automatic cameras targeting moose gut piles. Blood lead concentration in ravens increased over time, indicating lead accumulation over the moose-hunting season. Using a contamination threshold of 100 µg x L(-1, more than 50% of individuals were lead-contaminated during the moose hunting period. Lead concentration was twice as high in one year compared to the other, matching the number of rifle-shot moose in the area. Non-contaminated birds exhibited no ammunition isotope signatures. The isotope signature of the lead detected in contaminated ravens tended towards the signature from lead ammunition. We also found that black bears (Ursus americanus, golden eagles and bald eagles (Aquila chrysaetos and Haliaeetus leucocephalus, two species of conservation concern scavenged heavily on moose viscera left by hunters. Our unequivocal results agree with other studies and further motivate the use of non-toxic ammunition for big game hunting.

Controllability for Variational Inequalities of Parabolic Type with Nonlinear Perturbation

Directory of Open Access Journals (Sweden)

Jeong Jin-Mun

2010-01-01

Full Text Available We deal with the approximate controllability for the nonlinear functional differential equation governed by the variational inequality in Hilbert spaces and present a general theorems under which previous results easily follow. The common research direction is to find conditions on the nonlinear term such that controllability is preserved under perturbation.

Common Courses for Common Purposes:

DEFF Research Database (Denmark)

Schaub Jr, Gary John

2014-01-01

(PME)? I suggest three alternative paths that increased cooperation in PME at the level of the command and staff course could take: a Nordic Defence College, standardized national command and staff courses, and a core curriculum of common courses for common purposes. I conclude with a discussion of how...

Variation in radiographic protocols in paediatric interventional cardiology

International Nuclear Information System (INIS)

McFadden, S L; Hughes, C M; Winder, R J

2013-01-01

The aim of this work is to determine current radiographic protocols in paediatric interventional cardiology (IC) in the UK and Ireland. To do this we investigated which imaging parameters/protocols are commonly used in IC in different hospitals, to identify if a standard technique is used and illustrate any variation in practice. A questionnaire was sent to all hospitals in the UK and Ireland which perform paediatric IC to obtain information on techniques used in each clinical department and on the range of clinical examinations performed. Ethical and research governance approval was sought from the Office for Research Ethics Committees Northern Ireland and the individual trusts. A response rate of 79% was achieved, and a wide variation in technique was found between hospitals. The main differences in technique involved variations in the use of an anti-scatter grid and the use of additional filtration to the radiation beam, frame rates for digital acquisition and pre-programmed projections/paediatric specific programming in the equipment. We conclude that there is no standard protocol for carrying out paediatric IC in the UK or Ireland. Each hospital carries out the IC procedure according to its own local protocols resulting in a wide variation in radiation dose. (paper)

Variation in radiographic protocols in paediatric interventional cardiology.

Science.gov (United States)

McFadden, S L; Hughes, C M; Winder, R J

2013-06-01

The aim of this work is to determine current radiographic protocols in paediatric interventional cardiology (IC) in the UK and Ireland. To do this we investigated which imaging parameters/protocols are commonly used in IC in different hospitals, to identify if a standard technique is used and illustrate any variation in practice. A questionnaire was sent to all hospitals in the UK and Ireland which perform paediatric IC to obtain information on techniques used in each clinical department and on the range of clinical examinations performed. Ethical and research governance approval was sought from the Office for Research Ethics Committees Northern Ireland and the individual trusts. A response rate of 79% was achieved, and a wide variation in technique was found between hospitals. The main differences in technique involved variations in the use of an anti-scatter grid and the use of additional filtration to the radiation beam, frame rates for digital acquisition and pre-programmed projections/paediatric specific programming in the equipment. We conclude that there is no standard protocol for carrying out paediatric IC in the UK or Ireland. Each hospital carries out the IC procedure according to its own local protocols resulting in a wide variation in radiation dose.

Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

Directory of Open Access Journals (Sweden)

Shulan Fu

Full Text Available BACKGROUND: Monosomic alien addition lines (MAALs can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP and methylation-sensitive amplification polymorphism (MSAP analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. CONCLUSIONS/SIGNIFICANCE: The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations

International Nuclear Information System (INIS)

Tsai, Yi-Chien; Chiao, Chun-Hui; Chang, Ian Yi-Feng; Chen, Dow-Tien; Liu, Tze-Tze; Hua, Kate; Chang, Chuan-Hsiung; Hsu, Ming-Ta

2011-01-01

We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis)

Complex patterns of geographic variation in heat tolerance and Hsp70 expression levels in the common frog Rana temporaria

DEFF Research Database (Denmark)

Sørensen, Jesper Givskov; Pekkonen, Minna; Lindgren, Beatrice

2009-01-01

1. We tested for geographical variation in heat tolerance and Hsp70 expression levels of Rana temporaria tadpoles along a 1500 km long latitudinal gradient in Sweden.   2. Temperature tolerance of the hatchling tadpoles did not differ among populations, but they tolerated stressful hot temperatur...

Dynamics of nonholonomic systems from variational principles embedded variation identity

International Nuclear Information System (INIS)

Guo Yongxin; Liu Shixing; Liu Chang; Chang Peng

2009-01-01

Nondeterminacy of dynamics, i.e., the nonholonomic or the vakonomic, fundamental variational principles, e.g., the Lagrange-d'Alembert or Hamiltonian, and variational operators, etc., of nonholonomic mechanical systems can be attributed to the non-uniqueness of ways how to realize nonholonomic constraints. Making use of a variation identity of nonholonomic constraints embedded into the Hamilton's principle with the method of Lagrange undetermined multipliers, three kinds of dynamics for the nonholonomic systems including the vakonomic and nonholonomic ones and a new one are obtained if the variation is respectively reduced to three conditional variations: vakonomic variation, Hoelder's variation and Suslov's variation, defined by the identity. Therefore, different dynamics of nonholonomic systems can be derived from an integral variational principle, utilizing one way of embedding constraints into the principle, with different variations. It is verified that the similar embedding of the identity into the Lagrange-d'Alembert principle gives rise to the nonholonomic dynamics but fails to give the vakonomic one unless the constraints are integrable.

Quasi-static responses and variational principles in gradient plasticity

Science.gov (United States)

Nguyen, Quoc-Son

2016-12-01

Gradient models have been much discussed in the literature for the study of time-dependent or time-independent processes such as visco-plasticity, plasticity and damage. This paper is devoted to the theory of Standard Gradient Plasticity at small strain. A general and consistent mathematical description available for common time-independent behaviours is presented. Our attention is focussed on the derivation of general results such as the description of the governing equations for the global response and the derivation of related variational principles in terms of the energy and the dissipation potentials. It is shown that the quasi-static response under a loading path is a solution of an evolution variational inequality as in classical plasticity. The rate problem and the rate minimum principle are revisited. A time-discretization by the implicit scheme of the evolution equation leads to the increment problem. An increment of the response associated with a load increment is a solution of a variational inequality and satisfies also a minimum principle if the energy potential is convex. The increment minimum principle deals with stables solutions of the variational inequality. Some numerical methods are discussed in view of the numerical simulation of the quasi-static response.

Genetic variation at CHRNA5-CHRNA3-CHRNB4 interacts with smoking status to influence body mass index

DEFF Research Database (Denmark)

Freathy, Rachel M; Kazeem, Gbenga R; Morris, Richard W

2011-01-01

Cigarette smoking is associated with lower body mass index (BMI), and a commonly cited reason for unwillingness to quit smoking is a concern about weight gain. Common variation in the CHRNA5-CHRNA3-CHRNB4 gene region (chromosome 15q25) is robustly associated with smoking quantity in smokers, but ......, but its association with BMI is unknown. We hypothesized that genotype would accurately reflect smoking exposure and that, if smoking were causally related to weight, it would be associated with BMI in smokers, but not in never smokers.......Cigarette smoking is associated with lower body mass index (BMI), and a commonly cited reason for unwillingness to quit smoking is a concern about weight gain. Common variation in the CHRNA5-CHRNA3-CHRNB4 gene region (chromosome 15q25) is robustly associated with smoking quantity in smokers...

Clinal variation of some mammals during the Holocene in Missouri

Science.gov (United States)

Purdue, James R.

1980-03-01

Eastern cottontail ( Sylvilagus floridanus), fox squirrel ( Sciurus niger), and gray squirrel ( Sciurus carolinensis) were examined for clinal variation during the Holocene. Modern samples of all three species displayed strong east-west patterns along the western edge of the eastern deciduous forest: S. floridanus and S. niger decrease and S. carolinensis increases in size. Archeological samples of S. carolinensis from Rodgers Shelter (23BE125), Benton County, Missouri, and Graham Cave (23MT2), Montgomery County, Missouri, indicated an increase in size from early to middle Holocene. Sylvilagus floridanus from Rodgers Shelter decreased in size from early to middle Holocene and then increased during the late Holocene to modern proportions. A literature survey reveals that clinal variation is a common phenomenon among modern homeotherms. In introduced species, clinal variation has developed after relatively few generations, indicating rapid adaptations to environmental conditions; often winter climatic variables are implicated. Morphological variation in the study species during the Holocene is interpreted as a response to changing climates. Studies of morphological clines may lead to another valuable data source for reconstructing past ecologies.

Body size and allometric variation in facial shape in children.

Science.gov (United States)

Larson, Jacinda R; Manyama, Mange F; Cole, Joanne B; Gonzalez, Paula N; Percival, Christopher J; Liberton, Denise K; Ferrara, Tracey M; Riccardi, Sheri L; Kimwaga, Emmanuel A; Mathayo, Joshua; Spitzmacher, Jared A; Rolian, Campbell; Jamniczky, Heather A; Weinberg, Seth M; Roseman, Charles C; Klein, Ophir; Lukowiak, Ken; Spritz, Richard A; Hallgrimsson, Benedikt

2018-02-01

Morphological integration, or the tendency for covariation, is commonly seen in complex traits such as the human face. The effects of growth on shape, or allometry, represent a ubiquitous but poorly understood axis of integration. We address the question of to what extent age and measures of size converge on a single pattern of allometry for human facial shape. Our study is based on two large cross-sectional cohorts of children, one from Tanzania and the other from the United States (N = 7,173). We employ 3D facial imaging and geometric morphometrics to relate facial shape to age and anthropometric measures. The two populations differ significantly in facial shape, but the magnitude of this difference is small relative to the variation within each group. Allometric variation for facial shape is similar in both populations, representing a small but significant proportion of total variation in facial shape. Different measures of size are associated with overlapping but statistically distinct aspects of shape variation. Only half of the size-related variation in facial shape can be explained by the first principal component of four size measures and age while the remainder associates distinctly with individual measures. Allometric variation in the human face is complex and should not be regarded as a singular effect. This finding has important implications for how size is treated in studies of human facial shape and for the developmental basis for allometric variation more generally. © 2017 Wiley Periodicals, Inc.

Simultaneously Discovering and Localizing Common Objects in Wild Images.

Science.gov (United States)

Wang, Zhenzhen; Yuan, Junsong

2018-09-01

Motivated by the recent success of supervised and weakly supervised common object discovery, in this paper, we move forward one step further to tackle common object discovery in a fully unsupervised way. Generally, object co-localization aims at simultaneously localizing objects of the same class across a group of images. Traditional object localization/detection usually trains specific object detectors which require bounding box annotations of object instances, or at least image-level labels to indicate the presence/absence of objects in an image. Given a collection of images without any annotations, our proposed fully unsupervised method is to simultaneously discover images that contain common objects and also localize common objects in corresponding images. Without requiring to know the total number of common objects, we formulate this unsupervised object discovery as a sub-graph mining problem from a weighted graph of object proposals, where nodes correspond to object proposals, and edges represent the similarities between neighbouring proposals. The positive images and common objects are jointly discovered by finding sub-graphs of strongly connected nodes, with each sub-graph capturing one object pattern. The optimization problem can be efficiently solved by our proposed maximal-flow-based algorithm. Instead of assuming that each image contains only one common object, our proposed solution can better address wild images where each image may contain multiple common objects or even no common object. Moreover, our proposed method can be easily tailored to the task of image retrieval in which the nodes correspond to the similarity between query and reference images. Extensive experiments on PASCAL VOC 2007 and Object Discovery data sets demonstrate that even without any supervision, our approach can discover/localize common objects of various classes in the presence of scale, view point, appearance variation, and partial occlusions. We also conduct broad

Genotype variation in bark texture drives lichen community assembly across multiple environments.

Science.gov (United States)

Lamit, L J; Lau, M K; Naesborg, R Reese; Wojtowicz, T; Whitham, T G; Gehring, C A

2015-04-01

A major goal of community genetics is to understand the influence of genetic variation within a species on ecological communities. Although well-documented for some organisms, additional research is necessary to understand the relative and interactive effects of genotype and environment on biodiversity, identify mechanisms through which tree genotype influences communities, and connect this emerging field with existing themes in ecology. We employ an underutilized but ecologically significant group of organisms, epiphytic bark lichens, to understand the relative importance of Populus angustifolia (narrowleaf cottonwood) genotype and environment on associated organisms within the context of community assembly and host ontogeny. Several key findings emerged. (1) In a single common garden, tree genotype explained 18-33% and 51% of the variation in lichen community variables and rough bark cover, respectively. (2) Across replicated common gardens, tree genotype affected lichen species richness, total lichen cover, lichen species composition, and rough bark cover, whereas environment only influenced composition and there were no genotype by environment interactions. (3) Rough bark cover was positively correlated with total lichen cover and richness, and was associated with a shift in species composition; these patterns occurred with variation in rough bark cover among tree genotypes of the same age in common gardens and with increasing rough bark cover along a -40 year tree age gradient in a natural riparian stand. (4) In a common garden, 20-year-old parent trees with smooth bark had poorly developed lichen communities, similar to their 10-year-old ramets (root suckers) growing in close proximity, while parent trees with high rough bark cover had more developed communities than their ramets. These findings indicate that epiphytic lichens are influenced by host genotype, an effect that is robust across divergent environments. Furthermore, the response to tree genotype is

Large-Scale Evaluation of Common Variation in Regulatory T Cell-Related Genes and Ovarian Cancer Outcome

OpenAIRE

Charbonneau, Bridget; Moysich, Kirsten B.; Kalli, Kimberly R.; Oberg, Ann L.; Vierkant, Robert A.; Fogarty, Zachary C.; Block, Matthew S.; Maurer, Matthew J.; Goergen, Krista M.; Fridley, Brooke L.; Cunningham, Julie M.; Rider, David N.; Preston, Claudia; Hartmann, Lynn C.; Lawrenson, Kate

2014-01-01

The presence of regulatory T cells (Tregs) in solid tumors is known to play a role in patient survival in ovarian cancer and other malignancies. We assessed inherited genetic variations via 749 tag SNPs in 25 Treg-associated genes (CD28, CTLA4, FOXP3, IDO1, IL10, IL10RA, IL15, 1L17RA, IL23A, IL23R, IL2RA, IL6, IL6R, IL8, LGALS1, LGALS9, MAP3K8, STAT5A, STAT5B, TGFB1, TGFB2, TGFB3, TGFBR1, TGRBR2, and TGFBR3) in relation to ovarian cancer survival. We analyzed genotype and overall survival in ...

Dynamics of nonholonomic systems from variational principles embedded variation identity

Energy Technology Data Exchange (ETDEWEB)

Guo Yongxin, E-mail: yxguo@lnu.edu.c [College of Physics, Liaoning University, Shenyang 110036 (China); Liu Shixing [College of Physics, Liaoning University, Shenyang 110036 (China); Liu Chang; Chang Peng [Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081 (China)

2009-10-19

Nondeterminacy of dynamics, i.e., the nonholonomic or the vakonomic, fundamental variational principles, e.g., the Lagrange-d'Alembert or Hamiltonian, and variational operators, etc., of nonholonomic mechanical systems can be attributed to the non-uniqueness of ways how to realize nonholonomic constraints. Making use of a variation identity of nonholonomic constraints embedded into the Hamilton's principle with the method of Lagrange undetermined multipliers, three kinds of dynamics for the nonholonomic systems including the vakonomic and nonholonomic ones and a new one are obtained if the variation is respectively reduced to three conditional variations: vakonomic variation, Hoelder's variation and Suslov's variation, defined by the identity. Therefore, different dynamics of nonholonomic systems can be derived from an integral variational principle, utilizing one way of embedding constraints into the principle, with different variations. It is verified that the similar embedding of the identity into the Lagrange-d'Alembert principle gives rise to the nonholonomic dynamics but fails to give the vakonomic one unless the constraints are integrable.

Documenting Sociolinguistic Variation in Lesser-Studied Indigenous Communities: Challenges and Practical Solutions

Science.gov (United States)

Mansfield, John; Stanford, James

2017-01-01

Documenting sociolinguistic variation in lesser-studied languages presents methodological challenges, but also offers important research opportunities. In this paper we examine three key methodological challenges commonly faced by researchers who are outsiders to the community. We then present practical solutions for successful variationist…

Greening the Common Agricultural Policy. Impacts on farmland biodiversity on an EU scale

Energy Technology Data Exchange (ETDEWEB)

Van Zeijts, H.; Overmars, K.; Van der Bilt, W.; Schulp, N.; Notenboom, J.; Westhoek, H. [Netherlands Environmental Assessment Agency PBL, Den Haag (Netherlands); Helming, J.; Terluin, I. [LEI, Wageningen University and Research Centre WUR, Wageningen (Netherlands); Janssen, S. [Alterra Wageningen UR, Wageningen (Netherlands)

2011-08-15

'Greening' the EU Common Agricultural Policy (CAP), as proposed by the European Commission (EC), will slow down the decline in farmland biodiversity, most notably in intensive farming areas. Extensively farmed areas are better served by policies preserving their rich biodiversity. Regional variation in policies tailored to reflect local conditions could, therefore, result in a better outcome.

Genetic variation in WRN and ischemic stroke

DEFF Research Database (Denmark)

Christoffersen, Mette; Frikke-Schmidt, Ruth; Nordestgaard, Børge G.

