Composing Models of Geographic Physical Processes

Science.gov (United States)

Hofer, Barbara; Frank, Andrew U.

Processes are central for geographic information science; yet geographic information systems (GIS) lack capabilities to represent process related information. A prerequisite to including processes in GIS software is a general method to describe geographic processes independently of application disciplines. This paper presents such a method, namely a process description language. The vocabulary of the process description language is derived formally from mathematical models. Physical processes in geography can be described in two equivalent languages: partial differential equations or partial difference equations, where the latter can be shown graphically and used as a method for application specialists to enter their process models. The vocabulary of the process description language comprises components for describing the general behavior of prototypical geographic physical processes. These process components can be composed by basic models of geographic physical processes, which is shown by means of an example.

Superior and inferior vena cavae: Embryology, variants, and pathology

International Nuclear Information System (INIS)

Mendelson, D.S.; Mitty, H.; Janus, C.; Gendal, E.; Berson, B.

1987-01-01

The superior and inferior venae cavae may be involved in a host of disease processes. Knowledge of the normal anatomy and variants of these structures is valuable in interpreting plain films and the results of angiographic procedures and all cross-sectional modalities. The authors review the embryology of venae cavae and proceed to describe their normal anatomy and variants. An awareness of the variants can prevent mistaking variants for pathologic processes. Finally, the authors describe pathology involving these vessels and demonstrate the radiographic manifestations

The curation of genetic variants: difficulties and possible solutions.

Science.gov (United States)

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-12-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. Copyright © 2012. Published by Elsevier Ltd.

Congenital anomalies and normal skeletal variants

International Nuclear Information System (INIS)

Guebert, G.M.; Yochum, T.R.; Rowe, L.J.

1987-01-01

Congenital anomalies and normal skeletal variants are a common occurrence in clinical practice. In this chapter a large number of skeletal anomalies of the spine and pelvis are reviewed. Some of the more common skeletal anomalies of the extremities are also presented. The second section of this chapter deals with normal skeletal variants. Some of these variants may simulate certain disease processes. In some instances there are no clear-cut distinctions between skeletal variants and anomalies; therefore, there may be some overlap of material. The congenital anomalies are presented initially with accompanying text, photos, and references, beginning with the skull and proceeding caudally through the spine to then include the pelvis and extremities. The normal skeletal variants section is presented in an anatomical atlas format without text or references

Paraxial diffractive elements for space-variant linear transforms

Science.gov (United States)

Teiwes, Stephan; Schwarzer, Heiko; Gu, Ben-Yuan

1998-06-01

Optical linear transform architectures bear good potential for future developments of very powerful hybrid vision systems and neural network classifiers. The optical modules of such systems could be used as pre-processors to solve complex linear operations at very high speed in order to simplify an electronic data post-processing. However, the applicability of linear optical architectures is strongly connected with the fundamental question of how to implement a specific linear transform by optical means and physical imitations. The large majority of publications on this topic focusses on the optical implementation of space-invariant transforms by the well-known 4f-setup. Only few papers deal with approaches to implement selected space-variant transforms. In this paper, we propose a simple algebraic method to design diffractive elements for an optical architecture in order to realize arbitrary space-variant transforms. The design procedure is based on a digital model of scalar, paraxial wave theory and leads to optimal element transmission functions within the model. Its computational and physical limitations are discussed in terms of complexity measures. Finally, the design procedure is demonstrated by some examples. Firstly, diffractive elements for the realization of different rotation operations are computed and, secondly, a Hough transform element is presented. The correct optical functions of the elements are proved in computer simulation experiments.

A Time-Variant Reliability Model for Copper Bending Pipe under Seawater-Active Corrosion Based on the Stochastic Degradation Process

Directory of Open Access Journals (Sweden)

Bo Sun

2018-03-01

Full Text Available In the degradation process, the randomness and multiplicity of variables are difficult to describe by mathematical models. However, they are common in engineering and cannot be neglected, so it is necessary to study this issue in depth. In this paper, the copper bending pipe in seawater piping systems is taken as the analysis object, and the time-variant reliability is calculated by solving the interference of limit strength and maximum stress. We did degradation experiments and tensile experiments on copper material, and obtained the limit strength at each time. In addition, degradation experiments on copper bending pipe were done and the thickness at each time has been obtained, then the response of maximum stress was calculated by simulation. Further, with the help of one kind of Monte Carlo method we propose, the time-variant reliability of copper bending pipe was calculated based on the stochastic degradation process and interference theory. Compared with traditional methods and verified by maintenance records, the results show that the time-variant reliability model based on the stochastic degradation process proposed in this paper has better applicability in the reliability analysis, and it can be more convenient and accurate to predict the replacement cycle of copper bending pipe under seawater-active corrosion.

Multiphoton Processes and Attosecond Physics

CERN Document Server

Midorikawa, Katsumi; 12th International Conference on Multiphoton Processes; 3rd International Conference on Attosecond Physics

2012-01-01

Recent advances in ultrashort pulsed laser technology have opened new frontiers in atomic, molecular and optical sciences. The 12th International Conference on Multiphoton Processes (ICOMP12) and the 3rd International Conference on Attosecond Physics (ATTO3), held jointly in Sapporo, Japan, during July 3-8, showcased studies at the forefront of research on multiphoton processes and attosecond physics. This book summarizes presentations and discussions from these two conferences.

Glucocorticoid-regulated and constitutive trafficking of proteolytically processed cell surface-associated glycoproteins in wild type and variant rat hepatoma cells

International Nuclear Information System (INIS)

Amacher, S.L.; Goodman, L.J.; Bravo, D.A.; Wong, K.Y.; Goldfine, I.D.; Hawley, D.M.; Firestone, G.L.

1989-01-01

Glucocorticoids regulate the trafficking of mouse mammary tumor virus (MMTV) glycoproteins to the cell surface in the rat hepatoma cell line M1.54, but not in the immunoselected sorting variant CR4. To compare the localization of MMTV glycoproteins to another proteolytically processed glycoprotein, both wild type M1.54 cells and variant CR4 cells were transfected with a human insulin receptor (hIR) expression vector, pRSVhIR. The production of cell surface hIR was monitored in dexamethasone-treated and -untreated wild type M1.54 and variant CR4 cells by indirect immunofluorescence, direct plasma membrane immunoprecipitation, and by [125I] insulin binding. In both wild type and variant rat hepatoma cells, hIR were localized at the cell surface in the presence or in the absence of 1 microM dexamethasone. In contrast, the glucocorticoid-regulated trafficking of cell surface MMTV glycoproteins occurred only in wild type M1.54 cells. We conclude that the hIR, which undergoes posttranslational processing reactions similar to MMTV glycoproteins, does not require glucocorticoids to be transported to the plasma membrane and is representative of a subset of cell surface glycoproteins whose trafficking is constitutive in rat hepatoma cells. Thus, MMTV glycoproteins and hIR provide specific cell surface markers to characterize the glucocorticoid-regulated and constitutive sorting pathways

Simulation methods supporting homologation of Electronic Stability Control in vehicle variants

Science.gov (United States)

Lutz, Albert; Schick, Bernhard; Holzmann, Henning; Kochem, Michael; Meyer-Tuve, Harald; Lange, Olav; Mao, Yiqin; Tosolin, Guido

2017-10-01

Vehicle simulation has a long tradition in the automotive industry as a powerful supplement to physical vehicle testing. In the field of Electronic Stability Control (ESC) system, the simulation process has been well established to support the ESC development and application by suppliers and Original Equipment Manufacturers (OEMs). The latest regulation of the United Nations Economic Commission for Europe UN/ECE-R 13 allows also for simulation-based homologation. This extends the usage of simulation from ESC development to homologation. This paper gives an overview of simulation methods, as well as processes and tools used for the homologation of ESC in vehicle variants. The paper first describes the generic homologation process according to the European Regulation (UN/ECE-R 13H, UN/ECE-R 13/11) and U.S. Federal Motor Vehicle Safety Standard (FMVSS 126). Subsequently the ESC system is explained as well as the generic application and release process at the supplier and OEM side. Coming up with the simulation methods, the ESC development and application process needs to be adapted for the virtual vehicles. The simulation environment, consisting of vehicle model, ESC model and simulation platform, is explained in detail with some exemplary use-cases. In the final section, examples of simulation-based ESC homologation in vehicle variants are shown for passenger cars, light trucks, heavy trucks and trailers. This paper is targeted to give a state-of-the-art account of the simulation methods supporting the homologation of ESC systems in vehicle variants. However, the described approach and the lessons learned can be used as reference in future for an extended usage of simulation-supported releases of the ESC system up to the development and release of driver assistance systems.

Reduced Order Fractional Fourier Transform A New Variant to Fractional Signal Processing Definition and Properties

OpenAIRE

Kumar, Sanjay

2018-01-01

In this paper, a new variant to fractional signal processing is proposed known as the Reduced Order Fractional Fourier Transform. Various properties satisfied by its transformation kernel is derived. The properties associated with the proposed Reduced Order Fractional Fourier Transform like shift, modulation, time-frequency shift property are also derived and it is shown mathematically that when the rotation angle of Reduced Order Fractional Fourier Transform approaches 90 degrees, the propos...

Determination of uranium by luminescent method (tablet variant)

International Nuclear Information System (INIS)

Sergeev, A.N.; Yufa, B.Ya.

1985-01-01

A new tablet variant of luminescent determination of uranium in rocks is developed. The analytical process includes the following operations: sample decomposition, uranium separation from luminescence quencher impurities, preparation of luminescent sample (tablet), photometry of the tablet. The method has two variants developed: the first one is characterized by a more hard decomposition, sample mass being 0.2 g; the second variant has a better detection limit (5x10 -6 %), the sample mass being 0.2-1 g. Procedures of the sample preparation for both variants of analysis are described

Self-perception in a clinical sample of gender variant children.

Science.gov (United States)

Rijn, Anouk Balleur-van; Steensma, Thomas D; Kreukels, Baudewijntje P C; Cohen-Kettenis, Peggy T

2013-07-01

Gender variance (GV) in childhood has a negative impact on the self-concept of children in the general population and can lead to mental health problems and even suicidal ideation in adulthood. This study explored the self-concept of clinically referred gender variant children and examined potential risk factors. The Self-Perception Profile for Children was administered to 147 children, who were referred to a gender identity clinic. Their parents completed the Child Behaviour Checklist and the Gender Identity Questionnaire to assess the degree of GV. The referred children were at risk of developing a negative self-concept; more specifically gender variant girls had low scores on 'global self-worth', 'physical appearance' and 'behavioural conduct' compared to Dutch norms for girls. Gender variant boys had low scores on 'global self-worth', 'scholastic competence', 'athletic competence' and 'physical appearance' compared to Dutch norms for boys. Within the group of referred children, sex differences, but no age effects, were found. The referred girls felt more competent than the referred boys on 'athletic competence' and 'scholastic functioning'. For both boys and girls poor peer relations had a significant negative relationship with self-concept and more GV was related to a lower global self-worth. Clinically referred gender variant children seemed vulnerable to developing a negative self-concept. Poor peer relations and extreme GV might be mediating variables. Interventions might focus on enhancing acceptance of the environment and improving social skills of gender variant children.

Dissociation between controlled and automatic processes in the behavioral variant of fronto-temporal dementia.

Science.gov (United States)

Collette, Fabienne; Van der Linden, Martial; Salmon, Eric

2010-01-01

A decline of cognitive functioning affecting several cognitive domains was frequently reported in patients with frontotemporal dementia. We were interested in determining if these deficits can be interpreted as reflecting an impairment of controlled cognitive processes by using an assessment tool specifically developed to explore the distinction between automatic and controlled processes, namely the process dissociation procedure (PDP) developed by Jacoby. The PDP was applied to a word stem completion task to determine the contribution of automatic and controlled processes to episodic memory performance and was administered to a group of 12 patients with the behavioral variant of frontotemporal dementia (bv-FTD) and 20 control subjects (CS). Bv-FTD patients obtained a lower performance than CS for the estimates of controlled processes, but no group differences was observed for estimates of automatic processes. The between-groups comparison of the estimates of controlled and automatic processes showed a larger contribution of automatic processes to performance in bv-FTD, while a slightly more important contribution of controlled processes was observed in control subjects. These results are clearly indicative of an alteration of controlled memory processes in bv-FTD.

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

Noise and signal processing in a microstrip detector with a time variant readout system

International Nuclear Information System (INIS)

Cattaneo, P.W.

1995-01-01

This paper treats the noise and signal processing by a time variant filter in a microstrip detector. In particular, the noise sources in the detector-electronics chain and the signal losses that cause a substantial decrease of the original signal are thoroughly analyzed. This work has been motivated by the analysis of the data of the microstrip detectors designed for the ALEPH minivertex detector. Hence, even if the discussion will be kept as general as possible, concrete examples will be presented referring to the specific ALEPH design. (orig.)

Transport processes in space physics and astrophysics

CERN Document Server

Zank, Gary P

2014-01-01

Transport Processes in Space Physics and Astrophysics' is aimed at graduate level students to provide the necessary mathematical and physics background to understand the transport of gases, charged particle gases, energetic charged particles, turbulence, and radiation in an astrophysical and space physics context. Subjects emphasized in the work include collisional and collisionless processes in gases (neutral or plasma), analogous processes in turbulence fields and radiation fields, and allows for a simplified treatment of the statistical description of the system. A systematic study that addresses the common tools at a graduate level allows students to progress to a point where they can begin their research in a variety of fields within space physics and astrophysics. This book is for graduate students who expect to complete their research in an area of plasma space physics or plasma astrophysics. By providing a broad synthesis in several areas of transport theory and modeling, the work also benefits resear...

Accurate genotyping across variant classes and lengths using variant graphs

DEFF Research Database (Denmark)

Sibbesen, Jonas Andreas; Maretty, Lasse; Jensen, Jacob Malte

2018-01-01

of read k-mers to a graph representation of the reference and variants to efficiently perform unbiased, probabilistic genotyping across the variation spectrum. We demonstrate that BayesTyper generally provides superior variant sensitivity and genotyping accuracy relative to existing methods when used...... collecting a set of candidate variants across discovery methods, individuals and databases, and then realigning the reads to the variants and reference simultaneously. However, this realignment problem has proved computationally difficult. Here, we present a new method (BayesTyper) that uses exact alignment...... to integrate variants across discovery approaches and individuals. Finally, we demonstrate that including a ‘variation-prior’ database containing already known variants significantly improves sensitivity....

Mechanical reliability of structures subjected to time-variant physical phenomena

International Nuclear Information System (INIS)

Lemaire, Celine

1999-01-01

This work deals with two-phase critical flows in order to improve the way to dimension safety systems. It brings a numerical, physical and experimental contribution. We emphasized the importance to validate separately the numerical method and the physical model. Reference numerical solutions, assimilated to quasi-analytical solutions, were elaborated for a stationary one-dimensional restriction. They allowed to validate in space non stationary numerical schemes converged in time and constitute space convergence indicator (2 schemes validated). With this reliable numerical solution, we studied the physical model. The potential of a particular existing dispersed flow model has been validated thanks to experimental data. The validity domain of such a model is inevitably reduced. During this study, particular behaviors have been exhibited like the pseudo-critical nature of flow with a relaxation process, the non characteristic properties/nature of critical parameters where disequilibrium is largely reduced or the predominance of pressure due to interfacial transfers. The multidimensional aspect has been studied. A data base included local parameters corresponding to a simplify geometry has been constituted. The flow impact on the disk has been characterized and multidimensional effects identified. These effects form an additional step to the validation of multidimensional physical models. (author) [fr

Exoplanet atmospheres physical processes

CERN Document Server

Seager, Sara

2010-01-01

Over the past twenty years, astronomers have identified hundreds of extrasolar planets--planets orbiting stars other than the sun. Recent research in this burgeoning field has made it possible to observe and measure the atmospheres of these exoplanets. This is the first textbook to describe the basic physical processes--including radiative transfer, molecular absorption, and chemical processes--common to all planetary atmospheres, as well as the transit, eclipse, and thermal phase variation observations that are unique to exoplanets. In each chapter, Sara Seager offers a conceptual introduction, examples that combine the relevant physics equations with real data, and exercises. Topics range from foundational knowledge, such as the origin of atmospheric composition and planetary spectra, to more advanced concepts, such as solutions to the radiative transfer equation, polarization, and molecular and condensate opacities. Since planets vary widely in their atmospheric properties, Seager emphasizes the major p...

Impact of Pathogen Population Heterogeneity and Stress-Resistant Variants on Food Safety.

Science.gov (United States)

Abee, T; Koomen, J; Metselaar, K I; Zwietering, M H; den Besten, H M W

2016-01-01

This review elucidates the state-of-the-art knowledge about pathogen population heterogeneity and describes the genotypic and phenotypic analyses of persister subpopulations and stress-resistant variants. The molecular mechanisms underlying the generation of persister phenotypes and genetic variants are identified. Zooming in on Listeria monocytogenes, a comparative whole-genome sequence analysis of wild types and variants that enabled the identification of mutations in variants obtained after a single exposure to lethal food-relevant stresses is described. Genotypic and phenotypic features are compared to those for persistent strains isolated from food processing environments. Inactivation kinetics, models used for fitting, and the concept of kinetic modeling-based schemes for detection of variants are presented. Furthermore, robustness and fitness parameters of L. monocytogenes wild type and variants are used to model their performance in food chains. Finally, the impact of stress-resistant variants and persistence in food processing environments on food safety is discussed.

Cellulase variants

Science.gov (United States)

Blazej, Robert; Toriello, Nicholas; Emrich, Charles; Cohen, Richard N.; Koppel, Nitzan

2015-07-14

This invention provides novel variant cellulolytic enzymes having improved activity and/or stability. In certain embodiments the variant cellulotyic enzymes comprise a glycoside hydrolase with or comprising a substitution at one or more positions corresponding to one or more of residues F64, A226, and/or E246 in Thermobifida fusca Cel9A enzyme. In certain embodiments the glycoside hydrolase is a variant of a family 9 glycoside hydrolase. In certain embodiments the glycoside hydrolase is a variant of a theme B family 9 glycoside hydrolase.

Functional genetic variants in the vesicular monoamine transporter 1 (VMAT1) modulate emotion processing

Science.gov (United States)

Lohoff, Falk W.; Hodge, Rachel; Narasimhan, Sneha; Nall, Aleksandra; Ferraro, Thomas N.; Mickey, Brian J.; Heitzeg, Mary M.; Langenecker, Scott A.; Zubieta, Jon-Kar; Bogdan, Ryan; Nikolova, Yuliya S.; Drabant, Emily; Hariri, Ahmad R.; Bevilacqua, Laura; Goldman, David; Doyle, Glenn A.

2012-01-01

SUMMARY Emotional behavior is in part heritable and often disrupted in psychopathology. Identification of specific genetic variants that drive this heritability may provide important new insight into molecular and neurobiological mechanisms involved in emotionality. Our results demonstrate that the presynaptic vesicular monoamine transporter 1 (VMAT1) Thr136Ile (rs1390938) polymorphism is functional in vitro, with the Ile allele leading to increased monoamine transport into presynaptic vesicles. Moreover, we show that the Thr136Ile variant predicts differential responses in emotional brain circuits consistent with its effects in vitro. Lastly, deep sequencing of bipolar disorder (BPD) patients and controls identified several rare novel VMAT1 variants. The variant Phe84Ser was only present in individuals with BPD and leads to marked increase monoamine transport in vitro. Taken together, our data show that VMAT1 polymorphisms influence monoamine signaling, the functional response of emotional brain circuits, and risk for psychopathology. PMID:23337945

COMPARISON OF THE TEST VARIANTS IN ENTRANCE EXAMINATIONS

Directory of Open Access Journals (Sweden)

KLŮFA, Jindřich

2016-12-01

Full Text Available The paper contains an analysis of the differences of number of points in the test in mathematics between test variants, which were used in the entrance examinations at the Faculty of Business Administration at University of Economics in Prague in 2015. The differences may arise due to the varying difficulty of variants for students, but also because of the different level of knowledge of students who write these variants. This problem we shall study in present paper. The aim of this paper is to study dependence of the results of entrance examinations in mathematics on test variants. The results obtained will be used for further improvement of the admission process at University of Economics.

OVAS: an open-source variant analysis suite with inheritance modelling.

Science.gov (United States)

Mozere, Monika; Tekman, Mehmet; Kari, Jameela; Bockenhauer, Detlef; Kleta, Robert; Stanescu, Horia

2018-02-08

The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functionally important variants has now shifted towards identifying the critical differences between normal variants and disease-causing ones. The ever-increasing reliance on cloud-based services for sequence analysis and the non-transparent methods they utilize has prompted the need for more in-situ services that can provide a safer and more accessible environment to process patient data, especially in circumstances where continuous internet usage is limited. To address these issues, we herein propose our standalone Open-source Variant Analysis Sequencing (OVAS) pipeline; consisting of three key stages of processing that pertain to the separate modes of annotation, filtering, and interpretation. Core annotation performs variant-mapping to gene-isoforms at the exon/intron level, append functional data pertaining the type of variant mutation, and determine hetero/homozygosity. An extensive inheritance-modelling module in conjunction with 11 other filtering components can be used in sequence ranging from single quality control to multi-file penetrance model specifics such as X-linked recessive or mosaicism. Depending on the type of interpretation required, additional annotation is performed to identify organ specificity through gene expression and protein domains. In the course of this paper we analysed an autosomal recessive case study. OVAS made effective use of the filtering modules to recapitulate the results of the study by identifying the prescribed compound-heterozygous disease pattern from exome-capture sequence input samples. OVAS is an offline open-source modular-driven analysis environment designed to annotate and extract useful variants from Variant Call Format (VCF) files, and process them under an inheritance context through a top-down filtering schema of

Laser isotope separation: the physics of the process

International Nuclear Information System (INIS)

Lapierre, Y.

1990-01-01

The physics of the AVLIS process is analysed. The intricacy of physics considerations, technology and economic forecast is developed. The scaling of a production unit is a complicated optimization which takes into account the limitations imposed by physics laws (spectroscopy, plasma physics,...), technology (vapor production, laser industry,...), and economy. But the only philosophy which prevails for such R and D programs is to be cheaper than competitive processes and to reach the goal first to get the market

Somatic cancer variant curation and harmonization through consensus minimum variant level data

Directory of Open Access Journals (Sweden)

Deborah I. Ritter

2016-11-01

Full Text Available Abstract Background To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG of the Clinical Genome Resource (ClinGen, in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD. MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice. Methods We developed MVLD through a consensus approach by i reviewing clinical actionability interpretations from institutions participating in the WG, ii conducting extensive literature search of clinical somatic interpretation schemas, and iii survey of cancer variant web portals. A forthcoming guideline on cancer variant interpretation, from the Association of Molecular Pathology (AMP, can be incorporated into MVLD. Results Along with harmonizing standardized terminology for allele interpretive and descriptive fields that are collected by many databases, the MVLD includes unique fields for cancer variants such as Biomarker Class, Therapeutic Context and Effect. In addition, MVLD includes recommendations for controlled semantics and ontologies. The Somatic WG is collaborating with ClinVar to evaluate MVLD use for somatic variant submissions. ClinVar is an open and centralized repository where sequencing laboratories can report summary-level variant data with clinical significance, and ClinVar accepts cancer variant data. Conclusions We expect the use of the MVLD to streamline clinical interpretation of cancer variants, enhance interoperability among multiple redundant curation efforts, and increase submission of

CDKL5 variants

Science.gov (United States)

Kalscheuer, Vera M.; Hennig, Friederike; Leonard, Helen; Downs, Jenny; Clarke, Angus; Benke, Tim A.; Armstrong, Judith; Pineda, Mercedes; Bailey, Mark E.S.; Cobb, Stuart R.

2017-01-01

Objective: To provide new insights into the interpretation of genetic variants in a rare neurologic disorder, CDKL5 deficiency, in the contexts of population sequencing data and an updated characterization of the CDKL5 gene. Methods: We analyzed all known potentially pathogenic CDKL5 variants by combining data from large-scale population sequencing studies with CDKL5 variants from new and all available clinical cohorts and combined this with computational methods to predict pathogenicity. Results: The study has identified several variants that can be reclassified as benign or likely benign. With the addition of novel CDKL5 variants, we confirm that pathogenic missense variants cluster in the catalytic domain of CDKL5 and reclassify a purported missense variant as having a splicing consequence. We provide further evidence that missense variants in the final 3 exons are likely to be benign and not important to disease pathology. We also describe benign splicing and nonsense variants within these exons, suggesting that isoform hCDKL5_5 is likely to have little or no neurologic significance. We also use the available data to make a preliminary estimate of minimum incidence of CDKL5 deficiency. Conclusions: These findings have implications for genetic diagnosis, providing evidence for the reclassification of specific variants previously thought to result in CDKL5 deficiency. Together, these analyses support the view that the predominant brain isoform in humans (hCDKL5_1) is crucial for normal neurodevelopment and that the catalytic domain is the primary functional domain. PMID:29264392

Physical processes in the interstellar medium

CERN Document Server

Spitzer, Lyman

2008-01-01

Physical Processes in the Interstellar Medium discusses the nature of interstellar matter, with a strong emphasis on basic physical principles, and summarizes the present state of knowledge about the interstellar medium by providing the latest observational data. Physics and chemistry of the interstellar medium are treated, with frequent references to observational results. The overall equilibrium and dynamical state of the interstellar gas are described, with discussions of explosions produced by star birth and star death and the initial phases of cloud collapse leading to star formation.

Physics of Laser Materials Processing Theory and Experiment

CERN Document Server

Gladush, Gennady G

2011-01-01

This book describes the basic mechanisms, theory, simulations and technological aspects of Laser processing techniques. It covers the principles of laser quenching, welding, cutting, alloying, selective sintering, ablation, etc. The main attention is paid to the quantitative description. The diversity and complexity of technological and physical processes is discussed using a unitary approach. The book aims on understanding the cause-and-effect relations in physical processes in Laser technologies. It will help researchers and engineers to improve the existing and develop new Laser machining techniques. The book addresses readers with a certain background in general physics and mathematical analysis: graduate students, researchers and engineers practicing laser applications.

[The Process of Healing Child Physical Abuse: Sprouting and Twining].

Science.gov (United States)

Chang, Hsin-Yi; Feng, Jui-Ying; Tseng, Ren-Mei

2018-06-01

Child physical abuse impacts the physical and psychological health of survivors. Healing child abuse is an essential process that helps survivors reorganize the meaning of the trauma and pursue a normal life. Considering the trauma of child physical abuse within the social context allows the experiences of individual survivors to be reflected in their process of healing. To explore the social interaction and construction process of healing experienced by survivors of child physical abuse. A qualitative research design using grounded theory was applied. Purposive and theoretical sampling was used to recruit survivors of childhood physical abuse who had experienced healing. Semi-structured, in-depth interviews were used and data were analyzed using open, axial, and selective coding. The process of healing child physical abuse in this study was a process of sprouting and twining. Three core categories emerged: thriving, relationships, and ethics. The healing process was analogous to a seed growing in poor soil, sprouting out from the ground, and striving to live by seeking support. The survivors constantly established interactive relationships with their selves and with others and struggled to keep family bonds grounded and growing within the frame of ethics. The healing process of sprouting and twining for child physical abuse survivors in Taiwan integrates thriving, relationships, and ethics. Professionals working with child-physical-abuse survivors must recognize conflicts in ethics. Strategies should be developed to assist survivors to cope with the impact of childhood trauma in order to facilitate the healing process.

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

Directory of Open Access Journals (Sweden)

Tjaart A P de Beer

Full Text Available The 1000 Genomes Project data provides a natural background dataset for amino acid germline mutations in humans. Since the direction of mutation is known, the amino acid exchange matrix generated from the observed nucleotide variants is asymmetric and the mutabilities of the different amino acids are very different. These differences predominantly reflect preferences for nucleotide mutations in the DNA (especially the high mutation rate of the CpG dinucleotide, which makes arginine mutability very much higher than other amino acids rather than selection imposed by protein structure constraints, although there is evidence for the latter as well. The variants occur predominantly on the surface of proteins (82%, with a slight preference for sites which are more exposed and less well conserved than random. Mutations to functional residues occur about half as often as expected by chance. The disease-associated amino acid variant distributions in OMIM are radically different from those expected on the basis of the 1000 Genomes dataset. The disease-associated variants preferentially occur in more conserved sites, compared to 1000 Genomes mutations. Many of the amino acid exchange profiles appear to exhibit an anti-correlation, with common exchanges in one dataset being rare in the other. Disease-associated variants exhibit more extreme differences in amino acid size and hydrophobicity. More modelling of the mutational processes at the nucleotide level is needed, but these observations should contribute to an improved prediction of the effects of specific variants in humans.

Magnetic resonance angiography: infrequent anatomic variants

International Nuclear Information System (INIS)

Trejo, Mariano; Meli, Francisco; Lambre, Hector; Blessing, Ricardo; Gigy Traynor, Ignacio; Miguez, Victor

2002-01-01

We studied through RM angiography (3D TOF) with high magnetic field equipment (1.5 T) different infrequent intracerebral vascular anatomic variants. For their detection we emphasise the value of post-processed images obtained after conventional angiographic sequences. These post-processed images should be included in routine protocols for evaluation of the intracerebral vascular structures. (author)

DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

Science.gov (United States)

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

2017-07-01

Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/. © 2017 Wiley Periodicals, Inc.