2017-01-01

trends for ischemic cerebrovascular disease (P = 0.06). In meta-analyses including 59,190 individuals in 5 studies, the hazard ratio for ischemic stroke for C1367R TT homozygotes versus CC/CT was 1.14 (1.04–1.25; P = 0.008). Conclusions This study suggests that common genetic variation in WRN......Background Werner syndrome, a premature genetic aging syndrome, shares many clinical features reminiscent of normal physiological aging, and ischemic vascular disease is a frequent cause of death. We tested the hypothesis that genetic variation in the WRN gene was associated with risk of ischemic...... vascular disease in the general population. Methods We included 58,284 participants from two general population cohorts, the Copenhagen City Heart Study (CCHS) and the Copenhagen General Population Study (CGPS). Of these, 6,312 developed ischemic vascular disease during follow-up. In the CCHS (n = 10...

Interpretation of biological and mechanical variations between the Lowry versus Bradford method for protein quantification

OpenAIRE

Tzong-Shi Lu; Szu-Yu Yiao; Kenneth Lim; Roderick V. Jensen; Li-Li Hsiao

2010-01-01

Background: The identification of differences in protein expression resulting from methodical variations is an essential component to the interpretation of true, biologically significant results. Aims: We used the Lowry and Bradford methods- two most commonly used methods for protein quantification, to assess whether differential protein expressions are a result of true biological or methodical variations. Material & Methods: Differential protein expression patterns was assessed by western bl...

Salix transect of Europe: variation in ploidy and genome size in willow-associated common nettle, Urtica dioica L. sens. lat., from Greece to arctic Norway.

Science.gov (United States)

Cronk, Quentin; Hidalgo, Oriane; Pellicer, Jaume; Percy, Diana; Leitch, Ilia J

2016-01-01

The common stinging nettle, Urtica dioica L. sensu lato, is an invertebrate "superhost", its clonal patches maintaining large populations of insects and molluscs. It is extremely widespread in Europe and highly variable, and two ploidy levels (diploid and tetraploid) are known. However, geographical patterns in cytotype variation require further study. We assembled a collection of nettles in conjunction with a transect of Europe from the Aegean to Arctic Norway (primarily conducted to examine the diversity of Salix and Salix -associated insects). Using flow cytometry to measure genome size, our sample of 29 plants reveals 5 diploids and 24 tetraploids. Two diploids were found in SE Europe (Bulgaria and Romania) and three diploids in S. Finland. More detailed cytotype surveys in these regions are suggested. The tetraploid genome size (2C value) varied between accessions from 2.36 to 2.59 pg. The diploids varied from 1.31 to 1.35 pg per 2C nucleus, equivalent to a haploid genome size of c. 650 Mbp. Within the tetraploids, we find that the most northerly samples (from N. Finland and arctic Norway) have a generally higher genome size. This is possibly indicative of a distinct population in this region.

Nest occupation and prey grabbing by saker falcon (Falco cherrug on power lines in the province of Vojvodina (Serbia

Directory of Open Access Journals (Sweden)

Puzović S.

2008-01-01

Full Text Available Research on nest occupation and prey grabbing by saker falcon (Falco cherrug on power lines in Vojvodina (Serbia was done in the period from 1986 to 2004. During three specially analyzed periods, saker falcon took the nests of raven (Corvus corax in 91% of a total of 22 cases of nest occupation, and those of hooded crow (Corvus corone cornix in only 9%. Saker falcon regularly grabs prey from different birds that occasionally or constantly spend time around power lines [Kestrel (Falco tinnunculus, hobby (Falco subbuteo, hooded crow (Corvus corone cornix, jack-daw (Corvus monedula, marsh harrier (Circus aeruginosus, hen harrier (Circus cyaneus, buzzard (Buteo buteo, and raven (Corvus corax]. One year a studied pair of saker falcons on a power line in Donji Srem, Serbia grabbed prey from five different species of birds. Out of a total of 40 cases of prey grabbing in the period from January to December, as much 70% of the grabbed prey was taken from kestrel (Falco tinnunculus. During the winter and early spring, prey was grabbed predominantly by males; after May, prey was sometimes grabbed by females as well. Most of the grabbed prey was common vole (Microtus arvalis.

Determining Need for School-Based Physical Therapy Under IDEA: Commonalities Across Practice Guidelines.

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Vialu, Carlo; Doyle, Maura

2017-10-01

The Individuals with Disabilities Education Act (IDEA) includes physical therapy (PT) as a related service that may be provided to help students with disabilities benefit from their education. However, the IDEA does not provide specific guidance for the provision of school-based PT, resulting in variations in practice across the United States. The authors examined 22 state and local education agency guidelines available online to find commonalities related to the determination of a student's need for PT. Seven commonalities found: educational benefit, team decision, need for PT expertise, establishment of Individualized Education Program (IEP) goal before determining need for PT, distinction between medical and educational PT, the student's disability adversely affects education, and the student's potential for improvement. These commonalities are discussed in relation to current PT and special education literature. This article suggests applying these commonalities as procedural requirements and questions for discussion during an IEP team meeting.

Genetic and ontogenetic variation in an endangered tree structures dependent arthropod and fungal communities.

Directory of Open Access Journals (Sweden)

Benjamin J Gosney

Full Text Available Plant genetic and ontogenetic variation can significantly impact dependent fungal and arthropod communities. However, little is known of the relative importance of these extended genetic and ontogenetic effects within a species. Using a common garden trial, we compared the dependent arthropod and fungal community on 222 progeny from two highly differentiated populations of the endangered heteroblastic tree species, Eucalyptus morrisbyi. We assessed arthropod and fungal communities on both juvenile and adult foliage. The community variation was related to previous levels of marsupial browsing, as well as the variation in the physicochemical properties of leaves using near-infrared spectroscopy. We found highly significant differences in community composition, abundance and diversity parameters between eucalypt source populations in the common garden, and these were comparable to differences between the distinctive juvenile and adult foliage. The physicochemical properties assessed accounted for a significant percentage of the community variation but did not explain fully the community differences between populations and foliage types. Similarly, while differences in population susceptibility to a major marsupial herbivore may result in diffuse genetic effects on the dependent community, this still did not account for the large genetic-based differences in dependent communities between populations. Our results emphasize the importance of maintaining the populations of this rare species as separate management units, as not only are the populations highly genetically structured, this variation may alter the trajectory of biotic colonization of conservation plantings.

Investigation of switching frequency variations and EMI properties in self-oscillating class D amplifiers

OpenAIRE

Nielsen, Dennis; Knott, Arnold; Pfaffinger, Gerhard; Andersen, Michael A. E.

2009-01-01

Class D audio amplifiers have gained significant influence in sound reproduction due to their high efficiency. One of the most commonly used control methods in these amplifiers is self-oscillation. A parameter of key interest in self-oscillating amplifiers is the switching frequency, which is known for its variation. Knowledge of switching frequency variations is of great importance with respect to electromagnetic interference (EMI). This paper will investigate, whether the switching frequenc...

Structural genomic variation in ischemic stroke

Science.gov (United States)

Matarin, Mar; Simon-Sanchez, Javier; Fung, Hon-Chung; Scholz, Sonja; Gibbs, J. Raphael; Hernandez, Dena G.; Crews, Cynthia; Britton, Angela; Wavrant De Vrieze, Fabienne; Brott, Thomas G.; Brown, Robert D.; Worrall, Bradford B.; Silliman, Scott; Case, L. Douglas; Hardy, John A.; Rich, Stephen S.; Meschia, James F.; Singleton, Andrew B.

2008-01-01

Technological advances in molecular genetics allow rapid and sensitive identification of genomic copy number variants (CNVs). This, in turn, has sparked interest in the function such variation may play in disease. While a role for copy number mutations as a cause of Mendelian disorders is well established, it is unclear whether CNVs may affect risk for common complex disorders. We sought to investigate whether CNVs may modulate risk for ischemic stroke (IS) and to provide a catalog of CNVs in patients with this disorder by analyzing copy number metrics produced as a part of our previous genome-wide single-nucleotide polymorphism (SNP)-based association study of ischemic stroke in a North American white population. We examined CNVs in 263 patients with ischemic stroke (IS). Each identified CNV was compared with changes identified in 275 neurologically normal controls. Our analysis identified 247 CNVs, corresponding to 187 insertions (76%; 135 heterozygous; 25 homozygous duplications or triplications; 2 heterosomic) and 60 deletions (24%; 40 heterozygous deletions;3 homozygous deletions; 14 heterosomic deletions). Most alterations (81%) were the same as, or overlapped with, previously reported CNVs. We report here the first genome-wide analysis of CNVs in IS patients. In summary, our study did not detect any common genomic structural variation unequivocally linked to IS, although we cannot exclude that smaller CNVs or CNVs in genomic regions poorly covered by this methodology may confer risk for IS. The application of genome-wide SNP arrays now facilitates the evaluation of structural changes through the entire genome as part of a genome-wide genetic association study. PMID:18288507

MetaRanker 2.0: a web server for prioritization of genetic variation data.

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Pers, Tune H; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

2013-07-01

MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein-protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRanker-2.0.

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

Directory of Open Access Journals (Sweden)

Coutant Sophie

2012-09-01

Full Text Available Abstract Background Whole exome sequencing (WES has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of efficient algorithms has been developed to ensure the variant discovery. They generally lead to ~20,000 variations that have to be narrow down to find the potential pathogenic allelic variant(s and the affected gene(s. For this purpose, commonly adopted procedures which implicate various filtering strategies have emerged: exclusion of common variations, type of the allelics variants, pathogenicity effect prediction, modes of inheritance and multiple individuals for exome comparison. To deal with the expansion of WES in medical genomics individual laboratories, new convivial and versatile software tools have to implement these filtering steps. Non-programmer biologists have to be autonomous combining themselves different filtering criteria and conduct a personal strategy depending on their assumptions and study design. Results We describe EVA (Exome Variation Analyzer, a user-friendly web-interfaced software dedicated to the filtering strategies for medical WES. Thanks to different modules, EVA (i integrates and stores annotated exome variation data as strictly confidential to the project owner, (ii allows to combine the main filters dealing with common variations, molecular types, inheritance mode and multiple samples, (iii offers the browsing of annotated data and filtered results in various interactive tables, graphical visualizations and statistical charts, (iv and finally offers export files and cross-links to external useful databases and softwares for further prioritization of the small subset of sorted candidate variations and genes. We report a demonstrative case study that allowed to identify a new candidate gene

Intelligence and family marital structure: the case of adolescents from monogamous and polygamous families among Bedouin Arabs in Israel.

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Elbedour, Salman; Bart, William M; Hektner, Joel

2003-02-01

The levels of intelligence among Bedouin Arab adolescents from monogamous and polygamous families living in the Negev region of Israel were examined. A shortened version of the Raven's Progressive Matrices (RPM) test (S. Elbedour, T. J. Bouchard, & Y. Hur, 1997; J. Raven, J. C. Raven, & J. H. Court, 1998) was used to assess intelligence. There were no significant test score differences between adolescents from monogamous families and adolescents from polygamous families. In addition, participants with 2 mothers tended to have lower RPM scores than those with 3 or 4 mothers, and participants with related parents tended to have lower RPM scores than participants with unrelated parents. One major finding of this study is that polygamous family marital structures tended not to have deleterious effects on the Bedouin Arab adolescents' RPM test scores.

Common and Rare Variant Association Study for Plasma Lipids and Coronary Artery Disease.

Science.gov (United States)

Tada, Hayato; Kawashiri, Masa-aki; Konno, Tetsuo; Yamagishi, Masakazu; Hayashi, Kenshi

2016-01-01

Blood lipid levels are highly heritable and modifiable risk factors for coronary artery disease (CAD), and are the leading cause of death worldwide. These facts have motivated human genetic association studies that have the substantial potential to define the risk factors that are causal and to identify pathways and therapeutic targets for lipids and CAD.The success of the HapMap project that provided an extensive catalog of human genetic variations and the development of microarray based genotyping chips (typically containing variations with allele frequencies ＞ 5%) facilitated common variant association study (CVAS; formerly termed genome-wide association study, GWAS) identifying disease-associated variants in a genome-wide manner. To date, 157 loci associated with blood lipids and 46 loci with CAD have been successfully identified, accounting for approximately 12%-14% of heritability for lipids and 10% of heritability for CAD. However, there is yet a major challenge termed "missing heritability problem," namely the observation that loci detected by CVAS explain only a small fraction of the inferred genetic variations. To explain such missing portions, focuses in genetic association studies have shifted from common to rare variants. However, it is challenging to apply rare variant association study (RVAS) in an unbiased manner because such variants typically lack the sufficient number to be identified statistically.In this review, we provide a current understanding of the genetic architecture mostly derived from CVAS, and several updates on the progress and limitations of RVAS for lipids and CAD.

Meiotic sex ratio variation in natural populations of Ceratodon purpureus (Ditrichaceae).

Science.gov (United States)

Norrell, Tatum E; Jones, Kelly S; Payton, Adam C; McDaniel, Stuart F

2014-09-01

• Sex ratio variation is a common but often unexplained phenomenon in species across the tree of life. Here we evaluate the hypothesis that meiotic sex ratio variation can contribute to the biased sex ratios found in natural populations of the moss Ceratodon purpureus.• We obtained sporophytes from several populations of C. purpureus from eastern North America. From each sporophyte, we estimated the mean spore viability by germinating replicate samples on agar plates. We estimated the meiotic sex ratio of each sporophyte by inferring the sex of a random sample of germinated spores (mean = 77) using a PCR-RFLP test. We tested for among-sporophyte variation in viability using an ANOVA and for deviations from 1:1 sex ratio using a χ(2)-test and evaluated the relationship between these quantities using a linear regression.• We found among-sporophyte variation in spore viability and meiotic sex ratio, suggesting that genetic variants that contribute to variation in both of these traits segregate within populations of this species. However, we found no relationship between these quantities, suggesting that factors other than sex ratio distorters contribute to variation in spore viability within populations.• These results demonstrate that sex ratio distortion may partially explain the population sex ratio variation seen in C. purpureus, but more generally that genetic conflict over meiotic segregation may contribute to fitness variation in this species. Overall, this study lays the groundwork for future studies on the genetic basis of meiotic sex ratio variation. © 2014 Botanical Society of America, Inc.

Calculus of variations

CERN Document Server

Elsgolc, L E; Stark, M

1961-01-01

Calculus of Variations aims to provide an understanding of the basic notions and standard methods of the calculus of variations, including the direct methods of solution of the variational problems. The wide variety of applications of variational methods to different fields of mechanics and technology has made it essential for engineers to learn the fundamentals of the calculus of variations. The book begins with a discussion of the method of variation in problems with fixed boundaries. Subsequent chapters cover variational problems with movable boundaries and some other problems; sufficiency

Limitations Of The Current State Space Modelling Approach In Multistage Machining Processes Due To Operation Variations

Science.gov (United States)

Abellán-Nebot, J. V.; Liu, J.; Romero, F.

2009-11-01

The State Space modelling approach has been recently proposed as an engineering-driven technique for part quality prediction in Multistage Machining Processes (MMP). Current State Space models incorporate fixture and datum variations in the multi-stage variation propagation, without explicitly considering common operation variations such as machine-tool thermal distortions, cutting-tool wear, cutting-tool deflections, etc. This paper shows the limitations of the current State Space model through an experimental case study where the effect of the spindle thermal expansion, cutting-tool flank wear and locator errors are introduced. The paper also discusses the extension of the current State Space model to include operation variations and its potential benefits.

Limits of principal components analysis for producing a common trait space: implications for inferring selection, contingency, and chance in evolution.

Directory of Open Access Journals (Sweden)

Kevin J Parsons

2009-11-01

Full Text Available Comparing patterns of divergence among separate lineages or groups has posed an especially difficult challenge for biologists. Recently a new, conceptually simple methodology called the "ordered-axis plot" approach was introduced for the purpose of comparing patterns of diversity in a common morphospace. This technique involves a combination of principal components analysis (PCA and linear regression. Given the common use of these statistics the potential for the widespread use of the ordered axis approach is high. However, there are a number of drawbacks to this approach, most notably that lineages with the greatest amount of variance will largely bias interpretations from analyses involving a common morphospace. Therefore, without meeting a set of a priori requirements regarding data structure the ordered-axis plot approach will likely produce misleading results.Morphological data sets from cichlid fishes endemic to Lakes Tanganyika, Malawi, and Victoria were used to statistically demonstrate how separate groups can have differing contributions to a common morphospace produced by a PCA. Through a matrix superimposition of eigenvectors (scale-free trajectories of variation identified by PCA we show that some groups contribute more to the trajectories of variation identified in a common morphospace. Furthermore, through a set of randomization tests we show that a common morphospace model partitions variation differently than group-specific models. Finally, we demonstrate how these limitations may influence an ordered-axis plot approach by performing a comparison on data sets with known alterations in covariance structure. Using these results we provide a set of criteria that must be met before a common morphospace can be reliably used.Our results suggest that a common morphospace produced by PCA would not be useful for producing biologically meaningful results unless a restrictive set of criteria are met. We therefore suggest biologists be aware

Higher order total variation regularization for EIT reconstruction.

Science.gov (United States)

Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Zhang, Fan; Mueller-Lisse, Ullrich; Moeller, Knut

2018-01-08

Electrical impedance tomography (EIT) attempts to reveal the conductivity distribution of a domain based on the electrical boundary condition. This is an ill-posed inverse problem; its solution is very unstable. Total variation (TV) regularization is one of the techniques commonly employed to stabilize reconstructions. However, it is well known that TV regularization induces staircase effects, which are not realistic in clinical applications. To reduce such artifacts, modified TV regularization terms considering a higher order differential operator were developed in several previous studies. One of them is called total generalized variation (TGV) regularization. TGV regularization has been successively applied in image processing in a regular grid context. In this study, we adapted TGV regularization to the finite element model (FEM) framework for EIT reconstruction. Reconstructions using simulation and clinical data were performed. First results indicate that, in comparison to TV regularization, TGV regularization promotes more realistic images. Graphical abstract Reconstructed conductivity changes located on selected vertical lines. For each of the reconstructed images as well as the ground truth image, conductivity changes located along the selected left and right vertical lines are plotted. In these plots, the notation GT in the legend stands for ground truth, TV stands for total variation method, and TGV stands for total generalized variation method. Reconstructed conductivity distributions from the GREIT algorithm are also demonstrated.