Secure and efficient multi-variant execution using hardware-assisted process virtualization

NARCIS (Netherlands)

Koning, Koen; Bos, Herbert; Giuffrida, Cristiano

2016-01-01

Memory error exploits rank among the most serious security threats. Of the plethora of memory error containment solutions proposed over the years, most have proven to be too weak in practice. Multi-Variant eXecution (MVX) solutions can potentially detect arbitrary memory error exploits via divergent

Effect of Variant End of Injection Period on Combustion Process of Biodiesel Combustion

Directory of Open Access Journals (Sweden)

Khalid Amir

2016-01-01

Full Text Available Biodiesel is an alternative fuel as a replacement to the standard diesel fuel in combustion diesel engine. The biodiesel fuel has a significantly influences throughout the combustion process and exhaust emission. The purpose of this research is to investigate the combustion process behavior during the End of Injection (EOI period and operates under variant conditions using Rapid Compression Machine (RCM. Experimental of RCM is used to simulate a combustion process and combustion characteristics of diesel engine combustion. Three types of biodiesel blend which are B5, B10 and B15 were tested at several injection pressures of 80 MPa, 90 MPa and 130 MPa under different ambient temperatures, 750 K to 1100 K. The results of this study showed that the ignition delay slightly reduced with increasing the content of biodiesel blends from B5, B10 and B15 and became more shorten as the injection pressure been enhanced. As the injection pressure increased, the behavior of combustion pressure at end of injection is reduced, radically increased the NOX emission. It is noted that the process of combustion at the end of injection increased as the ambient temperature is rising. In fact, higher initial ambient temperature improved the fuel atomization and mixing process. Under the biodiesel combustion with higher ambient temperature condition, the exhaust emission of CO, O2, and HC became less but increased in NOX emission. Besides, increased in blends of biodiesel ratio are found to enhance the combustion process, resulted a decreased in HC emissions.

Numerically-quantified two dimensionality of microstructure evolution accompanying variant selection of FePd

International Nuclear Information System (INIS)

Ueshima, N; Yoshiya, M; Yasuda, H; Fukuda, T; Kakeshita, T

2015-01-01

Through three-dimensional (3D) simulations of microstructure evolution by phase-field modeling (PFM), microstructures have been quantified during their time evolution by an image processing technique with particular attention to the shape of variants in the course of variant selection. It is found that the emerging variants exhibit planar shapes rather than 3D shapes due to the elastic field around the variants arising upon disorder-to-order transition to the L1 0 phase. The two-dimensionality is more pronounced as variant selection proceeds. Although three equivalent variants compete for dominance under an external field, one of the three variants vanishes before final competition occurs between the remaining variants, which can be explained by the elastic strain energy. These numerical analyses provide better understanding of the microstructure evolution in a more quantitative manner, including the small influence of the third variant, and the results obtained confirm that the understanding of variant selection obtained from two-dimensional (2D) simulations by PFM is valid. (paper)

Delineation of concentration ranges and longitudinal changes of human plasma protein variants.

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Olgica Trenchevska

Full Text Available Human protein diversity arises as a result of alternative splicing, single nucleotide polymorphisms (SNPs and posttranslational modifications. Because of these processes, each protein can exists as multiple variants in vivo. Tailored strategies are needed to study these protein variants and understand their role in health and disease. In this work we utilized quantitative mass spectrometric immunoassays to determine the protein variants concentration of beta-2-microglobulin, cystatin C, retinol binding protein, and transthyretin, in a population of 500 healthy individuals. Additionally, we determined the longitudinal concentration changes for the protein variants from four individuals over a 6 month period. Along with the native forms of the four proteins, 13 posttranslationally modified variants and 7 SNP-derived variants were detected and their concentration determined. Correlations of the variants concentration with geographical origin, gender, and age of the individuals were also examined. This work represents an important step toward building a catalog of protein variants concentrations and examining their longitudinal changes.

Differential Expression Profile of ZFX Variants Discriminates Breast Cancer Subtypes

Science.gov (United States)

Pourkeramati, Fatemeh; Asadi, Malek Hossein; Shakeri, Shahryar; Farsinejad, Alireza

2018-05-13

ZFX is a transcriptional regulator in embryonic stem cells that plays an important role in pluripotency and self-renewal. ZFX is widely expressed in pluripotent stem cells and is down-regulated during differentiation of embryonic stem cells. ZFX has five different variants that encode three different protein isoforms. While several reports have determined the overexpression of ZFX in a variety of somatic cancers, the expression of ZFX-spliced variants in cancer cells is not well-understood. We investigated the expression of ZFX variants in a series of breast cancer tissues and cell lines using quantitative PCR. The expression of ZFX variant 1/3 was higher in tumor tissue compared to marginal tissue. In contrast, the ZFX variant 5 was down-regulated in tumor tissues. While the ZFX variant 1/3 and ZFX variant 5 expression significantly increased in low-grade tumors, ZFX variant 4 was strongly expressed in high-grade tumors and demonstrating lymphatic invasion. In addition, our result revealed a significant association between the HER2 status and the expression of ZFX-spliced variants. Our data suggest that the expression of ZFX-spliced transcripts varies between different types of breast cancer and may contribute to their tumorigenesis process. Hence, ZFX-spliced transcripts could be considered as novel tumor markers with a probable value in diagnosis, prognosis, and therapy of breast cancer.

Following of erosive wash of soil in variants with different intercrops

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Barbora Badalíková

2010-01-01

Full Text Available In a pilot experiment established in a sugar beet growing region the erosive washing away of soil was studied in the years 2006 to 2008. The area is located at an altitude of 246 m with the long-term mean precipitation of 500 mm and the mean annual temperature of 8.4 °C. The soils are classified as Chernozem, moderately heavy, loamy, with a good supply of nutrients, humus content of 2.30 % and an alkaline soil reaction. Slope gradient is 12 %, exposition is NE. To study the role of intercrops in erosion control, three variants were established after the harvest of the main crop, two variants with different intercrops and one (control with no intercrop. These were Variant 1 with Secale cereale L. var. multicaule METZG. ex ALEF., a non-freezing intercrop, Variant 2 with cluster mallow (Malva verticillata L., a freezing intercrop, and a control variant with no intercrop. In Variant 1 Secale cereale L. var. multicaule was desiccated with the herbicide Roundup in early spring. All the variants involved maize as the main crop. In variants 1 and 2, maize was sown in intercrop residues after seedbed preparation by Vario and a compactor. In Variant 3 maize was sown after conventional seedbed preparation. For assessment of soil conditions soil samples were taken to determine soil physical and chemical properties and water content in the soil. Soil loss by erosion was determined using specially-designed pockets. Erosive washing away of soil was monitored during the entire growing season of maize. The variants in which intercrops were used were found very effective in soil erosion control. In Variant 3 (control without surface crop residues, the washing away of soil was recorded with each heavy torrential rain. During the all years the total amount of soil loss by erosion in this treatment was 2.25 t . ha−1.

PHYSICAL RESOURCES OF INFORMATION PROCESSES AND TECHNOLOGIES

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Mikhail O. Kolbanev

2014-11-01

Full Text Available Subject of study. The paper describes basic information technologies for automating of information processes of data storage, distribution and processing in terms of required physical resources. It is shown that the study of these processes with such traditional objectives of modern computer science, as the ability to transfer knowledge, degree of automation, information security, coding, reliability, and others, is not enough. The reasons are: on the one hand, the increase in the volume and intensity of information exchange in the subject of human activity and, on the other hand, drawing near to the limit of information systems efficiency based on semiconductor technologies. Creation of such technologies, which not only provide support for information interaction, but also consume a rational amount of physical resources, has become an actual problem of modern engineering development. Thus, basic information technologies for storage, distribution and processing of information to support the interaction between people are the object of study, and physical temporal, spatial and energy resources required for implementation of these technologies are the subject of study. Approaches. An attempt is made to enlarge the possibilities of traditional cybernetics methodology, which replaces the consideration of material information component by states search for information objects. It is done by taking explicitly into account the amount of physical resources required for changes in the states of information media. Purpose of study. The paper deals with working out of a common approach to the comparison and subsequent selection of basic information technologies for storage, distribution and processing of data, taking into account not only the requirements for the quality of information exchange in particular subject area and the degree of technology application, but also the amounts of consumed physical resources. Main findings. Classification of resources

Relaxation processes and physical aging in metallic glasses

Science.gov (United States)

Ruta, B.; Pineda, E.; Evenson, Z.

2017-12-01

Since their discovery in the 1960s, metallic glasses have continuously attracted much interest across the physics and materials science communities. In the forefront are their unique properties, which hold the alluring promise of broad application in fields as diverse as medicine, environmental science and engineering. However, a major obstacle to their wide-spread commercial use is their inherent temporal instability arising from underlying relaxation processes that can dramatically alter their physical properties. The result is a physical aging process which can bring about degradation of mechanical properties, namely through embrittlement and catastrophic mechanical failure. Understanding and controlling the effects of aging will play a decisive role in our on-going endeavor to advance the use of metallic glasses as structural materials, as well as in the more general comprehension of out-of-equilibrium dynamics in complex systems. This review presents an overview of the current state of the art in the experimental advances probing physical aging and relaxation processes in metallic glasses. Similarities and differences between other hard and soft matter glasses are highlighted. The topic is discussed in a multiscale approach, first presenting the key features obtained in macroscopic studies, then connecting them to recent novel microscopic investigations. Particular emphasis is put on the occurrence of distinct relaxation processes beyond the main structural process in viscous metallic melts and their fate upon entering the glassy state, trying to disentangle results and formalisms employed by the different groups of the glass-science community. A microscopic viewpoint is presented, in which physical aging manifests itself in irreversible atomic-scale processes such as avalanches and intermittent dynamics, ascribed to the existence of a plethora of metastable glassy states across a complex energy landscape. Future experimental challenges and the comparison with

Physical processes in the Indian seas

Digital Repository Service at National Institute of Oceanography (India)

Swamy, G.N.; Das, V.K.; Antony, M.K.

The proceedings volume comprise 38 papers covering air-sea boundary problems, open-ocean dynamics, nearshore processes, observational and analysis techniques, etc. This volume helps in taking stock of physical oceanographic activities in India...

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 1; referees: 2 approved, 1 approved with reservations

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Laura Oikkonen

2017-01-01

Full Text Available Identifying variants from RNA-seq (transcriptome sequencing data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available.

Physical processes in hot cosmic plasmas

International Nuclear Information System (INIS)

Fabian, A.G.; Giovannelli, F.

1990-01-01

The interpretation of many high energy astrophysical phenomena relies on a detailed knowledge of radiation and transport processes in hot plasmas. The understanding of these plasma properties is one of the aims of terrestrial plasma physics. While the microscopic properties of astrophysical plasmas can hardly be determined experimentally, laboratory plasmas are more easily accessible to experimental techniques, but transient phenomena and the interaction of the plasma with boundaries often make the interpretation of measurements cumbersome. This book contains the talks given at the NATO Advanced Research Workshop on astro- and plasma-physics in Vulcano, Sicily, May 29-June 2, 1989. The book focuses on three main areas: radiation transport processes in hot (astrophysical and laboratory) plasmas; magnetic fields; their generation, reconnection and their effects on plasma transport properties; relativistic and ultra-high density plasmas

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 2; referees: 2 approved, 1 approved with reservations

Directory of Open Access Journals (Sweden)

Laura Oikkonen

2017-03-01

Full Text Available Identifying variants from RNA-seq (transcriptome sequencing data is a cost-effective and versatile complement to whole-exome (WES and whole-genome sequencing (WGS analysis. RNA-seq (transcriptome sequencing is primarily considered a method of gene expression analysis but it can also be used to detect DNA variants in expressed regions of the genome. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available.

Physics as Information Processing

International Nuclear Information System (INIS)

D'Ariano, Giacomo Mauro

2011-01-01

I review some recent advances in foundational research at Pavia QUIT group. The general idea is that there is only Quantum Theory without quantization rules, and the whole Physics - including space-time and relativity - is emergent from the quantum-information processing. And since Quantum Theory itself is axiomatized solely on informational principles, the whole Physics must be reformulated in information-theoretical terms: this is the It from bit of J. A. Wheeler.The review is divided into four parts: a) the informational axiomatization of Quantum Theory; b) how space-time and relativistic covariance emerge from quantum computation; c) what is the information-theoretical meaning of inertial mass and of (ℎ/2π), and how the quantum field emerges; d) an observational consequence of the new quantum field theory: a mass-dependent refraction index of vacuum. I will conclude with the research lines that will follow in the immediate future.

Differential involvement of glutamate-gated chloride channel splice variants in the olfactory memory processes of the honeybee Apis mellifera.

Science.gov (United States)

Démares, Fabien; Drouard, Florian; Massou, Isabelle; Crattelet, Cindy; Lœuillet, Aurore; Bettiol, Célia; Raymond, Valérie; Armengaud, Catherine

2014-09-01

Glutamate-gated chloride channels (GluCl) belong to the cys-loop ligand-gated ion channel superfamily and their expression had been described in several invertebrate nervous systems. In the honeybee, a unique gene amel_glucl encodes two alternatively spliced subunits, Amel_GluCl A and Amel_GluCl B. The expression and differential localization of those variants in the honeybee brain had been previously reported. Here we characterized the involvement of each variant in olfactory learning and memory processes, using specific small-interfering RNA (siRNA) targeting each variant. Firstly, the efficacy of the two siRNAs to decrease their targets' expression was tested, both at mRNA and protein levels. The two proteins showed a decrease of their respective expression 24h after injection. Secondly, each siRNA was injected into the brain to test whether or not it affected olfactory memory by using a classical paradigm of conditioning the proboscis extension reflex (PER). Amel_GluCl A was found to be involved only in retrieval of 1-nonanol, whereas Amel_GluCl B was involved in the PER response to 2-hexanol used as a conditioned stimulus or as new odorant. Here for the first time, a differential behavioral involvement of two highly similar GluCl subunits has been characterized in an invertebrate species. Copyright © 2014 Elsevier Inc. All rights reserved.

The -250G>A promoter variant in hepatic lipase associates with elevated fasting serum high-density lipoprotein cholesterol modulated by interaction with physical activity in a study of 16,156 Danish subjects

DEFF Research Database (Denmark)

Grarup, Niels; Andreasen, Camilla H; Andersen, Mette K

2008-01-01

-tolerant control subjects (n = 360). RESULTS: In the Inter99 study, the A allele of rs2070895 associated with a 0.057 mmol/liter [95% confidence interval (CI) 0.039-0.075] increase in fasting serum HDL-cholesterol (HDL-c) (P = 8 x 10(-10)) supported by association in the Anglo-Danish-Dutch Study of Intensive...... Treatment in People with Screen Detected Diabetes in Primary Care study [0.038 mmol/liter per allele (95% CI 0.024-0.053); P = 2 x 10(-7)). The allelic effect on HDL-c was modulated by interaction with self-reported physical activity (P(interaction) = 0.002) because vigorous physically active homozygous A...... of variants in LIPC on metabolic traits and type 2 diabetes in a large sample of Danes. Because behavioral factors influence hepatic lipase activity, we furthermore examined possible gene-environment interactions in the population-based Inter99 study. DESIGN: The LIPC -250G>A (rs2070895) variant was genotyped...

Soil Heat Flow. Physical Processes in Terrestrial and Aquatic Ecosystems, Transport Processes.

Science.gov (United States)

Simpson, James R.