A systematic review and meta-analysis of variations in branching patterns of the adult aortic arch.

Science.gov (United States)

Popieluszko, Patrick; Henry, Brandon Michael; Sanna, Beatrice; Hsieh, Wan Chin; Saganiak, Karolina; Pękala, Przemysław A; Walocha, Jerzy A; Tomaszewski, Krzysztof A

2018-07-01

The aortic arch (AA) is the main conduit of the left side of the heart, providing a blood supply to the head, neck, and upper limbs. As it travels through the thorax, the pattern in which it gives off the branches to supply these structures can vary. Variations of these branching patterns have been studied; however, a study providing a comprehensive incidence of these variations has not yet been conducted. The objective of this study was to perform a meta-analysis of all the studies that report prevalence data on AA variants and to provide incidence data on the most common variants. A systematic search of online databases including PubMed, Embase, Scopus, ScienceDirect, Web of Science, SciELO, BIOSIS, and CNKI was performed for literature describing incidence of AA variations in adults. Studies including prevalence data on adult patients or cadavers were collected and their data analyzed. A total of 51 articles were included (N = 23,882 arches). Seven of the most common variants were analyzed. The most common variants found included the classic branching pattern, defined as a brachiocephalic trunk, a left common carotid, and a left subclavian artery (80.9%); the bovine arch variant (13.6%); and the left vertebral artery variant (2.8%). Compared by geographic data, bovine arch variants were noted to have a prevalence as high as 26.8% in African populations. Although patients who have an AA variant are often asymptomatic, they compose a significant portion of the population of patients and pose a greater risk of hemorrhage and ischemia during surgery in the thorax. Because of the possibility of encountering such variants, it is prudent for surgeons to consider potential variations in planning procedures, especially of an endovascular nature, in the thorax. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

A novel quantitative approach for eliminating sample-to-sample variation using a hue saturation value analysis program.

Science.gov (United States)

Yabusaki, Katsumi; Faits, Tyler; McMullen, Eri; Figueiredo, Jose Luiz; Aikawa, Masanori; Aikawa, Elena

2014-01-01

As computing technology and image analysis techniques have advanced, the practice of histology has grown from a purely qualitative method to one that is highly quantified. Current image analysis software is imprecise and prone to wide variation due to common artifacts and histological limitations. In order to minimize the impact of these artifacts, a more robust method for quantitative image analysis is required. Here we present a novel image analysis software, based on the hue saturation value color space, to be applied to a wide variety of histological stains and tissue types. By using hue, saturation, and value variables instead of the more common red, green, and blue variables, our software offers some distinct advantages over other commercially available programs. We tested the program by analyzing several common histological stains, performed on tissue sections that ranged from 4 µm to 10 µm in thickness, using both a red green blue color space and a hue saturation value color space. We demonstrated that our new software is a simple method for quantitative analysis of histological sections, which is highly robust to variations in section thickness, sectioning artifacts, and stain quality, eliminating sample-to-sample variation.

Fine-Mapping the HOXB Region Detects Common Variants Tagging a Rare Coding Allele

DEFF Research Database (Denmark)

Saunders, Edward J; Dadaev, Tokhir; Leongamornlert, Daniel A

2014-01-01

The HOXB13 gene has been implicated in prostate cancer (PrCa) susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs u...

Working memory capacity and fluid abilities: The more difficult the item, the more more is better

OpenAIRE

Daniel R Little; Stephan eLewandowsky; Stephan eLewandowsky; Stewart eCraig

2014-01-01

The relationship between fluid intelligence and working memory is of fundamental importance to understanding how capacity-limited structures such as working memory interact with inference abilities to determine intelligent behaviour. Recent evidence has suggested that the relationship between a fluid abilities test, Raven's Progressive Matrices, and working memory capacity (WMC) may be invariant across difficulty levels of the Raven's items. We show that this invariance can only be observed i...

Macrophytes shape trophic niche variation among generalist fishes.

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Ivana Vejříková

Full Text Available Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N and carbon (δ13C isotopic mixing models, perch (Perca fluviatilis L. and rudd (Scardinius erythrophthalmus (L. showed larger individual variation (i.e., variance in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.. Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence

Macrophytes shape trophic niche variation among generalist fishes

Science.gov (United States)

Vejřík, Lukáš; Šmejkal, Marek; Čech, Martin; Sajdlová, Zuzana; Frouzová, Jaroslava; Kiljunen, Mikko; Peterka, Jiří

2017-01-01

Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N) and carbon (δ13C) isotopic mixing models, perch (Perca fluviatilis L.) and rudd (Scardinius erythrophthalmus (L.)) showed larger individual variation (i.e., variance) in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.)). Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence the overall

Variation in human recombination rates and its genetic determinants.

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Adi Fledel-Alon

Full Text Available Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution.Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation.These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.

Variational and quasi-variational inequalities in mechanics

CERN Document Server

Kravchuk, Alexander S

2007-01-01

The essential aim of the present book is to consider a wide set of problems arising in the mathematical modelling of mechanical systems under unilateral constraints. In these investigations elastic and non-elastic deformations, friction and adhesion phenomena are taken into account. All the necessary mathematical tools are given: local boundary value problem formulations, construction of variational equations and inequalities, and the transition to minimization problems, existence and uniqueness theorems, and variational transformations (Friedrichs and Young-Fenchel-Moreau) to dual and saddle-point search problems. Important new results concern contact problems with friction. The Coulomb friction law and some others are considered, in which relative sliding velocities appear. The corresponding quasi-variational inequality is constructed, as well as the appropriate iterative method for its solution. Outlines of the variational approach to non-stationary and dissipative systems and to the construction of the go...

Common ataxia telangiectasia mutated haplotypes and risk of breast cancer: a nested case–control study

International Nuclear Information System (INIS)

Tamimi, Rulla M; Hankinson, Susan E; Spiegelman, Donna; Kraft, Peter; Colditz, Graham A; Hunter, David J

2004-01-01

The ataxia telangiectasia mutated (ATM) gene is a tumor suppressor gene with functions in cell cycle arrest, apoptosis, and repair of DNA double-strand breaks. Based on family studies, women heterozygous for mutations in the ATM gene are reported to have a fourfold to fivefold increased risk of breast cancer compared with noncarriers of the mutations, although not all studies have confirmed this association. Haplotype analysis has been suggested as an efficient method for investigating the role of common variation in the ATM gene and breast cancer. Five biallelic haplotype tagging single nucleotide polymorphisms are estimated to capture 99% of the haplotype diversity in Caucasian populations. We conducted a nested case–control study of breast cancer within the Nurses' Health Study cohort to address the role of common ATM haplotypes and breast cancer. Cases and controls were genotyped for five haplotype tagging single nucleotide polymorphisms. Haplotypes were predicted for 1309 cases and 1761 controls for which genotype information was available. Six unique haplotypes were predicted in this study, five of which occur at a frequency of 5% or greater. The overall distribution of haplotypes was not significantly different between cases and controls (χ 2 = 3.43, five degrees of freedom, P = 0.63). There was no evidence that common haplotypes of ATM are associated with breast cancer risk. Extensive single nucleotide polymorphism detection using the entire genomic sequence of ATM will be necessary to rule out less common variation in ATM and sporadic breast cancer risk

Technological quality of common bean grains obtained in different growing seasons

Directory of Open Access Journals (Sweden)

Eliana Francischinelli Perina

2014-03-01

Full Text Available The traits that provide technological quality to common bean grains exhibit genetic and environmental variation and variation in the genotype x environment interaction. In this context, the aim of this study was to assess the effect of different periods of the growing season on the technological quality of common bean grains. The experiment was conducted with 25 bean genotypes (carioca [beige with brown stripes] and black commercial group that are part of the Value for Cultivation and Use (Valor de Cultivo e Uso - VCU trials in three growing seasons, namely, the 2009/2010 rainy season, the 2010/2011 dry season and the 2010/2011 winter season, in a randomized block experimental design with three replications in which the following items were assessed: cooking time (CT, water absorption capacity before cooking (Peanc and after cooking (Peapc, percentage of whole grains (PWG, total soluble solids in the broth (TSSb, volume expansion before cooking (EXPVbc and after cooking (EXPVac, and dry grain density (DD, grain density after maceration (SD and grain density after cooking (CD. Assessments showed that the different growing seasons for obtaining grains for the purpose of analysis of technological quality have an effect on the results and on differentiation among genotypes, indicating genotype x environment interaction. They also showed that the genotypes C2-1-6-1, C4-8-1-1, LP04-03, IAC-Imperador, P5-4-4-1 and Pr11-6-4-1-2 had the best results in relation to cooking time in the mean values of the three growing seasons. The use of early selection based on phenotypic correlations that exist among the technological features is not expressive, due to the variation of magnitude among the different growing seasons.

Quantifying variation in speciation and extinction rates with clade data.

Science.gov (United States)

Paradis, Emmanuel; Tedesco, Pablo A; Hugueny, Bernard

2013-12-01

High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Variational principles for particles and fields in Heisenberg matrix mechanics

International Nuclear Information System (INIS)

Klein, A.; Li, C.T.; Vassanji, M.

1980-01-01

For many years we have advocated a form of quantum mechanics based on the application of sum rule methods (completeness) to the equations of motion and to the commutation relations, i.e., to Heisenberg matrix mechanics. Sporadically we have discussed or alluded to a variational foundation for this method. In this paper we present a series of variational principles applicable to a range of systems from one-dimensional quantum mechanics to quantum fields. The common thread is that the stationary quantity is the trace of the Hamiltonian over Hilbert space (or over a subspace of interest in an approximation) expressed as a functional of matrix elements of the elementary operators of the theory. These parameters are constrained by the kinematical relations of the theory introduced by the method of Lagrange multipliers. For the field theories, variational principles in which matrix elements of the density operators are chosen as fundamental are also developed. A qualitative discussion of applications is presented

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

Science.gov (United States)

Carpenter, Danielle; Mitchell, Laura M; Armour, John A L

2017-02-20

Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P structure may affect expression, but this was not significant in our data.

Calculus of variations

CERN Document Server

Elsgolc, Lev D

2007-01-01

This concise text offers both professionals and students an introduction to the fundamentals and standard methods of the calculus of variations. In addition to surveys of problems with fixed and movable boundaries, it explores highly practical direct methods for the solution of variational problems.Topics include the method of variation in problems with fixed boundaries; variational problems with movable boundaries and other problems; sufficiency conditions for an extremum; variational problems of constrained extrema; and direct methods of solving variational problems. Each chapter features nu

Genomic Features That Predict Allelic Imbalance in Humans Suggest Patterns of Constraint on Gene Expression Variation

Science.gov (United States)

Fédrigo, Olivier; Haygood, Ralph; Mukherjee, Sayan; Wray, Gregory A.

2009-01-01

Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In particular, measurements of gene expression usually do not reveal whether the genetic basis for any observed variation lies in cis or in trans to the gene, a distinction that has direct relevance to the physical location of the underlying genetic variant, and which may also impact its evolutionary trajectory. Allelic imbalance measurements identify cis-acting genetic effects by assaying the relative contribution of the two alleles of a cis-regulatory region to gene expression within individuals. Identification of patterns that predict commonly imbalanced genes could therefore serve as a useful tool and also shed light on the evolution of cis-regulatory variation itself. Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set. Reduction of this feature set to four factors revealed that only one factor significantly differentiated between commonly imbalanced and nonimbalanced genes. We demonstrate that these results are consistent between the original data set and a second published data set in humans obtained using different technical and statistical methods. Finally, we show that variation in the single allelic imbalance-associated factor is partially explained by the density of genes in the region of a target gene (allelic imbalance is less probable for genes in gene-dense regions), and, to a lesser extent, the evenness of expression of the gene across tissues and the magnitude of negative selection on putative regulatory regions of the gene. These results suggest that the genomic distribution of functional cis-regulatory variants in the human genome is nonrandom, perhaps due to local differences in evolutionary

Genetic regulation of the variation of circulating insulin-like growth factors and leptin in human pedigrees.

Science.gov (United States)

Pantsulaia, Ia; Pantsulaia, I; Trofimov, Svetlana; Kobyliansky, Eugene; Livshits, Gregory

2005-07-01

Recent literature has shown that circulating levels of insulin-like growth factor I (IGF-I) and/or IGF binding proteins (IGF-BPs) may be of importance in the risk assessment of several chronic diseases including cancer, cardiovascular disease, diabetes mellitus and so on. The present study examined the extent of genetic and environmental influences on the populational variation of circulating IGF-I and IGF-BP-1 in apparently healthy and ethnically homogeneous white families. The plasma levels of each of the studied biochemical indices were determined by enzyme-linked immunoassay in 563 individuals aged 18 to 80 years. Quantitative genetic analysis showed that the IGF-I variation was appreciably attributable to genetic effects (47.1% +/- 9.0%), whereas for IGF-BP-1, only 23.3% +/- 7.8% of the interindividual variation was explained by genetic determinants. Common familial environment factors contributed significantly only to IGF-BP-1 variation (23.3% +/- 7.8%). In addition, we examined the covariations between these molecules and between them and IGF-BP-3 and leptin that were previously studied in the same sample. The analysis revealed that the pleiotropic genetic effects were significant for 2 pairs of traits, namely for IGF-I and IGF-BP-3, and for IGF-BP-1 and leptin. The bivariate heritability estimates were 0.21 +/- 0.04 and 0.15 +/- 0.05. The common environmental factors were consistently a significant source of correlation between all pairs (barring IGF-I and leptin) of the studied molecules; they were the sole predictors of correlation between IGF-I and IGF-BP-1, and between IGF-BP-1 and IGF-BP-3. Our results affirm the existence of specific and common genetic pathways that in combination determine a substantial proportion of the circulating variation of these molecules.

Seasonal and spatial variations in fish and macrocrustacean assemblage structure in Mad Island Marsh estuary, Texas

Science.gov (United States)

Akin, S.; Winemiller, K. O.; Gelwick, F. P.

2003-05-01

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998-August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter-early spring when water temperature and salinity were low and dissolved oxygen high. During summer-early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab ( Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer-fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad ( Dorosoma cepedianum) and gars ( Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large

Diurnal changes of earthquake activity and geomagnetic Sq-variations

Directory of Open Access Journals (Sweden)

G. Duma

2003-01-01

Full Text Available Statistic analyses demonstrate that the probability of earthquake occurrence in many earthquake regions strongly depends on the time of day, that is on Local Time (e.g. Conrad, 1909, 1932; Shimshoni, 1971; Duma, 1997; Duma and Vilardo, 1998. This also applies to strong earthquake activity. Moreover, recent observations reveal an involvement of the regular diurnal variations of the Earth’s magnetic field, commonly known as Sq-variations, in this geodynamic process of changing earthquake activity with the time of day (Duma, 1996, 1999. In the article it is attempted to quantify the forces which result from the interaction between the induced Sq-variation currents in the Earth’s lithosphere and the regional Earth’s magnetic field, in order to assess the influence on the tectonic stress field and on seismic activity. A reliable model is obtained, which indicates a high energy involved in this process. The effect of Sq-induction is compared with the results of the large scale electromagnetic experiment "Khibiny" (Velikhov, 1989, where a giant artificial current loop was activated in the Barents Sea.

Assessment of inter- and intra-cultivar variations in olive using SSR markers

Directory of Open Access Journals (Sweden)

Ahmet Ipek

2012-10-01

Full Text Available Olive (Olea europaea L. production in the world has been made by using many cultivars, and the genetic uniformity of commercial cultivars is important for standard olive oil and table olive production. The genetic variation among and within commonly cultivated olive cultivars in Turkey was analyzed using SSR markers. A total of 135 leaf samples were collected from 11 commonly cultivated olive cultivars from 11 provinces in four geographical regions of Turkey. Seven SSR primer pairs generated 46 SSR markers, and the number of SSR markers per primer pair ranged from 4 (UDO-14 to 9 (GAPU-89 with an average of 6.57. This high level of SSR polymorphism suggests that olive production in Turkey has been made using genetically diverse olive cultivars and this high level of genetic variation is probably due to the location of Turkey in the center of the origin of olive. The UPGMA dendrogram, developed to visualize the estimated genetic relationships among the 135 samples, demonstrated that the clustering of olive cultivars was not based on geographical regions of cultivation. Presence of genetic variation was detected within a nationwide grown Turkish olive cultivar, called 'Gemlik'. Olive growers successfully discriminated olive cultivars with distinct morphological and pomological characters. However, there was some confusion about the identification of cultivars with similar phenotypic traits. To prevent misidentification of olive cultivars and to minimize intra-cultivar variation, certified propagation materials which were characterized using DNA based molecular markers should be used during the establishment of new olive orchards.

Variations in gynecologic oncology training in low (LIC and middle income (MIC countries (LMICs: Common efforts and challenges

Directory of Open Access Journals (Sweden)

Carolyn Johnston

2017-05-01

Full Text Available Gynecologic cancer, cervical cancer in particular, is disproportionately represented in the developing world where mortality is also high. Screening programs, increased availability of chemotherapy, and an awareness of HIV-related cancers have in part accelerated a need for physicians who can treat these cancers, yet the infrastructure for such training is often lacking. In this paper, we address the variations in gynecology oncology training in LMICs as well as the ubiquitous challenges, in an effort to guide future agendas.

Diet and mortality from common cancers in Brazil: an ecological study

Directory of Open Access Journals (Sweden)

Sichieri Rosely

1996-01-01

Full Text Available A prospective ecological evaluation of mortality from common malignancies with dietary risk factors and alcohol consumption was carried out among 10 state capitals of Brazil. Regression analysis was used to examine the association of dietary intake with mortality rates of the most common cancers among adults age 30 years and older. Age-adjusted cancer mortality rates varied 2.4 to 3.3 fold across the state capitals. A positive relationship was observed between energy intake and colon, lung, and esophageal cancer (p<=0.02 for each. Colon cancer mortality was positively associated with consumption of total fat, eggs, alcohol, mate tea, cereals, and vegetables (p<=0.01. Lung cancer was positively associated with mate and cereal intake (p<0.05. Stomach cancer was associated with consumption of eggs (p=0.04; and negatively associated with consumption of high fiber foods, fruits, and vitamin A and C (p<=0.05. Esophageal cancer was positively associated with fat intake, mate and cereals (p<=0.05 and negatively associated with vitamin A (p=0.02; prostate cancer was negatively associated with vitamin C (p=0.007. Breast cancer was not associated with any of the factors studied. The marked variation in cancer mortality rates in Brazil may be partially related to the high variation in dietary components or other diet associated factors.