These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. Soil heat flow and the resulting soil temperature distributions have ecological consequences…

Physics students' approaches to learning and cognitive processes in solving physics problems

Science.gov (United States)

Bouchard, Josee

This study examined traditional instruction and problem-based learning (PBL) approaches to teaching and the extent to which they foster the development of desirable cognitive processes, including metacognition, critical thinking, physical intuition, and problem solving among undergraduate physics students. The study also examined students' approaches to learning and their perceived role as physics students. The research took place in the context of advanced courses of electromagnetism at a Canadian research university. The cognitive science, expertise, physics and science education, instructional psychology, and discourse processes literature provided the framework and background to conceptualize and structure this study. A within-stage mixed-model design was used and a number of instruments, including a survey, observation grids, and problem sets were developed specifically for this study. A special one-week long problem-based learning (PBL) intervention was also designed. Interviews with the instructors participating in the study provided complementary data. Findings include evidence that students in general engage in metacognitive processes in the organization of their personal study time. However, this potential, including the development of other cognitive processes, might not be stimulated as much as it could in the traditional lecture instructional context. The PBL approach was deemed as more empowering for the students. An unexpected finding came from the realisation that a simple exposure to a structured exercise of problem-solving (pre-test) was sufficient to produce superior planning and solving strategies on a second exposure (post-test) even for the students who had not been exposed to any special treatment. Maturation was ruled out as a potential threat to the validity of this finding. Another promising finding appears to be that the problem-based learning (PBL) intervention tends to foster the development of cognitive competencies, particularly

Physical and mathematical modelling of extrusion processes

DEFF Research Database (Denmark)

Arentoft, Mogens; Gronostajski, Z.; Niechajowics, A.

2000-01-01

The main objective of the work is to study the extrusion process using physical modelling and to compare the findings of the study with finite element predictions. The possibilities and advantages of the simultaneous application of both of these methods for the analysis of metal forming processes...

ERP differences between processing of physical characteristics and personality attributes

Science.gov (United States)

2012-01-01

Background Limited data from behavioral and brain-imaging studies indicate that personality traits and physical characteristics are processed differently by the brain. Additionally, electrophysiological results of studies comparing the processing of positive and negative words have produced mixed results. It is therefore not clear how physical and personality attributes with emotional valence (i.e., positive and negative valence) are processed. Thus, this study aimed to examine the neural activity associated with words describing personality traits and physical characteristics with positive or negative emotional valence using Event Related Potentials (ERPs). Methods A sample of 15 healthy adults (7 men, 8 women) participated in a computerized word categorization task. Participants were asked to categorize visual word stimuli as physical characteristics or personality traits, while ERPs were recorded synchronously. Results Behavioral reaction times to negative physical stimuli were shorter compared to negative personality words, however reaction times did not significantly differ for positive stimuli. Electrophysiological results showed that personality stimuli elicited larger P2 and LPC (Late Positive Component) amplitudes compared to physical stimuli, regardless of negative or positive valence. Moreover, negative as compared with positive stimuli elicited larger P2 and LPC amplitudes. Conclusion Personality and physical stimuli were processed differently regardless of positive or negative valence. These findings suggest that personality traits and physical characteristics are differentially classified and are associated with different motivational significance. PMID:22967478

Electrical Storm Simulation to Improve the Learning Physics Process

Science.gov (United States)

Martínez Muñoz, Miriam; Jiménez Rodríguez, María Lourdes; Gutiérrez de Mesa, José Antonio

2013-01-01

This work is part of a research project whose main objective is to understand the impact that the use of Information and Communication Technology (ICT) has on the teaching and learning process on the subject of Physics. We will show that, with the use of a storm simulator, physics students improve their learning process on one hand they understand…

Variant selection of martensites in steel welded joints with low transformation temperature weld metals

International Nuclear Information System (INIS)

Takahashi, Masaru; Yasuda, Hiroyuki Y.

2013-01-01

Highlights: ► We examined the variant selection of martensites in the weld metals. ► We also measured the residual stress developed in the butt and box welded joints. ► 24 martensite variants were randomly selected in the butt welded joint. ► High tensile residual stress in the box welded joint led to the strong variant selection. ► We discussed the rule of the variant selection focusing on the residual stress. -- Abstract: Martensitic transformation behavior in steel welded joints with low transformation temperature weld (LTTW) metal was examined focusing on the variant selection of martensites. The butt and box welded joints were prepared with LTTW metals and 980 MPa grade high strength steels. The residual stress of the welded joints, which was measured by a neutron diffraction technique, was effectively reduced by the expansion of the LTTW metals by the martensitic transformation during cooling after the welding process. In the LTTW metals, the retained austenite and martensite phases have the Kurdjumov–Sachs (K–S) orientation relationship. The variant selection of the martensites in the LTTW metals depended strongly on the type of welded joints. In the butt welded joint, 24 K–S variants were almost randomly selected while a few variants were preferentially chosen in the box welded joint. This suggests that the high residual stress developed in the box welded joint accelerated the formation of specific variants during the cooling process, in contrast to the butt welded joint with low residual stress

Applying automatic item generation to create cohesive physics testlets

Science.gov (United States)

Mindyarto, B. N.; Nugroho, S. E.; Linuwih, S.

2018-03-01

Computer-based testing has created the demand for large numbers of items. This paper discusses the production of cohesive physics testlets using an automatic item generation concepts and procedures. The testlets were composed by restructuring physics problems to reveal deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based testlet generator was used to generate the testlet variants. Using this methodology, 1248 testlet variants were effectively generated from 25 testlet templates. Some issues related to the effective application of the generated physics testlets in practical assessments were discussed.

Association of fat mass and obesity-associated gene variant with lifestyle factors and body fat in Indian Children

Directory of Open Access Journals (Sweden)

Lavanya S Parthasarthy

2017-01-01

Full Text Available Context: Common intronic variants of the fat mass and obesity-associated (FTO gene have been associated with obesity-related traits in humans. Aims: (1 The aim of this study is to study the distribution of FTO gene variants across different body mass index (BMI categories and (2 to explore the association between FTO gene variants and lifestyle factors in obese and normal weight Indian children. Subjects and Methods: Fifty-six children (26 boys, mean age 10.3 ± 2.2 years were studied. Height, weight, and waist and hip circumference were measured. Physical activity (questionnaire and food intake (food frequency questionnaire were assessed. Body fat percentage (%BF was measured by dual-energy X-ray absorptiometry. FTO allelic variants at rs9939609 site were detected by SYBR Green Amplification Refractory Mutation System real-time polymerase chain reaction using allele-specific primers. Generalized linear model was used to investigate the simultaneous influence of genetic and lifestyle factors on %BF. Results: Mean height, weight, and BMI of normal and obese children were 130.6 ± 7.1 versus 143.2 ± 15.6, 24.0 ± 5.2 versus 53.1 ± 15.8, and 13.9 ± 2.1 versus 25.3 ± 3.2, respectively. The frequency of AA allele was 57% among obese children and 35% in normal weight children. Children with the AA allele who were obese had least physical activity, whereas children with AT allele and obesity had the highest intake of calories when compared to children who had AT allele and were normal. %BF was positively associated with AA alleles and junk food intake and negatively with healthy food intake and moderate physical activity. Conclusions: Healthy lifestyle with high physical activity and diet low in calories and fat may help in modifying the risk imposed by FTO variants in children.

Product Variant Master as a Means to Handle Variant Design

DEFF Research Database (Denmark)

Hildre, Hans Petter; Mortensen, Niels Henrik; Andreasen, Mogens Myrup

1996-01-01

be implemented in the CAD system I-DEAS. A precondition for high degree of computer support is identification of a product variant master from which new variants can be derived. This class platform defines how a product build up fit certain production methods and rules governing determination of modules...

Rapid preparative separation of monoclonal antibody charge variants using laterally-fed membrane chromatography.

Science.gov (United States)

Sadavarte, Rahul; Madadkar, Pedram; Filipe, Carlos Dm; Ghosh, Raja

2018-01-15

Monoclonal antibodies undergo various forms of chemical transformation which have been shown to cause loss in efficacy and alteration in pharmacokinetic properties of these molecules. Such modified antibody molecules are known as variants. They also display physical properties such as charge that are different from intact antibody molecules. However, the difference in charge is very subtle and separation based on it is quite challenging. Charge variants are usually separated using ion-exchange column chromatography or isoelectric focusing. In this paper, we report a rapid and scalable method for fractionating monoclonal antibody charge variants, based on the use of cation exchange laterally-fed membrane chromatography (LFMC). Starting with a sample of monoclonal antibody hIgG1-CD4, three well-resolved fractions were obtained using either pH or salt gradient. These fractions were identified as acidic, neutral and basic variants. Each of these fractions contained intact heavy and light chains and so antibody fragmentation had no role in variant generation. The separation was comparable to that using column chromatography but was an order of magnitude faster. Copyright © 2017 Elsevier B.V. All rights reserved.

Adjustment of automatic control systems of production facilities at coal processing plants using multivariant physico- mathematical models

Science.gov (United States)

Evtushenko, V. F.; Myshlyaev, L. P.; Makarov, G. V.; Ivushkin, K. A.; Burkova, E. V.

2016-10-01

The structure of multi-variant physical and mathematical models of control system is offered as well as its application for adjustment of automatic control system (ACS) of production facilities on the example of coal processing plant.

Physical activity (PA) and the disablement process

DEFF Research Database (Denmark)

Schultz-Larsen, Kirsten; Rahmanfard, Naghmeh; Holst, Claus

2012-01-01

. Among older women, the association between RPA and incidence of disability was attenuated in analyses that controlled for baseline mobility function. Thus, the association between physical activity and mortality reflected processes different from those underlying a simple relation between physical...... activity, disability and mortality. Physical activity was an ubiquitous predictor of longevity, but only for women....... community-living persons, aged 75-83 years, we evaluated the 1021 who reported no disability in basic activities of daily living. Participants were followed for a median of 8.34 years in public registers to determine onset of disability and mortality. RPA predicted mortality in older women (HR=1.77, 95%CI=1...

Hairy cell leukemia-variant

International Nuclear Information System (INIS)

Quadri, Mohammad I.; Al-Sheikh, Iman H.

2001-01-01

Hairy cell leukaemia variant is a very rare chronic lymphoproliferative disorder and is closely related to hairy cell leukemia. We hereby describe a case of hairy cell leukaemia variant for the first time in Saudi Arabia. An elderly Saudi man presented with pallor, massive splenomegaly, and moderate hepatomegaly. Hemoglobin was 7.7 g/dl, Platelets were 134 x109/l and white blood count was 140x10 9/l with 97% being abnormal lymphoid cells with cytoplasmic projections. The morphology, cytochemistry, and immunophenotype of the lymphoid cells were classical of hairy cell leukaemia variant. The bone marrow was easily aspirated and findings were consistent with hairy cell leukaemia variant. (author)

Overcoming turbulence-induced space-variant blur by using phase-diverse speckle.

Science.gov (United States)

Thelen, Brian J; Paxman, Richard G; Carrara, David A; Seldin, John H

2009-01-01

Space-variant blur occurs when imaging through volume turbulence over sufficiently large fields of view. Space-variant effects are particularly severe in horizontal-path imaging, slant-path (air-to-ground or ground-to-air) geometries, and ground-based imaging of low-elevation satellites or astronomical objects. In these geometries, the isoplanatic angle can be comparable to or even smaller than the diffraction-limited resolution angle. We report on a postdetection correction method that seeks to correct for the effects of space-variant aberrations, with the goal of reconstructing near-diffraction-limited imagery. Our approach has been to generalize the method of phase-diverse speckle (PDS) by using a physically motivated distributed-phase-screen model. Simulation results are presented that demonstrate the reconstruction of near-diffraction-limited imagery under both matched and mismatched model assumptions. In addition, we present evidence that PDS could be used as a beaconless wavefront sensor in a multiconjugate adaptive optics system when imaging extended scenes.

A systematic approach to assessing the clinical significance of genetic variants.

Science.gov (United States)

Duzkale, H; Shen, J; McLaughlin, H; Alfares, A; Kelly, M A; Pugh, T J; Funke, B H; Rehm, H L; Lebo, M S

2013-11-01

Molecular genetic testing informs diagnosis, prognosis, and risk assessment for patients and their family members. Recent advances in low-cost, high-throughput DNA sequencing and computing technologies have enabled the rapid expansion of genetic test content, resulting in dramatically increased numbers of DNA variants identified per test. To address this challenge, our laboratory has developed a systematic approach to thorough and efficient assessments of variants for pathogenicity determination. We first search for existing data in publications and databases including internal, collaborative and public resources. We then perform full evidence-based assessments through statistical analyses of observations in the general population and disease cohorts, evaluation of experimental data from in vivo or in vitro studies, and computational predictions of potential impacts of each variant. Finally, we weigh all evidence to reach an overall conclusion on the potential for each variant to be disease causing. In this report, we highlight the principles of variant assessment, address the caveats and pitfalls, and provide examples to illustrate the process. By sharing our experience and providing a framework for variant assessment, including access to a freely available customizable tool, we hope to help move towards standardized and consistent approaches to variant assessment. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Physical and chemical characterization of bioaerosols - Implications for nucleation processes

Science.gov (United States)

Ariya, P. A.; Sun, J.; Eltouny, N. A.; Hudson, E. D.; Hayes, C. T.; Kos, G.

The importance of organic compounds in the oxidative capacity of the atmosphere, and as cloud condensation and ice-forming nuclei, has been recognized for several decades. Organic compounds comprise a significant fraction of the suspended matter mass, leading to local (e.g. toxicity, health hazards) and global (e.g. climate change) impacts. The state of knowledge of the physical chemistry of organic aerosols has increased during the last few decades. However, due to their complex chemistry and the multifaceted processes in which they are involved, the importance of organic aerosols, particularly bioaerosols, in driving physical and chemical atmospheric processes is still very uncertain and poorly understood. Factors such as solubility, surface tension, chemical impurities, volatility, morphology, contact angle, deliquescence, wettability, and the oxidation process are pivotal in the understanding of the activation processes of cloud droplets, and their chemical structures, solubilities and even the molecular configuration of the microbial outer membrane, all impact ice and cloud nucleation processes in the atmosphere. The aim of this review paper is to assess the current state of knowledge regarding chemical and physical characterization of bioaerosols with a focus on those properties important in nucleation processes. We herein discuss the potential importance (or lack thereof) of physical and chemical properties of bioaerosols and illustrate how the knowledge of these properties can be employed to study nucleation processes using a modeling exercise. We also outline a list of major uncertainties due to a lack of understanding of the processes involved or lack of available data. We will also discuss key issues of atmospheric significance deserving future physical chemistry research in the fields of bioaerosol characterization and microphysics, as well as bioaerosol modeling. These fundamental questions are to be addressed prior to any definite conclusions on the

Micromechanics of transformation-induced plasticity and variant coalescence

International Nuclear Information System (INIS)

Marketz, F.; Fischer, F.D.; University for Mining and Metallurgy, Leoben; Tanaka, K.