Diet and mortality from common cancers in Brazil: an ecological study

Directory of Open Access Journals (Sweden)

Rosely Sichieri

Full Text Available A prospective ecological evaluation of mortality from common malignancies with dietary risk factors and alcohol consumption was carried out among 10 state capitals of Brazil. Regression analysis was used to examine the association of dietary intake with mortality rates of the most common cancers among adults age 30 years and older. Age-adjusted cancer mortality rates varied 2.4 to 3.3 fold across the state capitals. A positive relationship was observed between energy intake and colon, lung, and esophageal cancer (p<=0.02 for each. Colon cancer mortality was positively associated with consumption of total fat, eggs, alcohol, mate tea, cereals, and vegetables (p<=0.01. Lung cancer was positively associated with mate and cereal intake (p<0.05. Stomach cancer was associated with consumption of eggs (p=0.04; and negatively associated with consumption of high fiber foods, fruits, and vitamin A and C (p<=0.05. Esophageal cancer was positively associated with fat intake, mate and cereals (p<=0.05 and negatively associated with vitamin A (p=0.02; prostate cancer was negatively associated with vitamin C (p=0.007. Breast cancer was not associated with any of the factors studied. The marked variation in cancer mortality rates in Brazil may be partially related to the high variation in dietary components or other diet associated factors.

Flanking Variation Influences Rates of Stutter in Simple Repeats

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August E. Woerner

2017-11-01

Full Text Available It has been posited that the longest uninterrupted stretch (LUS of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL. While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.

Characterization and potential functional significance of human-chimpanzee large INDEL variation

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Polavarapu Nalini

2011-10-01

Full Text Available Abstract Background Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression. Results Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them. Conclusions The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.

Inter-observer variation in delineation of the heart and left anterior descending coronary artery in radiotherapy for breast cancer

DEFF Research Database (Denmark)

Laugaard Lorenzen, Ebbe; Taylor, C. W.; Maraldo, M.

2013-01-01

receiving left breast radiotherapy. The delineations were carried out twice, first without guidelines and then with a set of common guidelines. RESULTS: For the heart, most spatial variation in delineation was near the base of the heart whereas for the LADCA most variation was in its length at the apex...

Periodical climate variations and their impact on Earth rotation for the last 800Kyr

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Chapanov, Yavor; Gambis, Daniel

2010-05-01

The Earth rotation variations are highly affected by climatic variations associated with the glacial cycles in the late Pleistocene. The processes of glaciation, followed by ice melting, are connected with significant changes of the mean sea level. These processes redistribute great amount of water masses between oceans and ice sheets, which lead to changes of the axial moment of inertia and corresponding variations of the Universal Time UT1 and Length of Day LOD, according to the law of angular momentum conservation. The climatic variations for the last 800Kyr are analyzed by means of time series of temperature changes, determined by deuterium data from Antarctica ice core. Reconstructed glacial sea level variations for the last 380Kyr, determined by the sediments from the Red sea, are used, too. Common periodicities of the temperature and mean sea level variations are determined. Time series of the long-periodical UT1 and LOD oscillations for the last 380Kyr and 800Kyr are reconstructed by means of empirical hydrological model of global water redistribution between the ocean and ice sheets during the last glacial events.

A Common LPA Null Allele Associates With Lower Lipoprotein(a) Levels and Coronary Artery Disease Risk

NARCIS (Netherlands)

Kyriakou, Theodosios; Seedorf, Udo; Goel, Anuj; Hopewell, Jemma C.; Clarke, Robert; Watkins, Hugh; Farrall, Martin; van der Hout, A.H.

Objective-Increased levels of lipoprotein(a) are a highly heritable risk factor for coronary artery disease (CAD). The genetic determinants of lipoprotein(a) levels are mainly because of genetic variation in the apolipoprotein(a) gene (LPA). We have tested the association of a relatively common null

The crowded magnetosphere of the post common envelope binary QS Virginis

OpenAIRE

Parsons, S. G.; Hill, C. A.; Marsh, T. R.; Gansicke, B. T.; Watson, C. A.; Steeghs, D.; Dhillon, V. S.; Littlefair, S. P.; Copperwheat, C. M.; Schreiber, M. R.; Zorotovic, M.

2016-01-01

We present high-speed photometry and high-resolution spectroscopy of the eclipsing post-common-envelope binary QS Virginis (QS Vir). Our Ultraviolet and Visual Echelle Spectrograph (UVES) spectra span multiple orbits over more than a year and reveal the presence of several large prominences passing in front of both the M star and its white dwarf companion, allowing us to triangulate their positions. Despite showing small variations on a time-scale of days, they persist for more than a year an...

Wandel und Variation in der Morphosyntax der schweizerdeutschen Dialekte

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Elvira Glaser

2014-12-01

Full Text Available Syntactic Variation and change in Swiss German dialects The article deals with the areal distribution of morphosyntactic variants in Swiss German dialects. The Zurich project “Syntaktischer Atlas der deutschen Schweiz” (SADS has provided a lot of evidence for the existence of syntactic isoglosses within the German-speaking regions of Switzerland. In the following, we will discuss several types of variant distribution. There are syntactic variables showing a division of Western and Eastern Swiss German dialects, a division well known from phonology and lexis. In addition, we find few archaic variants restricted to southern Highest Alemannic, again in line with other linguistic levels. Most interesting are some variants showing up in quite small – and differing – regions. These regions usually do not only show these specific variants but variation with a more common variant. This leads to a discussion of the implications of variation. Variation is not only seen as an indication of an ongoing change, but it is argued that there is evidence for a long lasting variational situation and largely stable variation respectively. Several possible types of comparison with older data and between age groups (apparent time analysis within the data are presented. There are relatively few cases where we can show larger shifts between two regional variants and there seem to be only some rare cases of syntactic influence by Standard German introducing new variants. With respect to the old question of morphosyntactic borrowing, Swiss German dialects show cases of resistance as well as cases of interference, the latter concerning loan translation and semantic adaptation if the structure favors it.

Implementation and Validation of Artificial Intelligence Techniques for Robotic Surgery

OpenAIRE

Aarshay Jain; Deepansh Jagotra; Vijayant Agarwal

2014-01-01

The primary focus of this study is implementation of Artificial Intelligence (AI) technique for developing an inverse kinematics solution for the Raven-IITM surgical research robot [1]. First, the kinematic model of the Raven-IITM robot was analysed along with the proposed analytical solution [2] for inverse kinematics problem. Next, The Artificial Neural Network (ANN) techniques was implemented. The training data for the same was careful selected by keeping manipulability constraints in mind...

The relationships between common measures of glucose meter performance.

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Wilmoth, Daniel R

2012-09-01

Glucose meter performance is commonly measured in several different ways, including the relative bias and coefficient of variation (CV), the total error, the mean absolute relative deviation (MARD), and the size of the interval around the reference value that would be necessary to contain a meter measurement at a specified probability. This fourth measure is commonly expressed as a proportion of the reference value and will be referred to as the necessary relative deviation. A deeper understanding of the relationships between these measures may aid health care providers, patients, and regulators in comparing meter performances when different measures are used. The relationships between common measures of glucose meter performance were derived mathematically. Equations are presented for calculating the total error, MARD, and necessary relative deviation using the reference value, relative bias, and CV when glucose meter measurements are normally distributed. When measurements are also unbiased, the CV, total error, MARD, and necessary relative deviation are linearly related and are therefore equivalent measures of meter performance. The relative bias and CV provide more information about meter performance than the other measures considered but may be difficult for some audiences to interpret. Reporting meter performance in multiple ways may facilitate the informed selection of blood glucose meters. © 2012 Diabetes Technology Society.

Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort

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Stallcup Michael R

2009-01-01

studies. Conclusion Our findings suggest that common coding variation in these candidate genes do not make a substantial contribution to breast cancer risk in the general population. Cataloging and testing of coding variants in coactivator and corepressor genes should continue and may serve as a valuable resource for investigations of other hormone-related phenotypes, such as inter-individual response to hormonal therapies used for cancer treatment and prevention.

Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort

International Nuclear Information System (INIS)

Haiman, Christopher A; Stallcup, Michael R; Greene, Geoffrey L; Press, Michael F; Garcia, Rachel R; Hsu, Chris; Xia, Lucy; Ha, Helen; Sheng, Xin; Le Marchand, Loic; Kolonel, Laurence N; Henderson, Brian E

2009-01-01

Only a limited number of studies have performed comprehensive investigations of coding variation in relation to breast cancer risk. Given the established role of estrogens in breast cancer, we hypothesized that coding variation in steroid receptor coactivator and corepressor genes may alter inter-individual response to estrogen and serve as markers of breast cancer risk. We sequenced the coding exons of 17 genes (EP300, CCND1, NME1, NCOA1, NCOA2, NCOA3, SMARCA4, SMARCA2, CARM1, FOXA1, MPG, NCOR1, NCOR2, CALCOCO1, PRMT1, PPARBP and CREBBP) suggested to influence transcriptional activation by steroid hormone receptors in a multiethnic panel of women with advanced breast cancer (n = 95): African Americans, Latinos, Japanese, Native Hawaiians and European Americans. Association testing of validated coding variants was conducted in a breast cancer case-control study (1,612 invasive cases and 1,961 controls) nested in the Multiethnic Cohort. We used logistic regression to estimate odds ratios for allelic effects in ethnic-pooled analyses as well as in subgroups defined by disease stage and steroid hormone receptor status. We also investigated effect modification by established breast cancer risk factors that are associated with steroid hormone exposure. We identified 45 coding variants with frequencies ≥ 1% in any one ethnic group (43 non-synonymous variants). We observed nominally significant positive associations with two coding variants in ethnic-pooled analyses (NCOR2: His52Arg, OR = 1.79; 95% CI, 1.05–3.05; CALCOCO1: Arg12His, OR = 2.29; 95% CI, 1.00–5.26). A small number of variants were associated with risk in disease subgroup analyses and we observed no strong evidence of effect modification by breast cancer risk factors. Based on the large number of statistical tests conducted in this study, the nominally significant associations that we observed may be due to chance, and will need to be confirmed in other studies. Our findings suggest that common coding

A BAYESIAN SPATIAL AND TEMPORAL MODELING APPROACH TO MAPPING GEOGRAPHIC VARIATION IN MORTALITY RATES FOR SUBNATIONAL AREAS WITH R-INLA.

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Khana, Diba; Rossen, Lauren M; Hedegaard, Holly; Warner, Margaret

2018-01-01

Hierarchical Bayes models have been used in disease mapping to examine small scale geographic variation. State level geographic variation for less common causes of mortality outcomes have been reported however county level variation is rarely examined. Due to concerns about statistical reliability and confidentiality, county-level mortality rates based on fewer than 20 deaths are suppressed based on Division of Vital Statistics, National Center for Health Statistics (NCHS) statistical reliability criteria, precluding an examination of spatio-temporal variation in less common causes of mortality outcomes such as suicide rates (SRs) at the county level using direct estimates. Existing Bayesian spatio-temporal modeling strategies can be applied via Integrated Nested Laplace Approximation (INLA) in R to a large number of rare causes of mortality outcomes to enable examination of spatio-temporal variations on smaller geographic scales such as counties. This method allows examination of spatiotemporal variation across the entire U.S., even where the data are sparse. We used mortality data from 2005-2015 to explore spatiotemporal variation in SRs, as one particular application of the Bayesian spatio-temporal modeling strategy in R-INLA to predict year and county-specific SRs. Specifically, hierarchical Bayesian spatio-temporal models were implemented with spatially structured and unstructured random effects, correlated time effects, time varying confounders and space-time interaction terms in the software R-INLA, borrowing strength across both counties and years to produce smoothed county level SRs. Model-based estimates of SRs were mapped to explore geographic variation.

Host genetic variation influences gene expression response to rhinovirus infection.

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Minal Çalışkan

2015-04-01

Full Text Available Rhinovirus (RV is the most prevalent human respiratory virus and is responsible for at least half of all common colds. RV infections may result in a broad spectrum of effects that range from asymptomatic infections to severe lower respiratory illnesses. The basis for inter-individual variation in the response to RV infection is not well understood. In this study, we explored whether host genetic variation is associated with variation in gene expression response to RV infections between individuals. To do so, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs from 98 individuals. We mapped local and distant genetic variation that is associated with inter-individual differences in gene expression levels (eQTLs in both uninfected and RV-infected cells. We focused specifically on response eQTLs (reQTLs, namely, genetic associations with inter-individual variation in gene expression response to RV infection. We identified local reQTLs for 38 genes, including genes with known functions in viral response (UBA7, OAS1, IRF5 and genes that have been associated with immune and RV-related diseases (e.g., ITGA2, MSR1, GSTM3. The putative regulatory regions of genes with reQTLs were enriched for binding sites of virus-activated STAT2, highlighting the role of condition-specific transcription factors in genotype-by-environment interactions. Overall, we suggest that the 38 loci associated with inter-individual variation in gene expression response to RV-infection represent promising candidates for affecting immune and RV-related respiratory diseases.

Host genetic variation influences gene expression response to rhinovirus infection.

Science.gov (United States)

Çalışkan, Minal; Baker, Samuel W; Gilad, Yoav; Ober, Carole

2015-04-01

Rhinovirus (RV) is the most prevalent human respiratory virus and is responsible for at least half of all common colds. RV infections may result in a broad spectrum of effects that range from asymptomatic infections to severe lower respiratory illnesses. The basis for inter-individual variation in the response to RV infection is not well understood. In this study, we explored whether host genetic variation is associated with variation in gene expression response to RV infections between individuals. To do so, we obtained genome-wide genotype and gene expression data in uninfected and RV-infected peripheral blood mononuclear cells (PBMCs) from 98 individuals. We mapped local and distant genetic variation that is associated with inter-individual differences in gene expression levels (eQTLs) in both uninfected and RV-infected cells. We focused specifically on response eQTLs (reQTLs), namely, genetic associations with inter-individual variation in gene expression response to RV infection. We identified local reQTLs for 38 genes, including genes with known functions in viral response (UBA7, OAS1, IRF5) and genes that have been associated with immune and RV-related diseases (e.g., ITGA2, MSR1, GSTM3). The putative regulatory regions of genes with reQTLs were enriched for binding sites of virus-activated STAT2, highlighting the role of condition-specific transcription factors in genotype-by-environment interactions. Overall, we suggest that the 38 loci associated with inter-individual variation in gene expression response to RV-infection represent promising candidates for affecting immune and RV-related respiratory diseases.

A cadaveric study involving variations in external morphology of gall bladder

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Anjankar Vaibhav Prakash, Panshewdikar Pradnyesh N, Joshi DS, Anjankar Ashish Prakash

2013-04-01

Full Text Available Background: Variations in the pattern of the extra hepatic biliary tract are usual and are commonly encountered during some radiological investigations or in operation theaters. Such Variations of the morphology of Gall bladder have been well documented in the literature for many years but a detail morphological study of variations of the gall bladder and its incidence is very rare. In this era of quick results, increasing use of diagnostic and interventional procedures makes it important to study variations of gall bladder morphology. Most of the interventional procedures in this modern era are done laparoscopically and there is tremendous increase in the number of laparoscopic cholecystectomies. So, sound knowledge of possible variations in morphology of gall bladder is important. Materials and Methods: This study was undertaken on 90 cadaveric liver and gall bladder specimens in terms of length, maximum transverse diameter, shape, external variations of gall bladder, Interior and length of gall bladder below the inferior border of the liver. Results: GB had length ranging between 7 and 10 cm, transverse diameter between 2 and 5 cm. The commonest shape observed in this study was pear shaped in 82.22% of cases. The length of gall bladder below the inferior border of liver varied between 0.4 and 2.5 cm. Conclusion: The growing importance of such variations, lie not only from the point of biliary disease but also with respect to the various invasive techniques in the diagnosis and treatment of gall bladder and extrahepatic bile duct disease.

A common copy number variation polymorphism in the CNTNAP2 gene: sexual dimorphism in association with healthy aging and disease.

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Iakoubov, Leonid; Mossakowska, Malgorzata; Szwed, Malgorzata; Puzianowska-Kuznicka, Monika

2015-01-01

New therapeutic targets are needed to fight aging-related diseases and increase life span. A new female-specific association with diseases and limited survival past 80 years was recently reported for a copy number variation (CNV) in the CNTNAP4 gene from the neurexin superfamily. We asked whether there are CNVs that are associated with aging phenotypes within other genes from the neurexin superfamily and whether this association is sex specific. Select CNV polymorphisms were genotyped with proprietary TaqMan qPCR assays. A case/control study, in which a group of 81- to 90-year-old community-dwelling Caucasians with no chronic diseases (case) was compared to a similar control group of 65- to 75-year-olds, revealed a negative association with healthy aging for the ins allele of common esv11910 CNV in the CNTNAP2 gene (n = 388; OR = 0.29, 95% CI: 0.14-0.59, p = 0.0004 for males, and OR = 0.82, 95% CI: 0.42-1.57, p = 0.625 for females). This male-specific association was validated in a study of an independent group of 76- to 80-year-olds. To look for a corresponding positive association of the allele with aging-related diseases, two case subgroups of 81- to 90-year-olds, one composed of individuals with cognitive impairment and the other with various diseases not directly related to the nervous system, such as cardiovascular diseases, etc., were compared to a healthy control subgroup of the same age. A positive male-specific association was found for both cases (OR = 2.75, p = 0.008 for association with cognitive impairment, and OR = 3.18, p = 0.002 for other diseases combined). A new male-specific association with aging is reported for a CNV in the CNTNAP2 gene. The polymorphism might be useful for diagnosing individual genetic predispositions to healthy aging versus aging complicated by chronic diseases. © 2014 S. Karger AG, Basel.

Ethnic and geographic variations in the epidemiology of childhood fractures in the United Kingdom

NARCIS (Netherlands)

Moon, Rebecca J; Harvey, Nicholas C; Curtis, Elizabeth M; de Vries, Frank; van Staa, Tjeerd; Cooper, Cyrus

BACKGROUND: Fractures are common in childhood, and there is considerable variation in the reported incidence across European countries, but few data relating to ethnic and geographic differences within a single country. We therefore aimed to determine the incidence of childhood fractures in the

Is there much variation in variation? Revisiting statistics of small area variation in health services research

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Ibáñez Berta

2009-04-01

Full Text Available Abstract Background The importance of Small Area Variation Analysis for policy-making contrasts with the scarcity of work on the validity of the statistics used in these studies. Our study aims at 1 determining whether variation in utilization rates between health areas is higher than would be expected by chance, 2 estimating the statistical power of the variation statistics; and 3 evaluating the ability of different statistics to compare the variability among different procedures regardless of their rates. Methods Parametric bootstrap techniques were used to derive the empirical distribution for each statistic under the hypothesis of homogeneity across areas. Non-parametric procedures were used to analyze the empirical distribution for the observed statistics and compare the results in six situations (low/medium/high utilization rates and low/high variability. A small scale simulation study was conducted to assess the capacity of each statistic to discriminate between different scenarios with different degrees of variation. Results Bootstrap techniques proved to be good at quantifying the difference between the null hypothesis and the variation observed in each situation, and to construct reliable tests and confidence intervals for each of the variation statistics analyzed. Although the good performance of Systematic Component of Variation (SCV, Empirical Bayes (EB statistic shows better behaviour under the null hypothesis, it is able to detect variability if present, it is not influenced by the procedure rate and it is best able to discriminate between different degrees of heterogeneity. Conclusion The EB statistics seems to be a good alternative to more conventional statistics used in small-area variation analysis in health service research because of its robustness.

Spatial Variation of Magnitude Scaling Factors During the 2010 Darfield and 2011 Christchurch, New Zealand, Earthquakes

OpenAIRE

Carter, William Lake

2016-01-01

Magnitude Scaling Factors (MSF) account for the durational effects of strong ground shaking on the inducement of liquefaction within the simplified liquefaction evaluation procedure which is the most commonly used approach for assessing liquefaction potential worldwide. Within the context of the simplified procedure, the spatial variation in the seismic demand imposed on the soil traditionally has been assumed to be solely a function of the spatial variation of the peak amplitude of the groun...

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure.

Science.gov (United States)

Hao, Dapeng; Ren, Cong; Li, Chuanxing

2012-05-01

A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling). Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn't show dependence of degree. Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to "deterministic model" of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

Postawy rodziców i płeć psychologiczna a preferencja stylu kierowania

OpenAIRE

Tylka, Joanna

2011-01-01

The article is concerned with the subject of gender, parental attitudes and styles of people management. Theoretical grounds of the article refer to Gender Schema Theory worked out by S. L. Bem, Power/Interaction Model of Interpersonal Influence by B. Raven and Parental Attitudes Theory by M. Plopa. In the researches participated 122 executives (60 woman, 62 man) from southern Poland. The author used „Sex Role Inventory” A. Kuczyńskiej (IPP), Raven Interpersonal Influence Inventory, adapted b...

VARIATIONAL ANATOMY OF PROFUNDA FEMORIS ARTERY AND ITS BRANCHES: A CADAVERIC STUDY

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Tapan Kumar

2015-09-01

Full Text Available BACKGROUND: Accurate knowledge of anatomical variations regarding origins of the profunda femoris, medial and lateral femoral circumflex femoral arteries are important for clinicians in the present modern era of interventional radiology. Our aim of this study was to observe and identify the variations in origin of the Profunda femoris artery and its circumflex br anches. MATERIALS & METHODS: 66 femoral triangles were dissected on 33 cadavers (Both sides. The profunda femoris vessel and its medial and lateral circumflex arteries were dissected and identified. The distance of the site of origin of Profunda Femoris A rtery was measured from mid - inguinal point (MIP in centimetres with scale, thread, and digital callipers. The sites of origin of Medial Circumflex Femoral Artery and Lateral Circumflex Femoral Artery were also studied and the distances of origin of each of them were measured from the origin of the Profunda Femoris Artery and from the mid - inguinal point. All the data were interpreted in tables. RESULTS : The data from the study was analyzed using statistical methods and analyzed by using the statistical pa ckage SPSS (Statistical Package for Social Sciences version 16.0 for windows in present study for analyzing the data contingency table were created first and then analyzed by using the Pearson’s chi - square test. The present study encountered that, in appr oximately 50% cases the profunda femoris artery originated from the lateral aspect of the common femoral artery. The lateral and medial circumflex femoral artery commonly originated from the profunda femoris nearly close to its origin from common femoral a rtery. CONCLUSION: This knowledge of variation and position would be very useful in preventing the iatrogenic injury to these vessels during surgical procedures of the femoral triangle. So, this study would be useful for the clinician for surgical and therapeutic interventi on.

Accessory mental foramen: A rare anatomical variation detected by cone-beam computed tomography

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Torres, Marianna Guanaes Gomes; De Faro Valverde, Ludmila; Vidal, Manuela Torres Andion; Crusoe-Rebello, Ieda Margarida [Dept. of Oral Radiology, School of Dentistry, Federal University of Bahia, Salvador (Brazil)

2015-03-15

The mental foramen is a bilateral opening in the vestibular portion of the mandible through which nerve endings, such as the mental nerve, emerge. In general, the mental foramen is located between the lower premolars. This region is a common area for the placement of dental implants. It is very important to identify anatomical variations in presurgical imaging exams since damage to neurovascular bundles may have a direct influence on treatment success. In the hemimandible, the mental foramen normally appears as a single structure, but there are some rare reports on the presence and number of anatomical variations; these variations may include accessory foramina. The present report describes the presence of accessory mental foramina in the right mandible, as detected by cone-beam computed tomography before dental implant placement.

Spatial Evolution of the Thickness Variations over a CFRP Laminated Structure

Science.gov (United States)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2017-10-01

Ply thickness is one of the main drivers of the structural performance of a composite part. For stress analysis calculations (e.g., finite element analysis), composite plies are commonly considered to have a constant thickness compared to the reality (coefficients of variation up to 9% of the mean ply thickness). Unless this variability is taken into account reliable property predictions cannot be made. A modelling approach of such variations is proposed using parameters obtained from a 16-ply quasi-isotropic CFRP plate cured in an autoclave. A discrete Fourier transform algorithm is used to analyse the frequency response of the observed ply and plate thickness profiles. The model inputs, obtained by a mathematical representation of the ply thickness profiles, permit the generation of a representative stratification considering the spatial continuity of the thickness variations that are in good agreement with the real ply profiles spread over the composite part. A residual deformation FE model of the composite plate is used to illustrate the feasibility of the approach.

The Source of Language Variation among Chagga People in Kilimanjaro Region, Tanzania

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Godson Robert Mtallo

2015-07-01

Full Text Available This paper intends to find out the source of language variation among Chagga people. The study was guided by four specific objectives which were: to investigate the extent to which language variation exists among the Chagga, to examine the areas (aspects which mark language variation among the Chagga, to find out the source of language variation among the Chagga, and to determine whether Chagga varieties constitute different languages or varieties (dialects of the same language. In this study, three techniques were used to collect the primary data, which were sociolinguistic interview (free conversation, reading passage, and the wordlist. Results show that, despite the difficulties that Chagga people experience in communicating through their mother tongue, they understand each other. Their differences in speaking are based on some of the lexicon (vocabulary. Further, the study propounded the following as the reasons as to why Chagga people seem to differ in some vocabulary: geographical location, differences in origin, lack of common socialization, the existence of hostility among them as well as political unrest and the Mangi rule.

Anatomic variations found on dissection of depressor septi nasi muscles in cadavers.

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Ebrahimi, Ali; Nejadsarvari, Nasrin; Motamedi, Mohammad Hosein Kalantar; Rezaee, Maryam; Koushki, Ehsan Shams

2012-01-01

To define variations of the depressor septi muscle in Iranians; to provide guidance for modification of this muscle during rhinoplasty in patients with an active muscle and short upper lip; and to correlate our findings with our clinical experience to develop the applied algorithms. This study was conducted by dissecting 82 depressor septi nasi muscles in 41 Iranian cadavers. Origin and insertion points of each muscle were studied. Three variations were found in muscle insertion points: periosteal, orbicularis oris, and floating. Forty-four percent of the muscles were inserted into the periosteum of the maxilla (n = 36); 39% of muscles were inserted into the orbicularis oris muscle (n = 32); and 17% were diminutive or floating (n = 14). Periosteal insertion was thicker and stronger than the other variations. In all cadavers, the origin of the muscle was medial crus of alar cartilage and caudal of the nasal septum. This cadaveric dissection showed that the percentage of depressor septi muscle insertions is not similar to that found in other surveys. In this study, periosteal insertion of the depressor septi muscle was the most common variation.

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster.

Science.gov (United States)

Lavington, Erik; Kern, Andrew D

2017-11-06

Chromosomal inversions are a ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel (DGRP) to explore the effects of two cosmopolitan inversions, In ( 2L ) t and In ( 3R ) Mo , on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion-affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In ( 3R ) Mo but do not have SNPs in linkage disequilibrium (LD) with the inversion. We speculate that this upregulation is driven by genetic variation in mod ( mdg4 ) that is in LD with In ( 3R ) Mo We find that there is little evidence for a regional or position effect of inversions on gene expression at the chromosomal level, but do find evidence for the distal breakpoint of In ( 3R ) Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements. Copyright © 2017 Lavington and Kern.

Longitudinal Variations in the Variability of Spread F Occurrence

Science.gov (United States)

Groves, K. M.; Bridgwood, C.; Carrano, C. S.

2017-12-01

The complex dynamics of the equatorial ionosphere have attracted the interest and attention of researchers for many decades. The relatively local processes that give rise to large meridional gradients have been well documented and the associated terminology has entered the common lexicon of ionospheric research (e.g., fountain effect, equatorial anomaly, bubbles, Spread F). Zonal variations have also been noted, principally at the level of determining longitudinal differences in seasonal activity patterns. Due to a historical lack of high resolution ground-based observations at low latitudes, the primary source of data for such analyses has been space-based observations from satellites such as ROCSAT, DMSP, C/NOFS that measure in situ electron density variations. An important longitudinal variation in electron density structure associated with non-migrating diurnal tides was discovered by Immel et al. in 2006 using data from the FUV sensor aboard the NASA IMAGE satellite. These satellite observations have been very helpful in identifying the structural characteristics of the equatorial ionosphere and the occurrence of Spread F, but they provide little insight into variations in scintillation features and potential differences in bubble development characteristics. Moreover space-based studies tend towards the statistics of occurrence frequency over periods of weeks to months. A recent analysis of daily spread F occurrence as determined by low latitude VHF scintillation activity shows that statistical results that are consistent with previous space-based observations, but the level of variability in the occurrence data show marked variations with longitude. For example, the American sector shows very low in-season variability while the African and Asian sectors exhibit true day-to-day variability regardless of seasonal variations. The results have significant implications for space weather as they suggest that long-term forecasts of equatorial scintillation may be

Learning a common dictionary for subject-transfer decoding with resting calibration.

Science.gov (United States)

Morioka, Hiroshi; Kanemura, Atsunori; Hirayama, Jun-ichiro; Shikauchi, Manabu; Ogawa, Takeshi; Ikeda, Shigeyuki; Kawanabe, Motoaki; Ishii, Shin

2015-05-01

Brain signals measured over a series of experiments have inherent variability because of different physical and mental conditions among multiple subjects and sessions. Such variability complicates the analysis of data from multiple subjects and sessions in a consistent way, and degrades the performance of subject-transfer decoding in a brain-machine interface (BMI). To accommodate the variability in brain signals, we propose 1) a method for extracting spatial bases (or a dictionary) shared by multiple subjects, by employing a signal-processing technique of dictionary learning modified to compensate for variations between subjects and sessions, and 2) an approach to subject-transfer decoding that uses the resting-state activity of a previously unseen target subject as calibration data for compensating for variations, eliminating the need for a standard calibration based on task sessions. Applying our methodology to a dataset of electroencephalography (EEG) recordings during a selective visual-spatial attention task from multiple subjects and sessions, where the variability compensation was essential for reducing the redundancy of the dictionary, we found that the extracted common brain activities were reasonable in the light of neuroscience knowledge. The applicability to subject-transfer decoding was confirmed by improved performance over existing decoding methods. These results suggest that analyzing multisubject brain activities on common bases by the proposed method enables information sharing across subjects with low-burden resting calibration, and is effective for practical use of BMI in variable environments. Copyright © 2015 Elsevier Inc. All rights reserved.

The African Genome Variation Project shapes medical genetics in Africa

Science.gov (United States)

Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

2015-01-01

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

The African Genome Variation Project shapes medical genetics in Africa.

Science.gov (United States)

Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

2015-01-15

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

A common-path phase-shift interferometry surface plasmon imaging system

Science.gov (United States)

Su, Y.-T.; Chen, Shean-Jen; Yeh, T.-L.

2005-03-01

A biosensing imaging system is proposed based on the integration of surface plasmon resonance (SPR) and common-path phase-shift interferometry (PSI) techniques to measure the two-dimensional spatial phase variation caused by biomolecular interactions upon a sensing chip. The SPR phase imaging system can offer high resolution and high-throughout screening capabilities to analyze microarray biomolecular interaction without the need for additional labeling. With the long-term stability advantage of the common-path PSI technique even with external disturbances such as mechanical vibration, buffer flow noise, and laser unstable issue, the system can match the demand of real-time kinetic study for biomolecular interaction analysis (BIA). The SPR-PSI imaging system has achieved a detection limit of 2×10-7 refraction index change, a long-term phase stability of 2.5x10-4π rms over four hours, and a spatial phase resolution of 10-3 π with a lateral resolution of 100μm.

Analysis of shared heritability in common disorders of the brain.

Science.gov (United States)