1996-01-01

Quantitative micromechanics descriptions of both transformation-induced plasticity (TRIP) associated with the martensitic transformation in an Fe-Ni alloy and of variant coalescence in a Cu-Al-Ni shape memory alloy are presented. The macroscopic deformation behavior of a polycrystalline aggregate as a result of the rearrangements within the crystallites is modelled with the help of a finite element based periodic microfield approach. In the case of TRIP the parent→martensite transformation is described by microscale thermodynamic and kinetic equations taking into account internal stress states. The simulation of a classical experiment on TRIP allows to quantify the Magee-effect and the Greenwood-Johnson effect. Furthermore, the development of the martensitic microstructure is studied with respect to the stress-assisted transformation of preferred variants. In the case of variant coalescence the strain energy due to internal stress states has an important influence on the mechanical behavior. Formulating the reorientation process on the size scale of self-accommodating plate groups in terms of the mobility of the boundaries between martensitic variants the macroscopic behavior in uniaxial tension is predicted by an incremental modelling procedure. Furthermore, influence of energy dissipation on the overall behavior is quantified. (orig.)

Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic

DEFF Research Database (Denmark)

Ahlborn, Lise B; Dandanell, Mette; Steffensen, Ane Y

2015-01-01

by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c......Pathogenic germline mutations in the BRCA1 gene predispose carriers to early onset breast and ovarian cancer. Clinical genetic screening of BRCA1 often reveals variants with uncertain clinical significance, complicating patient and family management. Therefore, functional examinations are urgently...... needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined...

Designing quantum information processing via structural physical approximation.

Science.gov (United States)

Bae, Joonwoo

2017-10-01

In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of quantum mechanics is more restrictive than classical systems, identified to a specific form of dynamics, that is, unitary transformations and, consequently, positive and completely positive maps to subsystems. This also characterizes classes of disallowed transformations on quantum systems, among which positive but not completely maps are of particular interest as they characterize entangled states, a general resource in quantum information processing. Structural physical approximation offers a systematic way of approximating those non-physical maps, positive but not completely positive maps, with quantum channels. Since it has been proposed as a method of detecting entangled states, it has stimulated fundamental problems on classifications of positive maps and the structure of Hermitian operators and quantum states, as well as on quantum measurement such as quantum design in quantum information theory. It has developed efficient and feasible methods of directly detecting entangled states in practice, for which proof-of-principle experimental demonstrations have also been performed with photonic qubit states. Here, we present a comprehensive review on quantum information processing with structural physical approximations and the related progress. The review mainly focuses on properties of structural physical approximations and their applications toward practical information applications.

HGVS Recommendations for the Description of Sequence Variants: 2016 Update.

Science.gov (United States)

den Dunnen, Johan T; Dalgleish, Raymond; Maglott, Donna R; Hart, Reece K; Greenblatt, Marc S; McGowan-Jordan, Jean; Roux, Anne-Francoise; Smith, Timothy; Antonarakis, Stylianos E; Taschner, Peter E M

2016-06-01

The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD-WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD-WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here, we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen. © 2016 WILEY PERIODICALS, INC.

Roles of medical image processing in medical physics

International Nuclear Information System (INIS)

Arimura, Hidetaka

2011-01-01

Image processing techniques including pattern recognition techniques play important roles in high precision diagnosis and radiation therapy. The author reviews a symposium on medical image information, which was held in the 100th Memorial Annual Meeting of the Japan Society of Medical Physics from September 23rd to 25th. In this symposium, we had three invited speakers, Dr. Akinobu Shimizu, Dr. Hideaki Haneishi, and Dr. Hirohito Mekata, who are active engineering researchers of segmentation, image registration, and pattern recognition, respectively. In this paper, the author reviews the roles of the medical imaging processing in medical physics field, and the talks of the three invited speakers. (author)

The common FTO variant rs9939609 is not associated with BMI in a longitudinal study on a cohort of Swedish men born 1920-1924

Directory of Open Access Journals (Sweden)

Lannfelt Lars

2009-12-01

Full Text Available Abstract Background Common FTO (fat mass and obesity associated gene variants have recently been strongly associated with body mass index and obesity in several large studies. Here we set out to examine the association of the FTO variant rs9939609 with BMI in a 32 year follow up study of men born 1920-1924. Moreover, we analyzed the effect of physical activity on the different genotypes. Methods The FTO rs9936609 was genotyped using an Illumina golden gate assay. BMI was calculated using standard methods and body fat was estimated by measuring skinfold thickness using a Harpenden caliper. Physical activity was assessed using a four question medical questionnaire. Results FTO rs9939609 was genotyped in 1153 elderly Swedish men taking part of a population-based cohort study, the ULSAM cohort. The risk of obesity and differences in BMI according to genotype at the ages of 50, 60, 70, 77 and 82 were investigated. We found no increased risk of obesity and no association with BMI at any age with the FTO rs9939609 variant. We found however interaction between physical activity at the age of 50 years and genotype on BMI levels (p = 0.039 and there was a clear trend towards larger BMI differences between the TT and AA carriers as well as between AT and AA carriers in the less physically active subjects. Conclusion Here we found that the well established obesity risk allele for a common variant in FTO does not associate with increased BMI levels in a Swedish population of adult men which reached adulthood before the appearance of today's obesogenic enviroment. There is an interaction between physical activity and the effect of the FTO genotype on BMI levels suggesting that lack of physical activity is a requirement for an association of FTO gene variants to obesity.

MR imaging of acute disseminated encephalomyelitis, cerebellitis and myelitis in infancy: likely topographic variant of a single process

International Nuclear Information System (INIS)

Fortuno, J. R.; Menor, F.; Esteban, M. J.; Pamies, J.; Gomez-Gosalvez, F. A.; Jover, J.

2003-01-01

To describe MR images of acute disseminated encephalomyelitis (ADE) in a paediatric group, particularly focused on its likely topographic variants, cerebellitis and myelitis, its evolution, and the differential diagnosis between it an an initial outbreak of multiple sclerosis. Initial and follow-up cranial MR images were retrospectively reviewed for 14 paediatric patients diagnosed with either ADE, cerebellitis or myelitis. In 9 patients, a spinal cord monitoring was included. Three topographic variants have been considered: ADE (7 patients). In the case of ADE, the supratentorial white matter was always affected, the brain stem in five (71%) and the cerebellum in two (28,5%). Basal ganglionic lesions were detected in 5 patients (71%) and cortical lesions in one (14%). Associated spinal cord abnormality was found in five of the six cases in which this study was included (83%). ADE lesions tended to be nodular and poorly differentiated whereas in cerebellitis and myelitis the predominant pattern was one of diffuse damage. Evolution of the lesions was toward reduction/resolution. Follow-up using MR in the medium-term in 6 patients (four ADE and two cerebellitis) did not detect any new lesions. Clinical follow-up of the patients did not show any neurological recurrences in any of them. ADE, cerebillits and myelitis could be topographic variants of a single process with a common pathogeny. As the spinal cord often seems to play a role in ADE, spinal cord monitoring would be recommended, even in the absence of the above-mentioned symptoms. This spinal cord abnormality, which is usually diffuse, plus deep gray matter damage, as well as the disease of monophase course, corroborated by a sequential MR follow-up, is all helpful in the differential diagnosis with multiple sclerosis. Nonetheless, the differential diagnosis between a recurring form of ADE and an encephalomyelitis is practically impossible to make. (Author) 33 refs

A rabies virus vampire bat variant shows increased neuroinvasiveness in mice when compared to a carnivore variant.

Science.gov (United States)

Mesquita, Leonardo Pereira; Gamon, Thais Helena Martins; Cuevas, Silvia Elena Campusano; Asano, Karen Miyuki; Fahl, Willian de Oliveira; Iamamoto, Keila; Scheffer, Karin Correa; Achkar, Samira Maria; Zanatto, Dennis Albert; Mori, Cláudia Madalena Cabrera; Maiorka, Paulo César; Mori, Enio

2017-12-01

Rabies is one of the most important zoonotic diseases and is caused by several rabies virus (RABV) variants. These variants can exhibit differences in neurovirulence, and few studies have attempted to evaluate the neuroinvasiveness of variants derived from vampire bats and wild carnivores. The aim of this study was to evaluate the neuropathogenesis of infection with two Brazilian RABV street variants (variant 3 and crab-eating fox) in mice. BALB/c mice were inoculated with RABV through the footpad, with the 50% mouse lethal dose (LD 50 ) determined by intracranial inoculation. The morbidity of rabies in mice infected with variant 3 and the crab-eating fox strain was 100% and 50%, respectively, with an incubation period of 7 and 6 days post-inoculation (dpi), respectively. The clinical disease in mice was similar with both strains, and it was characterized initially by weight loss, ruffled fur, hunched posture, and hind limb paralysis progressing to quadriplegia and recumbency at 9 to 12 dpi. Histological lesions within the central nervous system (CNS) characterized by nonsuppurative encephalomyelitis with neuronal degeneration and necrosis were observed in mice infected with variant 3 and those infected with the crab-eating fox variant. However, lesions and the presence of RABV antigen, were more widespread within the CNS of variant-3-infected mice, whereas in crab-eating fox-variant-infected mice, RABV antigens were more restricted to caudal areas of the CNS, such as the spinal cord and brainstem. In conclusion, the results shown here demonstrate that the RABV vampire bat strain (variant 3) has a higher potential for neuroinvasiveness than the carnivore variant.

An improved process for the production of highly purified recombinant thaumatin tagged-variants.

Science.gov (United States)

Healey, Robert D; Lebhar, Helene; Hornung, Simon; Thordarson, Pall; Marquis, Christopher P

2017-12-15

The sweetest tasting molecule known is the protein thaumatin, first isolated from the katemfe fruit, Thaumatococcus daniellii. Thaumatin is used in the food and beverage industry as a low-calorie sugar substitute. Thaumatin interacts with taste receptors in the oral cavity eliciting a persistent sweet taste and a bitter, liquorice flavor. Recombinant thaumatin was expressed in Pichia pastoris and through a co-expression strategy with a molecular chaperone, yields of one engineered thaumatin variant increased by greater than two-fold. A detailed purification strategy for thaumatin is reported resulting in a homogenous sample recovered at a yield of 42%. The recombinant thaumatins were extensively characterised using size exclusion chromatography for homogeneity, reversed-phase HPLC for purity (99%), peptide digest LC-MS/MS for sequence determination, and circular dichroism and tryptophan fluorescence spectroscopies for conformational characterisation. These new thaumatin variants are amenable for bioconjugation, providing chemical biology tools for thaumatin:taste receptor interaction studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

VIPER: a web application for rapid expert review of variant calls.

Science.gov (United States)

Wöste, Marius; Dugas, Martin

2018-01-15

With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10,000 calls. VIPER is implemented in Java and Javascript and is freely available at https://github.com/MarWoes/viper. Marius.Woeste@uni-muenster.de. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Development of industrial variant specification systems

DEFF Research Database (Denmark)

Hansen, Benjamin Loer

be developed from a holistic and strategically anchored point of view. Another assumption is that this is a challenge for many industrial companies. Even though the literature presents many considerations on general issues covering new information technology, little work is found on the business perspectives...... are discussed. A list of structural variables and solution components has been created. These are related to four design aspects in the holistic system design covering the aspects of process design, selection of resources (such as hardware, software and humans), the design of information structures...... solution elements and structural variables to be used in the design of variant specification systems. The thesis presents a “top-down” procedure to be used to develop variant specification systems from a strategically anchored and holistic point of view. A methodology and related task variables...

Standardizing the evaluation of scientific and academic performance in neurosurgery--critical review of the "h" index and its variants.

Science.gov (United States)

Aoun, Salah G; Bendok, Bernard R; Rahme, Rudy J; Dacey, Ralph G; Batjer, H Hunt

2013-11-01

Assessing the academic impact and output of scientists and physicians is essential to the academic promotion process and has largely depended on peer review. The inherent subjectivity of peer review, however, has led to an interest to incorporate objective measures into more established methods of academic assessment and promotion. Journal impact factor has been used to add objectivity to the process but this index alone does not capture all aspects of academic impact and achievement. The "h" index and its variants have been designed to compensate for these shortcomings, and have been successfully used in the fields of physics, mathematics, and biology, and more recently in medicine. Leaders in academic neurosurgery should be aware of the advantages offered by each of these indices, as well as of their individual shortcomings, to be able to efficiently use them to refine the peer-review process. This review critically analyzes indices that are currently available to evaluate the academic impact of scientists and physicians. These indices include the total citation count, the total number of papers, the impact factor, as well as the "h" index with eight of its most common variants. The analysis focuses on their use in the field of academic neurosurgery, and discusses means to implement them in current review processes. Copyright © 2013 Elsevier Inc. All rights reserved.

Diverse Functional Properties of Wilson Disease ATP7B Variants

Science.gov (United States)

Huster, Dominik; Kühne, Angelika; Bhattacharjee, Ashima; Raines, Lily; Jantsch, Vanessa; Noe, Johannes; Schirrmeister, Wiebke; Sommerer, Ines; Sabri, Osama; Berr, Frieder; Mössner, Joachim; Stieger, Bruno; Caca, Karel; Lutsenko, Svetlana

2012-01-01

BACKGROUND & AIMS Wilson disease is a severe disorder of copper metabolism caused by mutations in ATP7B, which encodes a copper-transporting adenosine triphosphatase. The disease presents with a variable phenotype that complicates the diagnostic process and treatment. Little is known about the mechanisms that contribute to the different phenotypes of the disease. METHODS We analyzed 28 variants of ATP7B from patients with Wilson disease that affected different functional domains; the gene products were expressed using the baculovirus expression system in Sf9 cells. Protein function was analyzed by measuring catalytic activity and copper (64Cu) transport into vesicles. We studied intracellular localization of variants of ATP7B that had measurable transport activities and were tagged with green fluorescent protein in mammalian cells using confocal laser scanning microscopy. RESULTS Properties of ATP7B variants with pathogenic amino-acid substitution varied greatly even if substitutions were in the same functional domain. Some variants had complete loss of catalytic and transport activity, whereas others lost transport activity but retained phosphor-intermediate formation or had partial losses of activity. In mammalian cells, transport-competent variants differed in stability and subcellular localization. CONCLUSIONS Variants in ATP7B associated with Wilson disease disrupt the protein’s transport activity, result in its mislocalization, and reduce its stability. Single assays are insufficient to accurately predict the effects of ATP7B variants the function of its product and development of Wilson disease. These findings will contribute to our understanding of genotype–phenotype correlation and mechanisms of disease pathogenesis. PMID:22240481

Variant Selection during Alpha Precipitation in Titanium Alloys: A Simulation Study

Science.gov (United States)