Anttila, Verneri; Bulik-Sullivan, Brendan; Finucane, Hilary K; Walters, Raymond K; Bras, Jose; Duncan, Laramie; Escott-Price, Valentina; Falcone, Guido J; Gormley, Padhraig; Malik, Rainer; Patsopoulos, Nikolaos A; Ripke, Stephan; Wei, Zhi; Yu, Dongmei; Lee, Phil H; Turley, Patrick; Grenier-Boley, Benjamin; Chouraki, Vincent; Kamatani, Yoichiro; Berr, Claudine; Letenneur, Luc; Hannequin, Didier; Amouyel, Philippe; Boland, Anne; Deleuze, Jean-François; Duron, Emmanuelle; Vardarajan, Badri N; Reitz, Christiane; Goate, Alison M; Huentelman, Matthew J; Kamboh, M Ilyas; Larson, Eric B; Rogaeva, Ekaterina; St George-Hyslop, Peter; Hakonarson, Hakon; Kukull, Walter A; Farrer, Lindsay A; Barnes, Lisa L; Beach, Thomas G; Demirci, F Yesim; Head, Elizabeth; Hulette, Christine M; Jicha, Gregory A; Kauwe, John S K; Kaye, Jeffrey A; Leverenz, James B; Levey, Allan I; Lieberman, Andrew P; Pankratz, Vernon S; Poon, Wayne W; Quinn, Joseph F; Saykin, Andrew J; Schneider, Lon S; Smith, Amanda G; Sonnen, Joshua A; Stern, Robert A; Van Deerlin, Vivianna M; Van Eldik, Linda J; Harold, Denise; Russo, Giancarlo; Rubinsztein, David C; Bayer, Anthony; Tsolaki, Magda; Proitsi, Petra; Fox, Nick C; Hampel, Harald; Owen, Michael J; Mead, Simon; Passmore, Peter; Morgan, Kevin; Nöthen, Markus M; Rossor, Martin; Lupton, Michelle K; Hoffmann, Per; Kornhuber, Johannes; Lawlor, Brian; McQuillin, Andrew; Al-Chalabi, Ammar; Bis, Joshua C; Ruiz, Agustin; Boada, Mercè; Seshadri, Sudha; Beiser, Alexa; Rice, Kenneth; van der Lee, Sven J; De Jager, Philip L; Geschwind, Daniel H; Riemenschneider, Matthias; Riedel-Heller, Steffi; Rotter, Jerome I; Ransmayr, Gerhard; Hyman, Bradley T; Cruchaga, Carlos; Alegret, Montserrat; Winsvold, Bendik; Palta, Priit; Farh, Kai-How; Cuenca-Leon, Ester; Furlotte, Nicholas; Kurth, Tobias; Ligthart, Lannie; Terwindt, Gisela M; Freilinger, Tobias; Ran, Caroline; Gordon, Scott D; Borck, Guntram; Adams, Hieab H H; Lehtimäki, Terho; Wedenoja, Juho; Buring, Julie E; Schürks, Markus; Hrafnsdottir, Maria; Hottenga, Jouke-Jan; Penninx, Brenda; Artto, Ville; Kaunisto, Mari; Vepsäläinen, Salli; Martin, Nicholas G; Montgomery, Grant W; Kurki, Mitja I; Hämäläinen, Eija; Huang, Hailiang; Huang, Jie; Sandor, Cynthia; Webber, Caleb; Muller-Myhsok, Bertram; Schreiber, Stefan; Salomaa, Veikko; Loehrer, Elizabeth; Göbel, Hartmut; Macaya, Alfons; Pozo-Rosich, Patricia; Hansen, Thomas; Werge, Thomas; Kaprio, Jaakko; Metspalu, Andres; Kubisch, Christian; Ferrari, Michel D; Belin, Andrea C; van den Maagdenberg, Arn M J M; Zwart, John-Anker; Boomsma, Dorret; Eriksson, Nicholas; Olesen, Jes; Chasman, Daniel I; Nyholt, Dale R; Avbersek, Andreja; Baum, Larry; Berkovic, Samuel; Bradfield, Jonathan; Buono, Russell; Catarino, Claudia B; Cossette, Patrick; De Jonghe, Peter; Depondt, Chantal; Dlugos, Dennis; Ferraro, Thomas N; French, Jacqueline; Hjalgrim, Helle; Jamnadas-Khoda, Jennifer; Kälviäinen, Reetta; Kunz, Wolfram S; Lerche, Holger; Leu, Costin; Lindhout, Dick; Lo, Warren; Lowenstein, Daniel; McCormack, Mark; Møller, Rikke S; Molloy, Anne; Ng, Ping-Wing; Oliver, Karen; Privitera, Michael; Radtke, Rodney; Ruppert, Ann-Kathrin; Sander, Thomas; Schachter, Steven; Schankin, Christoph; Scheffer, Ingrid; Schoch, Susanne; Sisodiya, Sanjay M; Smith, Philip; Sperling, Michael; Striano, Pasquale; Surges, Rainer; Thomas, G Neil; Visscher, Frank; Whelan, Christopher D; Zara, Federico; Heinzen, Erin L; Marson, Anthony; Becker, Felicitas; Stroink, Hans; Zimprich, Fritz; Gasser, Thomas; Gibbs, Raphael; Heutink, Peter; Martinez, Maria; Morris, Huw R; Sharma, Manu; Ryten, Mina; Mok, Kin Y; Pulit, Sara; Bevan, Steve; Holliday, Elizabeth; Attia, John; Battey, Thomas; Boncoraglio, Giorgio; Thijs, Vincent; Chen, Wei-Min; Mitchell, Braxton; Rothwell, Peter; Sharma, Pankaj; Sudlow, Cathie; Vicente, Astrid; Markus, Hugh; Kourkoulis, Christina; Pera, Joana; Raffeld, Miriam; Silliman, Scott; Boraska Perica, Vesna; Thornton, Laura M; Huckins, Laura M; William Rayner, N; Lewis, Cathryn M; Gratacos, Monica; Rybakowski, Filip; Keski-Rahkonen, Anna; Raevuori, Anu; Hudson, James I; Reichborn-Kjennerud, Ted; Monteleone, Palmiero; Karwautz, Andreas; Mannik, Katrin; Baker, Jessica H; O'Toole, Julie K; Trace, Sara E; Davis, Oliver S P; Helder, Sietske G; Ehrlich, Stefan; Herpertz-Dahlmann, Beate; Danner, Unna N; van Elburg, Annemarie A; Clementi, Maurizio; Forzan, Monica; Docampo, Elisa; Lissowska, Jolanta; Hauser, Joanna; Tortorella, Alfonso; Maj, Mario; Gonidakis, Fragiskos; Tziouvas, Konstantinos; Papezova, Hana; Yilmaz, Zeynep; Wagner, Gudrun; Cohen-Woods, Sarah; Herms, Stefan; Julià, Antonio; Rabionet, Raquel; Dick, Danielle M; Ripatti, Samuli; Andreassen, Ole A; Espeseth, Thomas; Lundervold, Astri J; Steen, Vidar M; Pinto, Dalila; Scherer, Stephen W; Aschauer, Harald; Schosser, Alexandra; Alfredsson, Lars; Padyukov, Leonid; Halmi, Katherine A; Mitchell, James; Strober, Michael; Bergen, Andrew W; Kaye, Walter; Szatkiewicz, Jin Peng; Cormand, Bru; Ramos-Quiroga, Josep Antoni; Sánchez-Mora, Cristina; Ribasés, Marta; Casas, Miguel; Hervas, Amaia; Arranz, Maria Jesús; Haavik, Jan; Zayats, Tetyana; Johansson, Stefan; Williams, Nigel; Dempfle, Astrid; Rothenberger, Aribert; Kuntsi, Jonna; Oades, Robert D; Banaschewski, Tobias; Franke, Barbara; Buitelaar, Jan K; Arias Vasquez, Alejandro; Doyle, Alysa E; Reif, Andreas; Lesch, Klaus-Peter; Freitag, Christine; Rivero, Olga; Palmason, Haukur; Romanos, Marcel; Langley, Kate; Rietschel, Marcella; Witt, Stephanie H; Dalsgaard, Soeren; Børglum, Anders D; Waldman, Irwin; Wilmot, Beth; Molly, Nikolas; Bau, Claiton H D; Crosbie, Jennifer; Schachar, Russell; Loo, Sandra K; McGough, James J; Grevet, Eugenio H; Medland, Sarah E; Robinson, Elise; Weiss, Lauren A; Bacchelli, Elena; Bailey, Anthony; Bal, Vanessa; Battaglia, Agatino; Betancur, Catalina; Bolton, Patrick; Cantor, Rita; Celestino-Soper, Patrícia; Dawson, Geraldine; De Rubeis, Silvia; Duque, Frederico; Green, Andrew; Klauck, Sabine M; Leboyer, Marion; Levitt, Pat; Maestrini, Elena; Mane, Shrikant; De-Luca, Daniel Moreno-; Parr, Jeremy; Regan, Regina; Reichenberg, Abraham; Sandin, Sven; Vorstman, Jacob; Wassink, Thomas; Wijsman, Ellen; Cook, Edwin; Santangelo, Susan; Delorme, Richard; Rogé, Bernadette; Magalhaes, Tiago; Arking, Dan; Schulze, Thomas G; Thompson, Robert C; Strohmaier, Jana; Matthews, Keith; Melle, Ingrid; Morris, Derek; Blackwood, Douglas; McIntosh, Andrew; Bergen, Sarah E; Schalling, Martin; Jamain, Stéphane; Maaser, Anna; Fischer, Sascha B; Reinbold, Céline S; Fullerton, Janice M; Guzman-Parra, José; Mayoral, Fermin; Schofield, Peter R; Cichon, Sven; Mühleisen, Thomas W; Degenhardt, Franziska; Schumacher, Johannes; Bauer, Michael; Mitchell, Philip B; Gershon, Elliot S; Rice, John; Potash, James B; Zandi, Peter P; Craddock, Nick; Ferrier, I Nicol; Alda, Martin; Rouleau, Guy A; Turecki, Gustavo; Ophoff, Roel; Pato, Carlos; Anjorin, Adebayo; Stahl, Eli; Leber, Markus; Czerski, Piotr M; Cruceanu, Cristiana; Jones, Ian R; Posthuma, Danielle; Andlauer, Till F M; Forstner, Andreas J; Streit, Fabian; Baune, Bernhard T; Air, Tracy; Sinnamon, Grant; Wray, Naomi R; MacIntyre, Donald J; Porteous, David; Homuth, Georg; Rivera, Margarita; Grove, Jakob; Middeldorp, Christel M; Hickie, Ian; Pergadia, Michele; Mehta, Divya; Smit, Johannes H; Jansen, Rick; de Geus, Eco; Dunn, Erin; Li, Qingqin S; Nauck, Matthias; Schoevers, Robert A; Beekman, Aartjan Tf; Knowles, James A; Viktorin, Alexander; Arnold, Paul; Barr, Cathy L; Bedoya-Berrio, Gabriel; Bienvenu, O Joseph; Brentani, Helena; Burton, Christie; Camarena, Beatriz; Cappi, Carolina; Cath, Danielle; Cavallini, Maria; Cusi, Daniele; Darrow, Sabrina; Denys, Damiaan; Derks, Eske M; Dietrich, Andrea; Fernandez, Thomas; Figee, Martijn; Freimer, Nelson; Gerber, Gloria; Grados, Marco; Greenberg, Erica; Hanna, Gregory L; Hartmann, Andreas; Hirschtritt, Matthew E; Hoekstra, Pieter J; Huang, Alden; Huyser, Chaim; Illmann, Cornelia; Jenike, Michael; Kuperman, Samuel; Leventhal, Bennett; Lochner, Christine; Lyon, Gholson J; Macciardi, Fabio; Madruga-Garrido, Marcos; Malaty, Irene A; Maras, Athanasios; McGrath, Lauren; Miguel, Eurípedes C; Mir, Pablo; Nestadt, Gerald; Nicolini, Humberto; Okun, Michael S; Pakstis, Andrew; Paschou, Peristera; Piacentini, John; Pittenger, Christopher; Plessen, Kerstin; Ramensky, Vasily; Ramos, Eliana M; Reus, Victor; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Roessner, Veit; Rosário, Maria; Samuels, Jack F; Sandor, Paul; Stein, Dan J; Tsetsos, Fotis; Van Nieuwerburgh, Filip; Weatherall, Sarah; Wendland, Jens R; Wolanczyk, Tomasz; Worbe, Yulia; Zai, Gwyneth; Goes, Fernando S; McLaughlin, Nicole; Nestadt, Paul S; Grabe, Hans-Jorgen; Depienne, Christel; Konkashbaev, Anuar; Lanzagorta, Nuria; Valencia-Duarte, Ana; Bramon, Elvira; Buccola, Nancy; Cahn, Wiepke; Cairns, Murray; Chong, Siow A; Cohen, David; Crespo-Facorro, Benedicto; Crowley, James; Davidson, Michael; DeLisi, Lynn; Dinan, Timothy; Donohoe, Gary; Drapeau, Elodie; Duan, Jubao; Haan, Lieuwe; Hougaard, David; Karachanak-Yankova, Sena; Khrunin, Andrey; Klovins, Janis; Kučinskas, Vaidutis; Lee Chee Keong, Jimmy; Limborska, Svetlana; Loughland, Carmel; Lönnqvist, Jouko; Maher, Brion; Mattheisen, Manuel; McDonald, Colm; Murphy, Kieran C; Nenadic, Igor; van Os, Jim; Pantelis, Christos; Pato, Michele; Petryshen, Tracey; Quested, Digby; Roussos, Panos; Sanders, Alan R; Schall, Ulrich; Schwab, Sibylle G; Sim, Kang; So, Hon-Cheong; Stögmann, Elisabeth; Subramaniam, Mythily; Toncheva, Draga; Waddington, John; Walters, James; Weiser, Mark; Cheng, Wei; Cloninger, Robert; Curtis, David; Gejman, Pablo V; Henskens, Frans; Mattingsdal, Morten; Oh, Sang-Yun; Scott, Rodney; Webb, Bradley; Breen, Gerome; Churchhouse, Claire; Bulik, Cynthia M; Daly, Mark; Dichgans, Martin; Faraone, Stephen V; Guerreiro, Rita; Holmans, Peter; Kendler, Kenneth S; Koeleman, Bobby; Mathews, Carol A; Price, Alkes; Scharf, Jeremiah; Sklar, Pamela; Williams, Julie; Wood, Nicholas W; Cotsapas, Chris; Palotie, Aarno; Smoller, Jordan W; Sullivan, Patrick; Rosand, Jonathan; Corvin, Aiden; Neale, Benjamin M

2018-06-22

Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Variations in the size of focal nodular hyperplasia on magnetic resonance imaging.

Science.gov (United States)

Ramírez-Fuentes, C; Martí-Bonmatí, L; Torregrosa, A; Del Val, A; Martínez, C

2013-01-01

To evaluate the changes in the size of focal nodular hyperplasia (FNH) during long-term magnetic resonance imaging (MRI) follow-up. We reviewed 44 FNHs in 30 patients studied with MRI with at least two MRI studies at least 12 months apart. We measured the largest diameter of the lesion (inmm) in contrast-enhanced axial images and calculated the percentage of variation as the difference between the maximum diameter in the follow-up and the maximum diameter in the initial study. We defined significant variation in size as variation greater than 20%. We also analyzed predisposing hormonal factors. The mean interval between the two imaging studies was 35±2 months (range: 12-94). Most lesions (80%) remained stable during follow-up. Only 9 of the 44 lesions (20%) showed a significant variation in diameter: 7 (16%) decreased in size and 2 (4%) increased, with variations that reached the double of the initial size. The change in size was not related to pregnancy, menopause, or the use of birth control pills or corticoids. Changes in the size of FNHs during follow-up are relatively common and should not lead to a change in the diagnosis. These variations in size seem to be independent of hormonal factors that are considered to predispose. Copyright © 2011 SERAM. Published by Elsevier Espana. All rights reserved.

Genetic variation shapes protein networks mainly through non-transcriptional mechanisms.

Directory of Open Access Journals (Sweden)

Eric J Foss

2011-09-01

Full Text Available Networks of co-regulated transcripts in genetically diverse populations have been studied extensively, but little is known about the degree to which these networks cause similar co-variation at the protein level. We quantified 354 proteins in a genetically diverse population of yeast segregants, which allowed for the first time construction of a coherent protein co-variation matrix. We identified tightly co-regulated groups of 36 and 93 proteins that were made up predominantly of genes involved in ribosome biogenesis and amino acid metabolism, respectively. Even though the ribosomal genes were tightly co-regulated at both the protein and transcript levels, genetic regulation of proteins was entirely distinct from that of transcripts, and almost no genes in this network showed a significant correlation between protein and transcript levels. This result calls into question the widely held belief that in yeast, as opposed to higher eukaryotes, ribosomal protein levels are regulated primarily by regulating transcript levels. Furthermore, although genetic regulation of the amino acid network was more similar for proteins and transcripts, regression analysis demonstrated that even here, proteins vary predominantly as a result of non-transcriptional variation. We also found that cis regulation, which is common in the transcriptome, is rare at the level of the proteome. We conclude that most inter-individual variation in levels of these particular high abundance proteins in this genetically diverse population is not caused by variation of their underlying transcripts.

Quantum Variational Calculus

OpenAIRE

Malinowska , Agnieszka B.; Torres , Delfim

2014-01-01

International audience; Introduces readers to the treatment of the calculus of variations with q-differences and Hahn difference operators Provides the reader with the first extended treatment of quantum variational calculus Shows how the techniques described can be applied to economic models as well as other mathematical systems This Brief puts together two subjects, quantum and variational calculi by considering variational problems involving Hahn quantum operators. The main advantage of it...

Human longevity and common variations in the LMNA gene: a meta-analysis

Science.gov (United States)

Conneely, Karen N.; Capell, Brian C.; Erdos, Michael R.; Sebastiani, Paola; Solovieff, Nadia; Swift, Amy J.; Baldwin, Clinton T.; Budagov, Temuri; Barzilai, Nir; Atzmon, Gil; Puca, Annibale A.; Perls, Thomas T.; Geesaman, Bard J.; Boehnke, Michael; Collins, Francis S.

2012-01-01

Summary A mutation in the LMNA gene is responsible for the most dramatic form of premature aging, Hutchinson-Gilford progeria syndrome (HGPS). Several recent studies have suggested that protein products of this gene might have a role in normal physiological cellular senescence. To explore further LMNA's possible role in normal aging, we genotyped 16 SNPs over a span of 75.4 kb of the LMNA gene on a sample of long-lived individuals (US Caucasians with age ≥95 years, N=873) and genetically matched younger controls (N=443). We tested all common non-redundant haplotypes (frequency ≥ 0.05) based on subgroups of these 16 SNPs for association with longevity. The most significant haplotype, based on 4 SNPs, remained significant after adjustment for multiple testing (OR = 1.56, P=2.5×10−5, multiple-testing-adjusted P=0.0045). To attempt to replicate these results, we genotyped 3448 subjects from four independent samples of long-lived individuals and control subjects from 1) the New England Centenarian Study (NECS) (N=738), 2) the Southern Italian Centenarian Study (SICS) (N=905), 3) France (N=1103), and 4) the Einstein Ashkenazi Longevity Study (N=702). We replicated the association with the most significant haplotype from our initial analysis in the NECS sample (OR = 1.60, P=0.0023), but not in the other three samples (P>.15). In a meta-analysis combining all five samples, the best haplotype remained significantly associated with longevity after adjustment for multiple testing in the initial and follow-up samples (OR = 1.18, P=7.5×10−4, multiple-testing-adjusted P=0.037). These results suggest that LMNA variants may play a role in human lifespan. PMID:22340368

Variation in the γ-glutamyltransferase 1 gene and risk of chronic pancreatitis.

Science.gov (United States)

Brand, Harrison; Diergaarde, Brenda; O'Connell, Michael R; Whitcomb, David C; Brand, Randall E

2013-07-01

Individuals with chronic pancreatitis are at increased risk for pancreatic cancer. We hypothesized that genetic variation in the γ-glutamyltransferase 1 (GGT1) gene, which was recently reported associated with pancreatic cancer risk in a genome-wide association study, is also associated with risk of chronic pancreatitis. Associations between common polymorphisms in GGT1 and chronic pancreatitis were evaluated using data and samples from the North American Pancreatitis Study 2. Patients (n = 496) and control subjects (n = 465) were genotyped for 4 single-nucleotide polymorphisms: rs4820599, rs2017869, rs8135987, and rs5751901. Odds ratios (ORs) and corresponding 95% confidence intervals (95% CI) for chronic pancreatitis risk were calculated using multiple logistic regression models. Interactions with cigarette smoking and alcohol use were explored. Single-nucleotide polymorphisms rs8135987 and rs4820599 were both statistically significantly associated with risk of chronic pancreatitis; compared with common allele homozygotes, individuals with at least 1 minor allele were at increased risk (rs8135987: OR, 1.36; 95% CI, 1.03-1.80 [P(trend) = 0.01]; rs4820599: OR, 1.39; 95% CI, 1.04-1.84 [P(trend) = 0.0]; adjusted for age, sex, race, smoking status, and alcohol use). No significant interactions with cigarette smoking and alcohol use were observed. Our results suggest that common variation in the GGT1 gene may also affect risk of chronic pancreatitis.

Data Analysis Approaches for the Risk-Informed Safety Margins Characterization Toolkit

International Nuclear Information System (INIS)

Mandelli, Diego; Alfonsi, Andrea; Maljovec, Daniel P.; Parisi, Carlo; Cogliati, Joshua J.; Talbot, Paul W.; Smith, Curtis L.; Rabiti, Cristian; Picoco, Claudia

2016-01-01

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, RELAP-7, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually called Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, ''extracting information'' means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework.