Shi, Rongpei

Variant selection of alpha phase during its precipitation from beta matrix plays a key role in determining transformation texture and final mechanical properties of alpha/beta and beta titanium alloys. In this study we develop a three-dimensional quantitative phase field model (PFM) to predict variant selection and microstructure evolution during beta to alpha transformation in polycrystalline Ti-6Al-4V under the influence of different processing variables. The model links its inputs directly to thermodynamic and mobility databases, and incorporates crystallography of BCC to HCP transformation, elastic anisotropy, defects within semi-coherent alpha/beta interfaces and elastic inhomogeneities among different beta grains. In particular, microstructure and transformation texture evolution are treated simultaneously via orientation distribution function (ODF) modeling of alpha/beta two-phase microstructure in beta polycrystalline obtained by PFM. It is found that, for a given undercooling, the development of transformation texture of the alpha phase due to variant selection during precipitation depends on both externally applied stress or strain, initial texture state of parent beta sample and internal stress generated by the precipitation reaction itself. Moreover, the growth of pre-existing widmanstatten alpha precipitates is accompanied by selective nucleation and growth of secondary alpha plates of preferred variants. We further develop a crystallographic model based on the ideal Burgers orientation relationship (BOR) between GBalpha and one of the two adjacent beta grains to investigate how a prior beta grain boundary contributes to variant selection of grain boundary allotriomorph (GBalpha). The model is able to predict all possible special beta grain boundaries where GBalpha is able to maintain BOR with two neighboring grain. In particular, the model has been used to evaluate the validity of all current empirical variant selection rules to obtain more insight of

Contextualization processes and the initial education of physics teachers

Directory of Open Access Journals (Sweden)

Cristina Cândida de Macedo

2014-03-01

Full Text Available Contextualization of school contents has been seen as a possibility of facilitating students’ learning, since it makes the educative process more significant to them. However, there is no agreement as to the meaning and the forms of applying such processes. Particularly in the area of Science teaching, the creation of thematic projects has been seen as a way of contextualizing school contents. It is noteworthy that the experience with the education of Physics teachers shows that the creation and execution of such projects brings many difficulties to teachers, the main obstacle being the understanding of what contextualized educative processes are. Having this in mind, a project has been elaborated with the objective of analyzing the comprehension Physics teachers that are going through teacher education courses have of the processes of contextualization. The data for this investigation has been obtained from students who attended a course of the Physics Teacher Education module at the Federal University of Itajubá. It is significant to mention that in this course students are asked to create three versions of a thematic project. In order to analyze the data, the procedure of Thematic Content and Category Analysis was adopted. This research shows that Physics teachers to be incorporate the discourses of the educative ideas throughout the course. However, there is a series of obstacles they face as they attempt to understand and carry out contextualized educative processes. Those difficulties are connected to their experience with this kind of educative process throughout the years they spend at school and in the teacher education course. We conclude thus that it is essential that contextualized educative activities be part of the reality of teacher education programs.

Space plasma physics stationary processes

CERN Document Server

Hasegawa, Akira

1989-01-01

During the 30 years of space exploration, important discoveries in the near-earth environment such as the Van Allen belts, the plasmapause, the magnetotail and the bow shock, to name a few, have been made. Coupling between the solar wind and the magnetosphere and energy transfer processes between them are being identified. Space physics is clearly approaching a new era, where the emphasis is being shifted from discoveries to understanding. One way of identifying the new direction may be found in the recent contribution of atmospheric science and oceanography to the development of fluid dynamics. Hydrodynamics is a branch of classical physics in which important discoveries have been made in the era of Rayleigh, Taylor, Kelvin and Helmholtz. However, recent progress in global measurements using man-made satellites and in large scale computer simulations carried out by scientists in the fields of atmospheric science and oceanography have created new activities in hydrodynamics and produced important new discover...

Variants of cellobiohydrolases

Energy Technology Data Exchange (ETDEWEB)

Bott, Richard R.; Foukaraki, Maria; Hommes, Ronaldus Wilhelmus; Kaper, Thijs; Kelemen, Bradley R.; Kralj, Slavko; Nikolaev, Igor; Sandgren, Mats; Van Lieshout, Johannes Franciscus Thomas; Van Stigt Thans, Sander

2018-04-10

Disclosed are a number of homologs and variants of Hypocrea jecorina Ce17A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

Lack of Association of CD55 Receptor Genetic Variants and Severe Malaria in Ghanaian Children

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Kathrin Schuldt

2017-03-01

Full Text Available In a recent report, the cellular receptor CD55 was identified as a molecule essential for the invasion of human erythrocytes by Plasmodium falciparum, the causal agent of the most severe form of malaria. As this invasion process represents a critical step during infection with the parasite, it was hypothesized that genetic variants in the gene could affect severe malaria (SM susceptibility. We performed high-resolution variant discovery of rare and common genetic variants in the human CD55 gene. Association testing of these variants in over 1700 SM cases and unaffected control individuals from the malaria-endemic Ashanti Region in Ghana, West Africa, were performed on the basis of single variants, combined rare variant analyses, and reconstructed haplotypes. A total of 26 genetic variants were detected in coding and regulatory regions of CD55. Five variants were previously unknown. None of the single variants, rare variants, or haplotypes showed evidence for association with SM or P. falciparum density. Here, we present the first comprehensive analysis of variation in the CD55 gene in the context of SM and show that genetic variants present in a Ghanaian study group appear not to influence susceptibility to the disease.

Girdler-sulfide process physical properties

International Nuclear Information System (INIS)

Neuburg, H.J.; Atherley, J.F.; Walker, L.G.

1977-05-01

Physical properties of pure hydrogen sulfide and of gaseous and liquid solutions of the H 2 S-H 2 O system have been formulated. Tables for forty-nine different properties in the pressure and temperature range of interest to the Girdler-Sulfide (GS) process for heavy water production are given. All properties are presented in SI units. A computer program capable of calculating properties of the pure components as well as gaseous mixtures and liquid solutions at saturated and non-saturated conditions is included. (author)

Dispersal from deep ocean sources: physical and related scientific processes

International Nuclear Information System (INIS)

Robinson, A.R.; Kupferman, S.L.

1985-02-01

This report presents the results of the workshop ''Dispersal from Deep Ocean Sources: Physical and Related Scientific Processes,'' together with subsequent developments and syntheses of the material discussed there. The project was undertaken to develop usable predictive descriptions of dispersal from deep oceanic sources. Relatively simple theoretical models embodying modern ocean physics were applied, and observational and experimental data bases were exploited. All known physical processes relevant to the dispersal of passive, conservative tracers were discussed, and contact points for inclusion of nonconservative processes (biological and chemical) were identified. Numerical estimates of the amplitude, space, and time scales of dispersion were made for various mechanisms that control the evolution of the dispersal as the material spreads from a bottom point source to small-, meso-, and world-ocean scales. Recommendations for additional work are given. The volume is presented as a handbook of dispersion processes. It is intended to be updated as new results become available

A Systematic Review of Human Bat Rabies Virus Variant Cases: Evaluating Unprotected Physical Contact with Claws and Teeth in Support of Accurate Risk Assessments.

Science.gov (United States)

Dato, Virginia M; Campagnolo, Enzo R; Long, Jonah; Rupprecht, Charles E

2016-01-01

In the United States and Canada, the most recent documented cases of rabies have been attributed to bat rabies viruses (RABV). We undertook this systematic review in an effort to summarize and enhance understanding of the risk of infection for individuals who have been potentially exposed to a suspect or confirmed rabid bat. United States rabies surveillance summaries documented a total of 41 human bat-rabies virus variant verified non-transplant cases between 1990 and 2015. All cases were fatal. Seven (17.1%) of 41 cases reported a bite from a bat. Ten (24.3%) cases had unprotected physical contact (UPC); these included seven cases that had a bat land or crawl on them (contact with claws) and one case that touched a bat's teeth. Seven (17.1%) cases had probable UPC. Insectivorous bat teeth are extremely sharp and highly efficient for predation upon arthropod prey. Bats also have sharp claws on the end of their thumbs and feet. One of the most common bat RABV variants has an ability to replicate in non-neural cells. Questioning individuals about unprotected contact with bat teeth and claws (including a bat landing or crawling on a person) may help identify additional exposures.

Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

Directory of Open Access Journals (Sweden)

Saumya Gupta

2015-06-01

Full Text Available Even with identification of multiple causal genetic variants for common human diseases, understanding the molecular processes mediating the causal variants' effect on the disease remains a challenge. This understanding is crucial for the development of therapeutic strategies to prevent and treat disease. While static profiling of gene expression is primarily used to get insights into the biological bases of diseases, it makes differentiating the causative from the correlative effects difficult, as the dynamics of the underlying biological processes are not monitored. Using yeast as a model, we studied genome-wide gene expression dynamics in the presence of a causal variant as the sole genetic determinant, and performed allele-specific functional validation to delineate the causal effects of the genetic variant on the phenotype. Here, we characterized the precise genetic effects of a functional MKT1 allelic variant in sporulation efficiency variation. A mathematical model describing meiotic landmark events and conditional activation of MKT1 expression during sporulation specified an early meiotic role of this variant. By analyzing the early meiotic genome-wide transcriptional response, we demonstrate an MKT1-dependent role of novel modulators, namely, RTG1/3, regulators of mitochondrial retrograde signaling, and DAL82, regulator of nitrogen starvation, in additively effecting sporulation efficiency. In the presence of functional MKT1 allele, better respiration during early sporulation was observed, which was dependent on the mitochondrial retrograde regulator, RTG3. Furthermore, our approach showed that MKT1 contributes to sporulation independent of Puf3, an RNA-binding protein that steady-state transcription profiling studies have suggested to mediate MKT1-pleiotropic effects during mitotic growth. These results uncover interesting regulatory links between meiosis and mitochondrial retrograde signaling. In this study, we highlight the advantage

Physics at a 100 TeV pp Collider: Standard Model Processes

Energy Technology Data Exchange (ETDEWEB)

Mangano, M. L. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Zanderighi, G. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Aguilar Saavedra, J. A. [Univ. of Granada (Spain); Alekhin, S. [Univ. of Hamburg (Germany). Inst. for Theoretical Physics; Inst. for High Energy Physics (IHEP), Moscow (Russian Federation); Badger, S. [Univ. of Edinburgh, Scotland (United Kingdom); Bauer, C. W. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Becher, T. [Univ. Bern (Switzerland); Bertone, V. [Univ. of Oxford (United Kingdom); Bonvini, M. [Univ. of Oxford (United Kingdom); Boselli, S. [Univ. of Pavia (Italy); Bothmann, E. [Gottingen Univ. (Germany); Boughezal, R. [Argonne National Lab. (ANL), Argonne, IL (United States); Cacciari, M. [Univ. Paris Diderot (France); Sorbonne Univ., Paris (France); Carloni Calame, C M. [Istituto Nazionale di Fisica Nucleare (INFN), Pavia (Italy); Caola, F. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Campbell, J. M. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Carrazza, S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Chiesa, M. [Istituto Nazionale di Fisica Nucleare (INFN), Pavia (Italy); Cieri, L. [Univ. of Zurich (Switzerland); Cimaglia, F. [Univ. degli Studi di Milano (Italy); Febres Cordero, F. [Physikalisches Inst., Freiburg (Germany); Ferrarese, P. [Gottingen Univ. (Germany); D' Enterria, D. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Ferrera, G. [Univ. degli Studi di Milano (Italy); Garcia i Tormo, X. [Univ. Bern (Switzerland); Garzelli, M. V. [Univ. of Hamburg (Germany); Germann, E. [Monash Univ., Melbourne, VIC (Australia); Hirschi, V. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Han, T. [Univ. of Pittsburgh, PA (United States); Ita, H. [Physikalisches Inst., Freiburg (Germany); Jager, B. [Univ. of Tubingen (Germany); Kallweit, S. [Johannes Gutenberg Univ., Mainz (Germany); Karlberg, A. [Univ. of Oxford (United Kingdom); Kuttimalai, S. [Durham Univ. (United Kingdom); Krauss, F. [Durham Univ. (United Kingdom); Larkoski, A. J. [Harvard Univ., Cambridge, MA (United States); Lindert, J. [Univ. of Zurich (Switzerland); Luisoni, G. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Maierhofer, P. [Univ. of Freiburg (Germany); Mattelaer, O. [Durham Univ. (United Kingdom); Martinez, H. [Univ. of Pavia (Italy); Moch, S. [Univ. of Hamburg (Germany); Montagna, G. [Univ. of Pavia (Italy); Moretti, M. [Univ. of Ferrara (Italy); Nason, P. [Univ. of Milano (Italy); Nicrosini, O. [Istituto Nazionale di Fisica Nucleare (INFN), Pavia (Italy); Oleari, C. [Univ. of Milano (Italy); Pagani, D. [Univ. Catholique de Louvain (Belgium); Papaefstathiou, A. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Petriello, F. [Northwestern Univ., Evanston, IL (United States); Piccinini, F. [Istituto Nazionale di Fisica Nucleare (INFN), Pavia (Italy); Pierini, M. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Pierog, T. [Karlsruhe Inst. of Technology (KIT) (Germany); Pozzorini, S. [Univ. of Zurich (Switzerland); Re, E. [National Centre for Scientific Research (CNRS), Annecy-le-Vieux (France). Lab. of Annecy-le-Vieux for Theoretical Physics (LAPTh); Robens, T. [Technische Universitat Dresden (Germany); Rojo, J. [Univ. of Oxford (United Kingdom); Ruiz, R. [Durham Univ. (United Kingdom); Sakurai, K. [Durham Univ. (United Kingdom); Salam, G. P. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Salfelder, L. [Univ. of Tubingen (Germany); Schonherr, M. [Univ. of Ferrara (Italy); Schulze, M. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Schumann, S. [Univ. Gottingen (Germany); Selvaggi, M. [Univ. Catholique de Louvain (Belgium); Shivaji, A. [Istituto Nazionale di Fisica Nucleare (INFN), Pavia (Italy); Siodmok, A. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Polish Academy of Sciences (PAS), Krakow (Poland); Skands, P. [Monash Univ., Melbourne, VIC (Australia); Torrielli, P. [Univ. of Torino (Italy); Tramontano, F. [Univ. of Napoli (Italy); Tsinikos, I. [Univ. Catholique de Louvain (Belgium); Tweedie, B. [Univ. of Pittsburgh, PA (United States); Vicini, A. [Univ. degli Studi di Milano (Italy); Westhoff, S. [Heidelberg Univ. (Germany); Zaro, M. [Sorbonne Univ., Paris (France); Zeppenfeld, D. [Forschungszentrum Karlsruhe (Germany)

2017-06-22

This report summarises the properties of Standard Model processes at the 100 TeV pp collider. We document the production rates and typical distributions for a number of benchmark Standard Model processes, and discuss new dynamical phenomena arising at the highest energies available at this collider. We discuss the intrinsic physics interest in the measurement of these Standard Model processes, as well as their role as backgrounds for New Physics searches.

Programs for low-energy nuclear physics data processing

International Nuclear Information System (INIS)

Antuf'ev, Yu.P.; Dejneko, A.S.; Ekhichev, O.I.; Kuz'menko, V.A.; Mashkarov, Yu.G.; Nemashkalo, B.A.; Skakun, E.A.; Storizhko, V.E.; Shlyakhov, N.A.