Data Analysis Approaches for the Risk-Informed Safety Margins Characterization Toolkit

Energy Technology Data Exchange (ETDEWEB)

Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Maljovec, Daniel P. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Parisi, Carlo [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cogliati, Joshua J. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Talbot, Paul W. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Smith, Curtis L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Picoco, Claudia [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2016-09-01

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, RELAP-7, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually called Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, “extracting information” means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework.

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

Science.gov (United States)

Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

2015-01-01

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

Directory of Open Access Journals (Sweden)

Brett eWagner Mackenzie

2015-02-01

Full Text Available The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation, with a smaller proportion of variation associated with DNA extraction method (technical variation and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis).

Science.gov (United States)

Johnson, M T J

2007-01-01

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Climate warming: a loss of variation in populations can accompany reproductive shifts.

Science.gov (United States)

Massot, Manuel; Legendre, Stéphane; Fédérici, Pierre; Clobert, Jean

2017-09-01

The most documented response of organisms to climate warming is a change in the average timing of seasonal activities (phenology). Although we know that these average changes can differ among species and populations, we do not know whether climate warming impacts within-population variation in phenology. Using data from five study sites collected during a 13-year survey, we found that the increase in spring temperatures is associated with a reproductive advance of 10 days in natural populations of common lizards (Zootoca vivipara). Interestingly, we show a correlated loss of variation in reproductive dates within populations. As illustrated by a model, this shortening of the reproductive period can have significant negative effects on population dynamics. Consequently, we encourage tests in other species to assess the generality of decreased variation in phenological responses to climate change. © 2017 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Genic intolerance to functional variation and the interpretation of personal genomes.

Directory of Open Access Journals (Sweden)

Slavé Petrovski

Full Text Available A central challenge in interpreting personal genomes is determining which mutations most likely influence disease. Although progress has been made in scoring the functional impact of individual mutations, the characteristics of the genes in which those mutations are found remain largely unexplored. For example, genes known to carry few common functional variants in healthy individuals may be judged more likely to cause certain kinds of disease than genes known to carry many such variants. Until now, however, it has not been possible to develop a quantitative assessment of how well genes tolerate functional genetic variation on a genome-wide scale. Here we describe an effort that uses sequence data from 6503 whole exome sequences made available by the NHLBI Exome Sequencing Project (ESP. Specifically, we develop an intolerance scoring system that assesses whether genes have relatively more or less functional genetic variation than expected based on the apparently neutral variation found in the gene. To illustrate the utility of this intolerance score, we show that genes responsible for Mendelian diseases are significantly more intolerant to functional genetic variation than genes that do not cause any known disease, but with striking variation in intolerance among genes causing different classes of genetic disease. We conclude by showing that use of an intolerance ranking system can aid in interpreting personal genomes and identifying pathogenic mutations.

Variations in C-heterochromatin and AgNOR distribution in the common vole (Microtus arvalis sensu lato) (Mammalia: Rodentia)

Czech Academy of Sciences Publication Activity Database

Yorulmaz, T.; Zima, Jan; Arslan, A.; Kankilic, T.

2013-01-01

Roč. 65, č. 3 (2013), s. 989-995 ISSN 0354-4664 Institutional support: RVO:68081766 Keywords : Common vole * Altai vole * Central Europe * Anatolia * C-banding * AgNOR staining Subject RIV: EG - Zoology Impact factor: 0.607, year: 2013

Multidetector computed tomography angiography of the renal arteries: normal anatomy and its variations

Directory of Open Access Journals (Sweden)

Carlos Fernando de Mello Júnior

2016-06-01

Full Text Available Abstract Conventional angiography is still considered the gold standard for the study of the anatomy and of vascular diseases of the abdomen. However, the advent of multidetector computed tomography and techniques of digital image reconstruction has provided an alternative means of performing angiography, without the risks inherent to invasive angiographic examinations. Therefore, within the field of radiology, there is an ever-increasing demand for deeper knowledge of the anatomy of the regional vasculature and its variations. Variations in the renal vascular system are relatively prevalent in the venous and arterial vessels. For various conditions in which surgical planning is crucial to the success of the procedure, knowledge of this topic is important. The aim of this study was to familiarize the general radiologist with variations in the renal vascular system. To that end, we prepared a pictorial essay comprising multidetector computed tomography images obtained in a series of cases. We show patterns representative of the most common anatomical variations in the arterial blood supply to the kidneys, calling attention to the nomenclature, as well as to the clinical and surgical implications of such variations.

Multidetector computed tomography angiography of the renal arteries: normal anatomy and its variations

International Nuclear Information System (INIS)

Mello Junior, Carlos Fernando de; Araujo Neto, Severino Aires; Carvalho Junior, Arlindo Monteiro de; Negromonte, Gustavo Ramalho Pessoa; Oliveira, Carollyne Dantas de; Reboucas, Rafael Batista

2016-01-01

Conventional angiography is still considered the gold standard for the study of the anatomy and of vascular diseases of the abdomen. However, the advent of multidetector computed tomography and techniques of digital image reconstruction has provided an alternative means of performing angiography, without the risks inherent to invasive angiographic examinations. Therefore, within the field of radiology, there is an ever-increasing demand for deeper knowledge of the anatomy of the regional vasculature and its variations. Variations in the renal vascular system are relatively prevalent in the venous and arterial vessels. For various conditions in which surgical planning is crucial to the success of the procedure, knowledge of this topic is important. The aim of this study was to familiarize the general radiologist with variations in the renal vascular system. To that end, we prepared a pictorial essay comprising multidetector computed tomography images obtained in a series of cases. We show patterns representative of the most common anatomical variations in the arterial blood supply to the kidneys, calling attention to the nomenclature, as well as to the clinical and surgical implications of such variations. (author)

Multidetector computed tomography angiography of the renal arteries: normal anatomy and its variations

Energy Technology Data Exchange (ETDEWEB)

Mello Junior, Carlos Fernando de; Araujo Neto, Severino Aires; Carvalho Junior, Arlindo Monteiro de; Negromonte, Gustavo Ramalho Pessoa; Oliveira, Carollyne Dantas de [Universidade Federal da Paraiba (UFPB), Joao Pessoa, PB (Brazil); Reboucas, Rafael Batista, E-mail: severinoaires@hotmail.com [Faculdade de Ciencias Medicas da Paraiba, Joao Pessoa, PB (Brazil)

2016-05-15

Conventional angiography is still considered the gold standard for the study of the anatomy and of vascular diseases of the abdomen. However, the advent of multidetector computed tomography and techniques of digital image reconstruction has provided an alternative means of performing angiography, without the risks inherent to invasive angiographic examinations. Therefore, within the field of radiology, there is an ever-increasing demand for deeper knowledge of the anatomy of the regional vasculature and its variations. Variations in the renal vascular system are relatively prevalent in the venous and arterial vessels. For various conditions in which surgical planning is crucial to the success of the procedure, knowledge of this topic is important. The aim of this study was to familiarize the general radiologist with variations in the renal vascular system. To that end, we prepared a pictorial essay comprising multidetector computed tomography images obtained in a series of cases. We show patterns representative of the most common anatomical variations in the arterial blood supply to the kidneys, calling attention to the nomenclature, as well as to the clinical and surgical implications of such variations. (author)

Induction of Genetic Variation with Recurrent Gamma Radiation in Centipedegrass (Eremochloa ophiuroides)

International Nuclear Information System (INIS)

Lim Keun- Bal; Rim Yong-Woo

1998-01-01

Centipedegrass (Eremochloa ophiuroides) is a popular lawn grass in the southeastern USA. It has a naturally light green color and grows well on a wide range of soil types. Studies show limited morphological variation present in centipedegrass germplasm. To obtain the high morphological variation, plants were established from the irradiated seed at 10 Kr, allowed to interpollinate and harvested bulk seed, and then irradiated again for the next cycles. Morphological characteristics were measured in the 5 genetic varition lines (TC201:cv. Common and non irradiated, TC202:4th cycles, TC241:6th cycles, TC306:8th cycles, and TC318:5th cycles) induced by recurrent gamma radiation. The ranges of variation of recurrently radiated centipedegrass lines TC202, TC241, and TC306 except TC318(TifBlair) for the stolons per plant, total stolon length per plant, longest stolon length, leaf length and width at top-most exposed internode were wider than those of non-irradiated line (TC201). Recurrent gamma radiation was very effective to enlarge the ranges of variation of morphological characteristics in reproductive organ like stolons of centipedegrass. The effect of quantity of gamma ray irradiation cycles on the means and ranges of variation in the morphological characteristics of centipedegrass was not regularly tended

Variation of the latissimus dorsi

Directory of Open Access Journals (Sweden)

Ishani P Shah

2014-01-01

Full Text Available A typical muscle variation of latissimus dorsi - the axillary arch is represented by the muscular or fibromuscular slip detached from the anteroinferior border of the musculus latissimus dorsi passing over the axilla under the axillary fascia crossing the medial side of the brachial plexus to continue as a septum intermusculare mediale brachii distally to the medial epicondyle of humerus. The full extent of the muscle is rarely present. Slips of muscle extend from the latissimus dorsi at the inferior angle of scapula to insert into pectoralis major (Langer, coracobrachilis, biceps or coracoid process forming what is described as a common variant - the muscular axillary arch. We report three cases of variants of latissimus dorsi, one of which has not been reported in the literature before.

Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk.

Science.gov (United States)

Chornokur, Ganna; Lin, Hui-Yi; Tyrer, Jonathan P; Lawrenson, Kate; Dennis, Joe; Amankwah, Ernest K; Qu, Xiaotao; Tsai, Ya-Yu; Jim, Heather S L; Chen, Zhihua; Chen, Ann Y; Permuth-Wey, Jennifer; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Bruinsma, Fiona; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A; Brooks-Wilson, Angela; Bunker, Clareann H; Butzow, Ralf; Campbell, Ian G; Carty, Karen; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; du Bois, Andreas; Despierre, Evelyn; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; Dürst, Matthias; Easton, Douglas F; Eccles, Diana M; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goodman, Marc T; Gronwald, Jacek; Harrington, Patricia; Harter, Philipp; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Claus K; Hogdall, Estrid; Hosono, Satoyo; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kelemen, Linda E; Kellar, Mellissa; Kiemeney, Lambertus A; Krakstad, Camilla; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lim, Boon Kiong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F A G; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Iain; Menon, Usha; Milne, Roger L; Modugno, Francesmary; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Eilber, Ursula; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Pelttari, Liisa M; Pike, Malcolm C; Poole, Elizabeth M; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schernhammer, Eva; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Spiewankiewicz, Beata; Sucheston, Lara; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Thomsen, Lotte; Tangen, Ingvild L; Tworoger, Shelley S; van Altena, Anne M; Vierkant, Robert A; Vergote, Ignace; Walsh, Christine S; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Wu, Anna H; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Hasmad, Hanis N; Berchuck, Andrew; Iversen, Edwin S; Schildkraut, Joellen M; Ramus, Susan J; Goode, Ellen L; Monteiro, Alvaro N A; Gayther, Simon A; Narod, Steven A; Pharoah, Paul D P; Sellers, Thomas A; Phelan, Catherine M

2015-01-01

Defective cellular transport processes can lead to aberrant accumulation of trace elements, iron, small molecules and hormones in the cell, which in turn may promote the formation of reactive oxygen species, promoting DNA damage and aberrant expression of key regulatory cancer genes. As DNA damage and uncontrolled proliferation are hallmarks of cancer, including epithelial ovarian cancer (EOC), we hypothesized that inherited variation in the cellular transport genes contributes to EOC risk. In total, DNA samples were obtained from 14,525 case subjects with invasive EOC and from 23,447 controls from 43 sites in the Ovarian Cancer Association Consortium (OCAC). Two hundred seventy nine SNPs, representing 131 genes, were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). SNP analyses were conducted using unconditional logistic regression under a log-additive model, and the FDR q<0.2 was applied to adjust for multiple comparisons. The most significant evidence of an association for all invasive cancers combined and for the serous subtype was observed for SNP rs17216603 in the iron transporter gene HEPH (invasive: OR = 0.85, P = 0.00026; serous: OR = 0.81, P = 0.00020); this SNP was also associated with the borderline/low malignant potential (LMP) tumors (P = 0.021). Other genes significantly associated with EOC histological subtypes (p<0.05) included the UGT1A (endometrioid), SLC25A45 (mucinous), SLC39A11 (low malignant potential), and SERPINA7 (clear cell carcinoma). In addition, 1785 SNPs in six genes (HEPH, MGST1, SERPINA, SLC25A45, SLC39A11 and UGT1A) were imputed from the 1000 Genomes Project and examined for association with INV EOC in white-European subjects. The most significant imputed SNP was rs117729793 in SLC39A11 (per allele, OR = 2.55, 95% CI = 1.5-4.35, p = 5.66x10-4). These results, generated on a large cohort of women, revealed associations between inherited cellular transport

Diel variations in zooplankton and their biochemical composition from Vengurla to Ratnagiri, west coast of India

Digital Repository Service at National Institute of Oceanography (India)

Goswami, S.C.; KrishnaKumari, L.; Shrivastava, Y.

Diel variations in zooplankton biomass, common groups and proximate composition zooplankton at stations between Vengurla to Ratnagiri, along west coast of India were studied. Higher biomass values were obtained for the night samples (av = 80 ml/100...

A cross-sectional analysis of variation in charges and prices across California for percutaneous coronary intervention.

Directory of Open Access Journals (Sweden)

Renee Y Hsia

Full Text Available Though past studies have shown wide variation in aggregate hospital price indices and specific procedures, few have documented or explained such variation for distinct and common episodes of care.We sought to examine the variability in charges for percutaneous coronary intervention (PCI with a drug-eluting stent and without major complications (MS-DRG-247, and determine whether hospital and market characteristics influenced these charges.We conducted a cross-sectional analysis of adults admitted to California hospitals in 2011 for MS-DRG-247 using patient discharge data from the California Office of Statewide Health Planning and Development. We used a two-part linear regression model to first estimate hospital-specific charges adjusted for patient characteristics, and then examine whether the between-hospital variation in those estimated charges was explained by hospital and market characteristics.Adjusted charges for the average California patient admitted for uncomplicated PCI ranged from $22,047 to $165,386 (median: $88,350 depending on which hospital the patient visited. Hospitals in areas with the highest cost of living, those in rural areas, and those with more Medicare patients had higher charges, while government-owned hospitals charged less. Overall, our model explained 43% of the variation in adjusted charges. Estimated discounted prices paid by private insurers ranged from $3,421 to $80,903 (median: $28,571.Charges and estimated discounted prices vary widely between hospitals for the average California patient undergoing PCI without major complications, a common and relatively homogeneous episode of care. Though observable hospital characteristics account for some of this variation, the majority remains unexplained.

Nationwide Multicenter Reference Interval Study for 28 Common Biochemical Analytes in China.

Science.gov (United States)

Xia, Liangyu; Chen, Ming; Liu, Min; Tao, Zhihua; Li, Shijun; Wang, Liang; Cheng, Xinqi; Qin, Xuzhen; Han, Jianhua; Li, Pengchang; Hou, Li'an; Yu, Songlin; Ichihara, Kiyoshi; Qiu, Ling

2016-03-01

A nationwide multicenter study was conducted in the China to explore sources of variation of reference values and establish reference intervals for 28 common biochemical analytes, as a part of the International Federation of Clinical Chemistry and Laboratory Medicine, Committee on Reference Intervals and Decision Limits (IFCC/C-RIDL) global study on reference values. A total of 3148 apparently healthy volunteers were recruited in 6 cities covering a wide area in China. Blood samples were tested in 2 central laboratories using Beckman Coulter AU5800 chemistry analyzers. Certified reference materials and value-assigned serum panel were used for standardization of test results. Multiple regression analysis was performed to explore sources of variation. Need for partition of reference intervals was evaluated based on 3-level nested ANOVA. After secondary exclusion using the latent abnormal values exclusion method, reference intervals were derived by a parametric method using the modified Box-Cox formula. Test results of 20 analytes were made traceable to reference measurement procedures. By the ANOVA, significant sex-related and age-related differences were observed in 12 and 12 analytes, respectively. A small regional difference was observed in the results for albumin, glucose, and sodium. Multiple regression analysis revealed BMI-related changes in results of 9 analytes for man and 6 for woman. Reference intervals of 28 analytes were computed with 17 analytes partitioned by sex and/or age. In conclusion, reference intervals of 28 common chemistry analytes applicable to Chinese Han population were established by use of the latest methodology. Reference intervals of 20 analytes traceable to reference measurement procedures can be used as common reference intervals, whereas others can be used as the assay system-specific reference intervals in China.

Interindividual variation in gene expression responses and metabolite formation in acetaminophen-exposed primary human hepatocytes

NARCIS (Netherlands)

Jetten, M.J.A.; Blanco Garcia, Ainhoa; Coonen, M.L.J.; Claessen, Sandra; Herwijnen, van M.H.M.; Lommen, Arjen; Delft, van J.H.M.; Peijnenburg, A.A.C.M.; Kleinjans, J.C.S.

2016-01-01

Acetaminophen (APAP) is a readily available over-the-counter drug and is one of the most commonly used analgesics/antipyretics worldwide. Large interindividual variation in susceptibility toward APAP-induced liver failure has been reported. However, the exact underlying factors causing this

Characterising phase variations in MALDI-TOF data and correcting

Directory of Open Access Journals (Sweden)

Michael C Fitzgerald

2005-01-01

Full Text Available Abstract: The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the development of robust data analysis algorithms is the variability in the location of protein ion signals along the x-axis. We studied technical variations of MALDI-TOF measurements in the context of proteomics profiling. By acquiring a benchmark data set with five replicates, we estimated 76% to 85% of the total variance is due to phase variation. We devised a lobster plot, so named because of the resemblance to a lobster claw, to help detect the phase variation in replicates. We also investigated a peak alignment algorithm to remove the phase variation. This operation is analogous to the normalization step in microarray data analysis. Only after this critical step can features of biological interest be clearly revealed. With the help of principal component analysis, we demonstrated that after peak alignment, the differences among replicates are reduced. We compared this approach to peak alignment with a model-based calibration approach in which there was known information about peaks in common among all spectra. Finally, we examined the potential value at each point in an analysis pipeline of having a set of methods available that includes parametric, semiparametric and nonparametric methods; among such methods are those that benefit from the use of prior information.

Common liability to addiction and “gateway hypothesis”: Theoretical, empirical and evolutionary perspective

Science.gov (United States)

Vanyukov, Michael M.; Tarter, Ralph E.; Kirillova, Galina P.; Kirisci, Levent; Reynolds, Maureen D.; Kreek, Mary Jeanne; Conway, Kevin P.; Maher, Brion S.; Iacono, William G.; Bierut, Laura; Neale, Michael C.; Clark, Duncan B.; Ridenour, Ty A.

2013-01-01

Background Two competing concepts address the development of involvement with psychoactive substances: the “gateway hypothesis” (GH) and common liability to addiction (CLA). Method The literature on theoretical foundations and empirical findings related to both concepts is reviewed. Results The data suggest that drug use initiation sequencing, the core GH element, is variable and opportunistic rather than uniform and developmentally deterministic. The association between risks for use of different substances, if any, can be more readily explained by common underpinnings than by specific staging. In contrast, the CLA concept is grounded in genetic theory and supported by data identifying common sources of variation in the risk for specific addictions. This commonality has identifiable neurobiological substrate and plausible evolutionary explanations. Conclusions Whereas the “gateway” hypothesis does not specify mechanistic connections between “stages”, and does not extend to the risks for addictions, the concept of common liability to addictions incorporates sequencing of drug use initiation as well as extends to related addictions and their severity, provides a parsimonious explanation of substance use and addiction co-occurrence, and establishes a theoretical and empirical foundation to research in etiology, quantitative risk and severity measurement, as well as targeted non-drug-specific prevention and early intervention. PMID:22261179

Revisiting the variation of clustering coefficient of biological networks suggests new modular structure

Directory of Open Access Journals (Sweden)

Hao Dapeng

2012-05-01

Full Text Available Abstract Background A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling. Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. Results We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn’t show dependence of degree. Conclusions Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to “deterministic model” of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

Tissue-specific and minor inter-individual variation in imprinting of IGF2R is a common feature of Bos taurus Concepti and not correlated with fetal weight.

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Daniela Bebbere

Full Text Available The insulin-like growth factor 2 receptor (IGF2R is essential for prenatal growth regulation and shows gene dosage effects on fetal weight that can be affected by in-vitro embryo culture. Imprinted maternal expression of murine Igf2r is well documented for all fetal tissues excluding brain, but polymorphic imprinting and biallelic expression were reported for IGF2R in human. These differences have been attributed to evolutionary changes correlated with specific reproductive strategies. However, data from species suitable for testing this hypothesis are lacking. The domestic cow (Bos taurus carries a single conceptus with a similar gestation length as human. We identified 12 heterozygous concepti informative for imprinting studies among 68 Bos taurus fetuses at Day 80 of gestation (28% term and found predominantly maternal IGF2R expression in all fetal tissues but brain, which escapes imprinting. Inter-individual variation in allelic expression bias, i.e. expression of the repressed paternal allele relative to the maternal allele, ranged from 4.6-8.9% in heart, 4.3-10.2% in kidney, 6.1-11.2% in liver, 4.6-15.8% in lung and 3.2-12.2% in skeletal muscle. Allelic bias for mesodermal tissues (heart, skeletal muscle differed significantly (P<0.05 from endodermal tissues (liver, lung. The placenta showed partial imprinting with allelic bias of 22.9-34.7% and differed significantly (P<0.001 from all other tissues. Four informative fetuses were generated by in-vitro fertilization (IVF with embryo culture and two individuals displayed fetal overgrowth. However, there was no evidence for changes in imprinting or DNA methylation after IVF, or correlations between allelic bias and fetal weight. In conclusion, imprinting of Bos taurus IGF2R is similar to mouse except in placenta, which could indicate an effect of reproductive strategy. Common minor inter-individual variation in allelic bias and absence of imprinting abnormalities in IVF fetuses suggest

Is tube repair of aortic aneurysm followed by aneurysmal change in the common iliac arteries?

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Provan, J L; Fialkov, J; Ameli, F M; St Louis, E L

1990-10-01

To address the concern that tube repair of an abdominal aortic aneurysm might be followed by aneurysmal change in the common iliac arteries, 23 patients who had undergone the operation were re-examined 3 to 5 years later. Although 9 had had minimal ectasia of these arteries preoperatively, in none of the 23 was there symptomatic or radiologic evidence of aneurysmal change on follow-up. Measurements of the maximum intraluminal diameters were made by computed tomography; they indicated no significant differences between the preoperative and follow-up sizes of the common iliac arteries. The variation in time to follow-up also showed no significant correlation with change in artery diameter.

Changes in hemoglobin-oxygen affinity with shape variations of red blood cells

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Chowdhury, Aniket; Dasgupta, Raktim; Majumder, Shovan K.

2017-10-01

Shape variations of red blood cells (RBCs) are known to occur upon exposure to various drugs or under diseased conditions. The commonly observed discocytic RBCs can be transformed to echinocytic or stomatocytic shape under such conditions. Raman spectra of the three major shape variations, namely discocyte, echinocyte, and stomatocyte, of RBCs were studied while subjecting the cells to oxygenated and deoxygenated conditions. Analysis of the recorded spectra suggests an increased level of hemoglobin (Hb)-oxygen affinity for the echinocytes. Also, some level of Hb degradation could be noticed for the deoxygenated echinocytes. The effects may arise from a reduced level of intracellular adenosine triphosphate in echinocytic cells and an increased fraction of submembrane Hb.

Examining the candidacy of ghrelin as a gene responsible for variation in adult stature in a United Kingdom population with type 2 diabetes.

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Gueorguiev, Maria; Wiltshire, Steven; Garcia, Edwin A; Mein, Charles; Lecoeur, Cecile; Kristen, Brigitte; Allotey, Rebecca; Hattersley, Andrew T; Walker, Mark; O'rahilly, Stephen; Froguel, Philippe; Grossman, Ashley B; McCarthy, Mark I; Hitman, Graham A; Korbonits, Márta

2007-06-01

Recently, a quantitative trait locus for stature was reported on chromosome 3p26 in patients with type 2 diabetes. Given that ghrelin is a peptide involved in GH release and located on 3p26, we hypothesized that variation within its gene (GHRL) may be responsible for the quantitative trait locus on 3p26. The evidence for linkage around GHRL was refined with the genotyping of an additional four microsatellites (D3S4545, D3S1537, D3S1597, and D3S3611), giving a total of 27 markers, followed by multipoint variance components linkage analysis. Probands from the linkage families were typed for five common single nucleotide polymorphisms (SNPs) within GHRL and tested for association with adult stature using haplotype trend regression. The maximum multipoint evidence for linkage between adult stature and the 27 microsatellites yielded an LOD score of 2.58 (P = 0.0003) between D3S1297 and D3S1304. Five common (frequency of > or =5%) SNPs were typed in the probands [two promoter SNPs (rs27647 and rs26802), two exonic (rs696217 and rs4684677), and one intronic (rs35683)] capturing 80% of the total common variation in GHRL. No association was found between any SNP (or haplotypes thereof) and adult stature. Common genetic variation within GHRL is not responsible for variation in adult stature in this population.

Hypotensive responses to common daily activities in institutionalized elderly. A potential risk for recurrent falls.

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Jonsson, P V; Lipsitz, L A; Kelley, M; Koestner, J

1990-07-01

Transient hypotension may be one of many factors contributing to the high prevalence of falls among elderly people. To determine the frequency and magnitude of hypotensive responses to common daily activities, and their potential relationship to falls in the elderly, we examined blood pressure (BP) and heart rate during a standardized series of activities in 38 institutionalized recurrent fallers (age, 87 +/- 6 years), 20 institutionalized nonfallers (age, 85 +/- 5 years), and 10 healthy young control subjects (age, 24 +/- 3 years). The coefficient of variation for systolic BP during all activities was higher in elderly subjects (fallers, 14% +/- 5%; nonfallers, 12% +/- 3%) than in young control subjects (8% +/- 1%). In contrast, the coefficient of variation for heart rate during all activities was higher in young subjects than in the elderly subjects. Elderly subjects had marked BP reduction following meals and nitroglycerin, which was significantly greater in fallers than in nonfallers, independent of the cause of the fall. Thus, institutionalized elderly have marked BP variability and hypotensive responses to meals and nitroglycerin. A decline in BP during common preload-reducing stresses may predispose some elderly people to falls.

Anatomical variations of the iliolumbar vein with application to the anterior retroperitoneal approach to the lumbar spine: a cadaver study.

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Unruh, Kenneth P; Camp, Christopher L; Zietlow, Scott P; Huddleston, Paul M

2008-10-01

Objectives of this study include identification of lumbosacral venous variations, designation of a critical area of dissection for surgical exposure, and comparison between both male/female and right/left-sided anatomy. Attempts were made to provide anatomic nomenclature that accurately describes these structures. Thirty-eight iliolumbar venous systems in 20 cadavers (11 females/9 males) were dissected. Each system was identified as one of three patterns of variation: common venous trunk (combining ascending lumbar and iliolumbar venous systems) with distal veins, common venous trunk without distal veins, and venous systems without a common venous trunk. Dimensions including distances to the inferior vena cava (IVC) confluence, the obturator nerve, and the lumbosacral trunk, and venous stem length were obtained to aid surgical dissection. Differences between males and females and those between right and left sides were compared. Anterior lumbosacral venous variations could be organized into three groups. A Type 1 venous system (common venous trunk with distal veins) was most common (53% of systems). The anatomical name "lateral lumbosacral veins" adequately describes the anatomical location of these veins and does not assume a direction of venous flow or the lack of individual distal veins. A critical area bordered by the obturator nerve anteriorly, the psoas muscle laterally, the spinal column medially, and sacrum posteriorly within 8.2 cm of the IVC confluence should be defined to adequately dissect the lateral lumbosacral veins. Differences in male and female lateral lumbosacral venous anatomy do not alter surgeon's approach to the anterior lumbar spine. (c) 2008 Wiley-Liss, Inc.

Genetics and variation

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John R. Jones; Norbert V. DeByle

1985-01-01

The broad genotypic variability in quaking aspen (Populus tremuloides Michx.), that results in equally broad phenotypic variability among clones is important to the ecology and management of this species. This chapter considers principles of aspen genetics and variation, variation in aspen over its range, and local variation among clones. For a more...

Variational principle for gravity with null and non-null boundaries: a unified boundary counter-term

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Parattu, Krishnamohan; Chakraborty, Sumanta; Padmanabhan, T. [IUCAA, Post Bag 4, Pune (India)

2016-03-15

It is common knowledge that the Einstein-Hilbert action does not furnish a well-posed variational principle. The usual solution to this problem is to add an extra boundary term to the action, called a counter-term, so that the variational principle becomes well-posed. When the boundary is spacelike or timelike, the Gibbons-Hawking-York counter-term is the most widely used. For null boundaries, we had proposed a counter-term in a previous paper. In this paper, we extend the previous analysis and propose a counter-term that can be used to eliminate variations of the ''off-the-surface'' derivatives of the metric on any boundary, regardless of its spacelike, timelike or null nature. (orig.)

Some remarks on variational and quasi-variational inequalities of monotone operators

International Nuclear Information System (INIS)

Siddiqi, A.H.

1990-08-01

In this paper we study a fairly general class of variational and quasi-variational inequalities problem which represent some important physical phenomena. Several well-known results concerning variational inequalities are special cases of our results. Existence, uniqueness and numerical analysis of this problem have been studied. (author). 39 refs

Morphological Variations in Conidia of Arthrobotrys oligospora on Different Media

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Singh, R. K.; Kumar, Niranjan; Singh, K. P.

2005-01-01

Most commonly occurring predacious fungus Arthrobotrys oligospora showed great variation in size and shape of conidia on some media. The formation of larger conidia was recorded on beef extract and nutrient agar media. The length of conidia in Richard's YPSS, Sabouraud's, PDA and corn meal agar media was of medium size while smaller conidia were produced on Czapek's, Jensen's, Martin's medium. Maximum width of conidia was recorded on YPSS medium followed by Sabouraud's medium. The average siz...

Ensembl variation resources

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Marin-Garcia Pablo

2010-05-01

Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

Evaluation of a new paleosecular variation activity index as a diagnostic tool for geomagnetic field variations

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Panovska, Sanja; Constable, Catherine

2015-04-01

. Currently reversals can only be detected after they have occurred. A baseline for the new index is established using modern and Holocene geomagnetic field data and models to analyze 'normal' variability. We extend our analyses to the 100 ka interval where several excursions have been identified. We discuss the diminished or absent signatures of excursions in some records, the apparent transgressive behavior of detected excursions, and implications for transitional field behavior. The absence of specific excursions in some sediment records is attributed to smoothing by the sedimentary remanence acquisition process and low sedimentation rates. Overall PSV activity index is inversely correlated with dipole moment, indicating stronger impacts of non-axial-dipole secular variations during periods of low axial dipole strength. Excursional events found with the PSV activity index are analyzed in the context of global probability density functions for VGP positions. We studied the appearance of VGP clusters of the excursions to find the common characteristics of these instabilities, including the non-axial dipole features of the geomagnetic field. A better understanding of geomagnetic excursions will aid attempts to predict when such events might occur in the future.

Variation and Mathematics Pedagogy

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Leung, Allen

2012-01-01

This discussion paper put forwards variation as a theme to structure mathematical experience and mathematics pedagogy. Patterns of variation from Marton's Theory of Variation are understood and developed as types of variation interaction that enhance mathematical understanding. An idea of a discernment unit comprising mutually supporting variation…

Interpretation of biological and mechanical variations between the Lowry versus Bradford method for protein quantification.

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Lu, Tzong-Shi; Yiao, Szu-Yu; Lim, Kenneth; Jensen, Roderick V; Hsiao, Li-Li

2010-07-01

The identification of differences in protein expression resulting from methodical variations is an essential component to the interpretation of true, biologically significant results. We used the Lowry and Bradford methods- two most commonly used methods for protein quantification, to assess whether differential protein expressions are a result of true biological or methodical variations. MATERIAL #ENTITYSTARTX00026; Differential protein expression patterns was assessed by western blot following protein quantification by the Lowry and Bradford methods. We have observed significant variations in protein concentrations following assessment with the Lowry versus Bradford methods, using identical samples. Greater variations in protein concentration readings were observed over time and in samples with higher concentrations, with the Bradford method. Identical samples quantified using both methods yielded significantly different expression patterns on Western blot. We show for the first time that methodical variations observed in these protein assay techniques, can potentially translate into differential protein expression patterns, that can be falsely taken to be biologically significant. Our study therefore highlights the pivotal need to carefully consider methodical approaches to protein quantification in techniques that report quantitative differences.

Variation in reaction norms: Statistical considerations and biological interpretation.

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Morrissey, Michael B; Liefting, Maartje

2016-09-01

Analysis of reaction norms, the functions by which the phenotype produced by a given genotype depends on the environment, is critical to studying many aspects of phenotypic evolution. Different techniques are available for quantifying different aspects of reaction norm variation. We examine what biological inferences can be drawn from some of the more readily applicable analyses for studying reaction norms. We adopt a strongly biologically motivated view, but draw on statistical theory to highlight strengths and drawbacks of different techniques. In particular, consideration of some formal statistical theory leads to revision of some recently, and forcefully, advocated opinions on reaction norm analysis. We clarify what simple analysis of the slope between mean phenotype in two environments can tell us about reaction norms, explore the conditions under which polynomial regression can provide robust inferences about reaction norm shape, and explore how different existing approaches may be used to draw inferences about variation in reaction norm shape. We show how mixed model-based approaches can provide more robust inferences than more commonly used multistep statistical approaches, and derive new metrics of the relative importance of variation in reaction norm intercepts, slopes, and curvatures. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Copy Number Variation of Cytokinin Oxidase Gene Tackx4 Associated with Grain Weight and Chlorophyll Content of Flag Leaf in Common Wheat.

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Chang, Cheng; Lu, Jie; Zhang, Hai-Ping; Ma, Chuan-Xi; Sun, Genlou

2015-01-01

As the main pigment in photosynthesis, chlorophyll significantly affects grain filling and grain weight of crop. Cytokinin (CTK) can effectively increase chlorophyll content and chloroplast stability, but it is irreversibly inactivated by cytokinin oxidase (CKX). In this study, therefore, twenty-four pairs of primers were designed to identify variations of wheat CKX (Tackx) genes associated with flag leaf chlorophyll content after anthesis, as well as grain weight in 169 recombinant inbred lines (RIL) derived from Triticum aestivum Jing 411 × Hongmangchun 21. Results indicated variation of Tackx4, identified by primer pair T19-20, was proven to significantly associate with chlorophyll content and grain weight in the RIL population. Here, two Tackx4 patterns were identified: one with two co-segregated fragments (Tackx4-1/Tackx4-2) containing 618 bp and 620 bp in size (as in Jing 411), and another with no PCR product. The two genotypes were designated as genotype-A and genotype-B, respectively. Grain weight and leaf chlorophyll content at 5~15 days after anthesis (DAA) were significantly higher in genotype-A lines than those in genotype-B lines. Mapping analysis indicated Tackx4 was closely linked to Xwmc169 on chromosome 3AL, as well as co-segregated with a major quantitative trait locus (QTL) for both grain weight and chlorophyll content of flag leaf at 5~15 DAA. This QTL explained 8.9~22.3% phenotypic variations of the two traits across four cropping seasons. Among 102 wheat varieties, a third genotype of Tackx4 was found and designated as genotype-C, also having two co-segregated fragments, Tackx4-2 and Tackx4-3 (615bp). The sequences of three fragments, Tackx4-1, Tackx4-2, and Tackx4-3, showed high identity (>98%). Therefore, these fragments could be considered as different copies at Tackx4 locus on chromosome 3AL. The effect of copy number variation (CNV) of Tackx4 was further validated. In general, genotype-A contains both significantly higher grain weight

AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation.

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Wu, Y Q; Taliaferro, C M; Bai, G H; Anderson, M P

2004-08-01

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45 degrees N and lat 45 degrees S, penetrating to about lat 53 degrees N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.