1978-01-01

Purpose of six computer programs developed in KhPTI of AN USSR for the processing of the experimental data on low energy nuclear physics ia friendly described. The programs are written in Algol-60 language. They are applied to some types of nuclear reactions and permit to process differential cross sections and γ spectra, to compute statistical tensors and excitation functions as well as to analyze some processes by means of theoretical models

MR imaging of the ankle: Normal variants

International Nuclear Information System (INIS)

Noto, A.M.; Cheung, Y.; Rosenberg, Z.S.; Norman, A.; Leeds, N.E.

1987-01-01

Thirty asymptomatic ankles were studied with high-resolution surface coil MR imaging. The thirty ankles were reviewed for identification or normal structures. The MR appearance of the deltoid and posterior to talo-fibular ligaments, peroneous brevis and longus tendons, and posterior aspect of the tibial-talar joint demonstrated several normal variants not previously described. These should not be misinterpreted as pathologic processes. The specific findings included (1) cortical irregularity of the posterior tibial-talar joint in 27 of 30 cases which should not be mistaken for osteonecrois; (2) normal posterior talo-fibular ligament with irregular and frayed inhomogeneity, which represents a normal variant in seven of ten cases; and (3) fluid in the shared peroneal tendons sheath which may be confused for a longitudinal tendon tear in three of 30 cases. Ankle imaging with the use of MR is still a relatively new procedure. Further investigation is needed to better define normal anatomy as well as normal variants. The authors described several structures that normally present with variable MR imaging appearances. This is clinically significant in order to maintain a high sensitivity and specificity in MR imaging interpretation

Bringing life to soil physical processes

Science.gov (United States)

Hallett, P. D.

2013-12-01

When Oklahoma's native prairie grass roots were replaced by corn, the greatest environmental (and social) disaster ever to hit America ensued. The soils lost structure, physical binding by roots was annihilated and when drought came the Great Dust Bowl commenced. This form of environmental disaster has repeated over history and although not always apparent, similar processes drive the degradation of seemingly productive farmland and forests. But just as negative impacts on biology are deleterious to soil physical properties, positive impacts could reverse these trends. In finding solutions to soil sustainability and food security, we should be able to exploit biological processes to improve soil physical properties. This talk will focus on a quantitative understanding of how biology changes soil physical behaviour. Like the Great Dust Bowl, it starts with reinforcement mechanisms by plant roots. We found that binding of soil by cereal (barley) roots within 5 weeks of planting can more than double soil shear strength, with greater plant density causing greater reinforcement. With time, however, the relative impact of root reinforcement diminishes due to root turnover and aging of the seedbed. From mechanical tests of individual roots, reasonable predictions of reinforcement by tree roots are possible with fibre bundle models. With herbaceous plants like cereals, however, the same parameters (root strength, stiffness, size and distribution) result in a poor prediction. We found that root type, root age and abiotic factors such as compaction and waterlogging affect mechanical behaviour, further complicating the understanding and prediction of root reinforcement. For soil physical stability, the interface between root and soil is an extremely important zone in terms of resistance of roots to pull-out and rhizosphere formation. Compounds analogous to root exudates have been found with rheological tests to initially decrease the shear stress where wet soils flow, but

The Processes of Inclusion and Exclusion in Physical Education

DEFF Research Database (Denmark)

Jensen, Mette Munk; Agergaard, Sine

2015-01-01

Existing research on inclusion and exclusion processes in physical education (PE) has particularly focused on exclusion from PE as something being done to students and attributed to specific social categories such as (female) gender, (low) physical skills or (minority) ethnic background....... This article aims to develop a social-relational perspective on inclusion and exclusion processes defined as students’ participation or non-participation in PE interpreted as a community of practice. In so doing, the article examines how students’ experiences of participation and non-participation in PE...... or non-participation is important not only in terms of how we talk about students as passive victims or active agents, but also in terms of future intervention aimed at promoting inclusion processes in PE....

Characterization of form variants of Xenorhabdus luminescens.

Science.gov (United States)

Gerritsen, L J; de Raay, G; Smits, P H

1992-01-01

From Xenorhabdus luminescens XE-87.3 four variants were isolated. One, which produced a red pigment and antibiotics, was luminescent, and could take up dye from culture media, was considered the primary form (XE-red). A pink-pigmented variant (XE-pink) differed from the primary form only in pigmentation and uptake of dye. Of the two other variants, one produced a yellow pigment and fewer antibiotics (XE-yellow), while the other did not produce a pigment or antibiotics (XE-white). Both were less luminescent, did not take up dye, and had small cell and colony sizes. These two variants were very unstable and shifted to the primary form after 3 to 5 days. It was not possible to separate the primary form and the white variant completely; subcultures of one colony always contained a few colonies of the other variant. The white variant was also found in several other X. luminescens strains. DNA fingerprints showed that all four variants are genetically identical and are therefore derivatives of the same parent. Protein patterns revealed a few differences among the four variants. None of the variants could be considered the secondary form. The pathogenicity of the variants decreased in the following order: XE-red, XE-pink, XE-yellow, and XE-white. The mechanism and function of this variability are discussed. Images PMID:1622273

Physical Abuse, Cognitive and Emotional Processes, and Aggressive/Disruptive Behavior Problems

Science.gov (United States)

Teisl, Michael; Cicchetti, Dante

2008-01-01

Cognitive and emotional processes were examined in maltreated children with a history of physical abuse (n = 76), children with a history of maltreatment other than physical abuse (i.e., sexual abuse, physical neglect, and emotional maltreatment; n = 91), and a group of non-maltreated comparison children (N = 100). Physical abuse was associated…

Microstructure evolution to reach the single variant in an ordered Fe–55at.%Pd alloy

International Nuclear Information System (INIS)

Farjami, Sahar; Fukuda, Takashi; Kakeshita, Tomoyuki

2013-01-01

Highlights: ► We confirmed formation of the single variant in Fe–55at.%Pd by XRD measurement and TEM observation. ► The size of each ordered domain is about 2 nm at the early stage of ordering. ► High density of antiphase boundaries has been observed after formation of the single variant. -- Abstract: Recently, we reported single variant formation in an Fe–55at.%Pd is certainly realized from a disordered fcc-phase to an ordered L1 0 -phase by heat-treatment under magnetic field. In the present study, we have investigated microstructure evolution during the process of the single variant formation by an X-ray diffraction and an electron microscopy observation. As a result, followings are obtained: size of the ordered particles at the early stage of ordering is about 2 nm and the nucleation ratio of preferable variant, whose easy axis lies in the field direction, is higher than that of other variants. Each of the ordered preferable variant grows by consuming the order variants and finally come together to become a single variant. Based on the observation, a model is proposed for the single variant formation of the ordered L1 0 -phase under magnetic field

m6AVar: a database of functional variants involved in m6A modification

OpenAIRE

Zheng, Yueyuan; Nie, Peng; Peng, Di; He, Zhihao; Liu, Mengni; Xie, Yubin; Miao, Yanyan; Zuo, Zhixiang; Ren, Jian

2017-01-01

Abstract Identifying disease-causing variants among a large number of single nucleotide variants (SNVs) is still a major challenge. Recently, N 6-methyladenosine (m6A) has become a research hotspot because of its critical roles in many fundamental biological processes and a variety of diseases. Therefore, it is important to evaluate the effect of variants on m6A modification, in order to gain a better understanding of them. Here, we report m6AVar (http://m6avar.renlab.org), a comprehensive da...

Bridging scales in polymer physics and processing

NARCIS (Netherlands)

Hütter, M.; Kröger, M.; Öttinger, H.C.; Schweizer, T.

2001-01-01

Understanding both the flow behavior of polymers during processing and the end-use properties offinished plastic products from a molecular picture of the constituent polymers has been a long-standing dreamin polymer engineering and science. It is the goal of our work in the Polymer Physics Group to

Physical education resources, class management, and student physical activity levels: a structure-process-outcome approach to evaluating physical education effectiveness.

Science.gov (United States)

Bevans, Katherine B; Fitzpatrick, Leslie-Anne; Sanchez, Betty M; Riley, Anne W; Forrest, Christopher

2010-12-01

This study was conducted to empirically evaluate specific human, curricular, and material resources that maximize student opportunities for physical activity during physical education (PE) class time. A structure-process-outcome model was proposed to identify the resources that influence the frequency of PE and intensity of physical activity during PE. The proportion of class time devoted to management was evaluated as a potential mediator of the relations between resource availability and student activity levels. Data for this cross-sectional study were collected from interviews conducted with 46 physical educators and the systematic observation of 184 PE sessions in 34 schools. Regression analyses were conducted to test for the main effects of resource availability and the mediating role of class management. Students who attended schools with a low student-to-physical educator ratio had more PE time and engaged in higher levels of physical activity during class time. Access to adequate PE equipment and facilities was positively associated with student activity levels. The availability of a greater number of physical educators per student was found to impact student activity levels by reducing the amount of session time devoted to class management. The identification of structure and process predictors of student activity levels in PE will support the allocation of resources and encourage instructional practices that best support increased student activity levels in the most cost-effective way possible. Implications for PE policies and programs are discussed. © 2010, American School Health Association.

[Specificities of the logopenic variant of primary progressive aphasia].

Science.gov (United States)

Magnin, E; Teichmann, M; Martinaud, O; Moreaud, O; Ryff, I; Belliard, S; Pariente, J; Moulin, T; Vandel, P; Démonet, J-F

2015-01-01

The logopenic variant of primary progressive aphasia is a syndrome with neuropsychological and linguistic specificities, including phonological loop impairment for which diagnosis is currently mainly based on the exclusion of the two other variants, semantic and nonfluent/agrammatic primary progressive aphasia. The syndrome may be underdiagnosed due (1) to mild language difficulties during the early stages of the disease or (2) to being mistaken for mild cognitive impairment or Alzheimer's disease when the evaluation of episodic memory is based on verbal material and (3) finally, it is not uncommon that the disorders are attributed to psychiatric co-morbidities such as, for example, anxiety. Moreover, compared to other variants of primary progressive aphasia, brain abnormalities are different. The left temporoparietal junction is initially affected. Neuropathology and biomarkers (cerebrospinal fluid, molecular amyloid nuclear imaging) frequently reveal Alzheimer's disease. Consequently this variant of primary progressive aphasia does not fall under the traditional concept of frontotemporal lobar degeneration. These distinctive features highlight the utility of correct diagnosis, classification, and use of biomarkers to show the neuropathological processes underlying logopenic primary progressive aphasia. The logopenic variant of primary progressive aphasia is a specific form of Alzheimer's disease frequently presenting a rapid decline; specific linguistic therapies are needed. Further investigation of this syndrome is needed to refine screening, improve diagnostic criteria and better understand the epidemiology and the biological mechanisms involved. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus.

Science.gov (United States)

Zhang, Xiao-Feng; Guo, Jiangbo; Zhang, Xiuchun; Meulia, Tea; Paul, Pierce; Madden, Laurence V; Li, Dawei; Qu, Feng

2015-10-20

Infection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs, and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants.

Screening of whole genome sequences identified high-impact variants for stallion fertility.

Science.gov (United States)

Schrimpf, Rahel; Gottschalk, Maren; Metzger, Julia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

2016-04-14

Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant

Semantic prioritization of novel causative genomic variants

KAUST Repository

Boudellioua, Imene

2017-04-17

Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.

Semantic prioritization of novel causative genomic variants

KAUST Repository

Boudellioua, Imene; Mohamad Razali, Rozaimi; Kulmanov, Maxat; Hashish, Yasmeen; Bajic, Vladimir B.; Goncalves-Serra, Eva; Schoenmakers, Nadia; Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert

2017-01-01

Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.

The application of the algorithm of the individualization of students’ physical education process

Directory of Open Access Journals (Sweden)

L.N. Barybina

2014-12-01

Full Text Available Purpose: theoretically and experimentally justify the use of the algorithm of physical education process individualization in universities taking into account the psychophysiological features of students. Material: the study involved 413 students. It was defined indicators of the level of physical fitness and functional status, psycho-physiological features. Results: it was worked out the algorithm of individualization of students’ physical education process. It was defined the structure of the complex preparedness and it was developed models of characteristics of students - representatives of different sports specializations. It was established that for the successful construction of the training process, it is necessary to combine the parameters of physical, functional training and physiological indicators into a single integral evaluation of the individual characteristics of students. It was shown that at the students of the experimental group was improved indicators of functional, psychophysiological capabilities and physical preparedness. Conclusions: the application of the algorithm of the individualization of process of physical education enhances the functionality of the students.

Advanced statistics to improve the physical interpretation of atomization processes

International Nuclear Information System (INIS)

Panão, Miguel R.O.; Radu, Lucian

2013-01-01

Highlights: ► Finite pdf mixtures improves physical interpretation of sprays. ► Bayesian approach using MCMC algorithm is used to find the best finite mixture. ► Statistical method identifies multiple droplet clusters in a spray. ► Multiple drop clusters eventually associated with multiple atomization mechanisms. ► Spray described by drop size distribution and not only its moments. -- Abstract: This paper reports an analysis of the physics of atomization processes using advanced statistical tools. Namely, finite mixtures of probability density functions, which best fitting is found using a Bayesian approach based on a Markov chain Monte Carlo (MCMC) algorithm. This approach takes into account eventual multimodality and heterogeneities in drop size distributions. Therefore, it provides information about the complete probability density function of multimodal drop size distributions and allows the identification of subgroups in the heterogeneous data. This allows improving the physical interpretation of atomization processes. Moreover, it also overcomes the limitations induced by analyzing the spray droplets characteristics through moments alone, particularly, the hindering of different natures of droplet formation. Finally, the method is applied to physically interpret a case-study based on multijet atomization processes

Behavioral and language variants of frontotemporal dementia: a review of key symptoms.

Science.gov (United States)

Laforce, Robert

2013-12-01

While recent advances in the development of neuroimaging and molecular biomarkers for studying neurodegenerative conditions have revolutionized the field, dementia remains a clinical diagnosis. No component of the diagnostic process is more crucial than obtaining a good history. Getting to know the first manifestations of the disease, tracking their evolution and functional impact, combined with a targeted neurological examination, further guides differential diagnosis. This paper summarizes the key symptoms of the behavioral and language variants of frontotemporal dementia. The behavioral variant of frontotemporal dementia (bvFTD) is characterized by severe changes in behavior and personality such as disinhibition, apathy, loss of empathy, or stereotypic behavior, leading to a loss of social competence. Executive functions are impaired, while memory and visuospatial skills are relatively better preserved. By contrast, the language variants or primary progressive aphasias (PPAs) are marked by prominent language disturbances that can be subclassified into a non-fluent/agrammatic variant (naPPA), a semantic variant (svPPA), and a logopenic variant (lvPPA). Although combined characterization of clinical, imaging, biological and genetic biomarkers is essential to establish a detailed diagnosis of such heterogeneous conditions, the author emphasizes the importance of accurate recognition of key symptoms that can lead to better identification of underlying neuropathology and appropriate treatment approaches.

Impaired Interoceptive Accuracy in Semantic Variant Primary Progressive Aphasia

Directory of Open Access Journals (Sweden)

Charles R. Marshall

2017-11-01

Full Text Available BackgroundInteroception (the perception of internal bodily sensations is strongly linked to emotional experience and sensitivity to the emotions of others in healthy subjects. Interoceptive impairment may contribute to the profound socioemotional symptoms that characterize frontotemporal dementia (FTD syndromes, but remains poorly defined.MethodsPatients representing all major FTD syndromes and healthy age-matched controls performed a heartbeat counting task as a measure of interoceptive accuracy. In addition, patients had volumetric MRI for voxel-based morphometric analysis, and their caregivers completed a questionnaire assessing patients’ daily-life sensitivity to the emotions of others.ResultsInteroceptive accuracy was impaired in patients with semantic variant primary progressive aphasia relative to healthy age-matched individuals, but not in behavioral variant frontotemporal dementia and nonfluent variant primary progressive aphasia. Impaired interoceptive accuracy correlated with reduced daily-life emotional sensitivity across the patient cohort, and with atrophy of right insula, cingulate, and amygdala on voxel-based morphometry in the impaired semantic variant group, delineating a network previously shown to support interoceptive processing in the healthy brain.ConclusionInteroception is a promising novel paradigm for defining mechanisms of reduced emotional reactivity, empathy, and self-awareness in neurodegenerative syndromes and may yield objective measures for these complex symptoms.

Swine Influenza/Variant Influenza Viruses

Science.gov (United States)

... Address What's this? Submit What's this? Submit Button Influenza Types Seasonal Avian Swine Variant Pandemic Other Information on Swine Influenza/Variant Influenza Virus Language: English (US) Español Recommend ...

Beta-glucosidase variants and polynucleotides encoding same

Science.gov (United States)

Wogulis, Mark; Harris, Paul; Osborn, David

2017-06-27

The present invention relates to beta-glucosidase variants, e.g. beta-glucosidase variants of a parent Family GH3A beta-glucosidase from Aspergillus fumigatus. The present invention also relates to polynucleotides encoding the beta-glucosidase variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the beta-glucosidase variants.

Advanced magnetic resonance imaging of the physical processes in human glioblastoma.

Science.gov (United States)

Kalpathy-Cramer, Jayashree; Gerstner, Elizabeth R; Emblem, Kyrre E; Andronesi, Ovidiu; Rosen, Bruce

2014-09-01

The most common malignant primary brain tumor, glioblastoma multiforme (GBM) is a devastating disease with a grim prognosis. Patient survival is typically less than two years and fewer than 10% of patients survive more than five years. Magnetic resonance imaging (MRI) can have great utility in the diagnosis, grading, and management of patients with GBM as many of the physical manifestations of the pathologic processes in GBM can be visualized and quantified using MRI. Newer MRI techniques such as dynamic contrast enhanced and dynamic susceptibility contrast MRI provide functional information about the tumor hemodynamic status. Diffusion MRI can shed light on tumor cellularity and the disruption of white matter tracts in the proximity of tumors. MR spectroscopy can be used to study new tumor tissue markers such as IDH mutations. MRI is helping to noninvasively explore the link between the molecular basis of gliomas and the imaging characteristics of their physical processes. We, here, review several approaches to MR-based imaging and discuss the potential for these techniques to quantify the physical processes in glioblastoma, including tumor cellularity and vascularity, metabolite expression, and patterns of tumor growth and recurrence. We conclude with challenges and opportunities for further research in applying physical principles to better understand the biologic process in this deadly disease. See all articles in this Cancer Research section, "Physics in Cancer Research." ©2014 American Association for Cancer Research.

The Process of Physics Teaching Assistants' Pedagogical Content Knowledge Development

Science.gov (United States)

Seung, Eulsun

2013-01-01

This study explored the process of physics teaching assistants' (TAs) PCK development in the context of teaching a new undergraduate introductory physics course. "Matter and Interactions" (M&I) has recently adopted a new introductory physics course that focuses on the application of a small number of fundamental physical…

Influence of different natural physical fields on biological processes

Science.gov (United States)

Mashinsky, A. L.

2001-01-01

In space flight conditions gravity, magnetic, and electrical fields as well as ionizing radiation change both in size, and in direction. This causes disruptions in the conduct of some physical processes, chemical reactions, and metabolism in living organisms. In these conditions organisms of different phylogenetic level change their metabolic reactions undergo changes such as disturbances in ionic exchange both in lower and in higher plants, changes in cell morphology for example, gyrosity in Proteus ( Proteus vulgaris), spatial disorientation in coleoptiles of Wheat ( Triticum aestivum) and Pea ( Pisum sativum) seedlings, mutational changes in Crepis ( Crepis capillaris) and Arabidopsis ( Arabidopsis thaliana) seedling. It has been found that even in the absence of gravity, gravireceptors determining spatial orientation in higher plants under terrestrial conditions are formed in the course of ontogenesis. Under weightlessness this system does not function and spatial orientation is determined by the light flux gradient or by the action of some other factors. Peculiarities of the formation of the gravireceptor apparatus in higher plants, amphibians, fish, and birds under space flight conditions have been observed. It has been found that the system in which responses were accompanied by phase transition have proven to be gravity-sensitive under microgravity conditions. Such reactions include also the process of photosynthesis which is the main energy production process in plants. In view of the established effects of microgravity and different natural physical fields on biological processes, it has been shown that these processes change due to the absence of initially rigid determination. The established biological effect of physical fields influence on biological processes in organisms is the starting point for elucidating the role of gravity and evolutionary development of various organisms on Earth.

Reflector antenna analysis using physical optics on Graphics Processing Units

DEFF Research Database (Denmark)

Borries, Oscar Peter; Sørensen, Hans Henrik Brandenborg; Dammann, Bernd

2014-01-01

The Physical Optics approximation is a widely used asymptotic method for calculating the scattering from electrically large bodies. It requires significant computational work and little memory, and is thus well suited for application on a Graphics Processing Unit. Here, we investigate the perform......The Physical Optics approximation is a widely used asymptotic method for calculating the scattering from electrically large bodies. It requires significant computational work and little memory, and is thus well suited for application on a Graphics Processing Unit. Here, we investigate...

Características morfoanatômicas da epiderme foliar de plantas variantes e não variantes somaclonais de bananeiras (Musa sp. Colla cv. Prata-anã cultivadas in vitro Morphoanatomical characteristics of the leaf epidermis of variant plants and somaclonal non-variants of banana trees (Musa sp. Colla cv. Prata-anã cultivated in vitro

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Guilherme Araújo Lacerda

2008-03-01

Full Text Available A variação somaclonal corresponde ao aparecimento de plantas anormais durante o processo de multiplicação in vitro, principalmente relacionada à estatura, no caso o gigantismo. O objetivo deste trabalho foi averiguar as diferenças morfoanatômicas da epiderme foliar na tentativa de diferenciar as plantas de 'Prata-anã' em relação aos seus variantes somaclonais. A análise por microscopia eletrônica de varredura mostrou uma diferença significativa entre o diâmetro polar dos estômatos da 'Prata-anã' não variante e suas variantes, ambas em condições in vitro, observando-se que o mesmo não ocorre para as plantas in vivo. O número médio de estômatos é menor nas plantas variantes somaclonais, porém sem diferenças significativas a não ser para a planta PIII. A descamação de cera é evidente somente nas plantas variantes de ambos os materiais (in vitro e in vivo. Conclui-se que os caracteres morfoanatômicos da epiderme foliar, como densidade estomática, diâmetro estomático polar e a uniformidade da cera atuam como marcadores morfológicos para caracterizar as plantas micropropagadas de 'Prata-anã' em relação aos seus variantes somaclonais para a característica gigantismo.Somaclonal variation corresponds to the emergence of abnormal plants during the process of multiplication in vitro, mainly related to stature, in the case the gigantism. The aim of this work was to discover morphoanatomical differences of the leaf epidermis in an attempt to differentiate plants of "Prata-anã" from their somaclonal variants. Analysis by scanning electronic microscopy showed significant difference between the polar diameter of the stomata of the "Prata-anã" non-variant and its variants, both in vitro. The same does not happen for plants in vivo. The average number of stomata is lower in the somaclonal variant plants, but without significant differences except for plant PIII. Wax peeling is only evident in the variant plants of both the

Time-resolved influences of functional DAT1 and COMT variants on visual perception and post-processing.

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Stephan Bender

Full Text Available BACKGROUND: Dopamine plays an important role in orienting and the regulation of selective attention to relevant stimulus characteristics. Thus, we examined the influences of functional variants related to dopamine inactivation in the dopamine transporter (DAT1 and catechol-O-methyltransferase genes (COMT on the time-course of visual processing in a contingent negative variation (CNV task. METHODS: 64-channel EEG recordings were obtained from 195 healthy adolescents of a community-based sample during a continuous performance task (A-X version. Early and late CNV as well as preceding visual evoked potential components were assessed. RESULTS: Significant additive main effects of DAT1 and COMT on the occipito-temporal early CNV were observed. In addition, there was a trend towards an interaction between the two polymorphisms. Source analysis showed early CNV generators in the ventral visual stream and in frontal regions. There was a strong negative correlation between occipito-temporal visual post-processing and the frontal early CNV component. The early CNV time interval 500-1000 ms after the visual cue was specifically affected while the preceding visual perception stages were not influenced. CONCLUSIONS: Late visual potentials allow the genomic imaging of dopamine inactivation effects on visual post-processing. The same specific time-interval has been found to be affected by DAT1 and COMT during motor post-processing but not motor preparation. We propose the hypothesis that similar dopaminergic mechanisms modulate working memory encoding in both the visual and motor and perhaps other systems.

Detonation Synthesis of Alpha-Variant Silicon Carbide

Science.gov (United States)

Langenderfer, Martin; Johnson, Catherine; Fahrenholtz, William; Mochalin, Vadym

2017-06-01

A recent research study has been undertaken to develop facilities for conducting detonation synthesis of nanomaterials. This process involves a familiar technique that has been utilized for the industrial synthesis of nanodiamonds. Developments through this study have allowed for experimentation with the concept of modifying explosive compositions to induce synthesis of new nanomaterials. Initial experimentation has been conducted with the end goal being synthesis of alpha variant silicon carbide (α-SiC) in the nano-scale. The α-SiC that can be produced through detonation synthesis methods is critical to the ceramics industry because of a number of unique properties of the material. Conventional synthesis of α-SiC results in formation of crystals greater than 100 nm in diameter, outside nano-scale. It has been theorized that the high temperature and pressure of an explosive detonation can be used for the formation of α-SiC in the sub 100 nm range. This paper will discuss in detail the process development for detonation nanomaterial synthesis facilities, optimization of explosive charge parameters to maximize nanomaterial yield, and introduction of silicon to the detonation reaction environment to achieve first synthesis of nano-sized alpha variant silicon carbide.

Physical processes in spin polarized plasmas

International Nuclear Information System (INIS)

Kulsrud, R.M.; Valeo, E.J.; Cowley, S.

1984-05-01

If the plasma in a nuclear fusion reactor is polarized, the nuclear reactions are modified in such a way as to enhance the reactor performance. We calculate in detail the modification of these nuclear reactions by different modes of polarization of the nuclear fuel. We also consider in detail the various physical processes that can lead to depolarization and show that they are by and large slow enough that a high degree of polarization can be maintained

Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

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Mengmeng Du

Full Text Available Genome-wide association studies (GWAS have identified many common single nucleotide polymorphisms (SNPs associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs. We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33. We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

Science.gov (United States)

Sendorek, Dorota H; Caloian, Cristian; Ellrott, Kyle; Bare, J Christopher; Yamaguchi, Takafumi N; Ewing, Adam D; Houlahan, Kathleen E; Norman, Thea C; Margolin, Adam A; Stuart, Joshua M; Boutros, Paul C

2018-01-31

The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs) predictions made by 21 teams as part of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. The median somatic SNV prediction set contained 4325 somatic SNVs and leaked one germline polymorphism. The level of germline leakage was inversely correlated with somatic SNV prediction accuracy and positively correlated with the amount of infiltrating normal cells. The specific germline variants leaked differed by tumour and algorithm. To aid in quantitation and correction of leakage, we created a tool, called GermlineFilter, for use in public-facing somatic SNV databases. The potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identification event could reshape public perceptions of the values of genomic data sharing. We find that modern somatic SNV prediction pipelines have low germline-leakage rates, which can be further reduced, especially for cloud-sharing, using pre-filtering software.

Graphene growth process modeling: a physical-statistical approach

Science.gov (United States)

Wu, Jian; Huang, Qiang

2014-09-01

As a zero-band semiconductor, graphene is an attractive material for a wide variety of applications such as optoelectronics. Among various techniques developed for graphene synthesis, chemical vapor deposition on copper foils shows high potential for producing few-layer and large-area graphene. Since fabrication of high-quality graphene sheets requires the understanding of growth mechanisms, and methods of characterization and control of grain size of graphene flakes, analytical modeling of graphene growth process is therefore essential for controlled fabrication. The graphene growth process starts with randomly nucleated islands that gradually develop into complex shapes, grow in size, and eventually connect together to cover the copper foil. To model this complex process, we develop a physical-statistical approach under the assumption of self-similarity during graphene growth. The growth kinetics is uncovered by separating island shapes from area growth rate. We propose to characterize the area growth velocity using a confined exponential model, which not only has clear physical explanation, but also fits the real data well. For the shape modeling, we develop a parametric shape model which can be well explained by the angular-dependent growth rate. This work can provide useful information for the control and optimization of graphene growth process on Cu foil.

Process evaluation of a worksite social and physical environmental intervention

NARCIS (Netherlands)

Coffeng, J.K.; Hendriksen, I.J.M.; Mechelen, W. van; Boot, C.R.L.

2013-01-01

OBJECTIVE:: To evaluate the process of implementation of a social and physical environmental intervention and to explore differences regarding this process between both interventions. METHODS:: Context, recruitment, dose delivered, fidelity, reach, dose received, satisfaction, and implementation

Acute physical exercise affected processing efficiency in an auditory attention task more than processing effectiveness.

Science.gov (United States)

Dutke, Stephan; Jaitner, Thomas; Berse, Timo; Barenberg, Jonathan

2014-02-01

Research on effects of acute physical exercise on performance in a concurrent cognitive task has generated equivocal evidence. Processing efficiency theory predicts that concurrent physical exercise can increase resource requirements for sustaining cognitive performance even when the level of performance is unaffected. This hypothesis was tested in a dual-task experiment. Sixty young adults worked on a primary auditory attention task and a secondary interval production task while cycling on a bicycle ergometer. Physical load (cycling) and cognitive load of the primary task were manipulated. Neither physical nor cognitive load affected primary task performance, but both factors interacted on secondary task performance. Sustaining primary task performance under increased physical and/or cognitive load increased resource consumption as indicated by decreased secondary task performance. Results demonstrated that physical exercise effects on cognition might be underestimated when only single task performance is the focus.

Introduction of a pyramid guiding process for general musculoskeletal physical rehabilitation

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Stark Timothy W

2006-06-01

Full Text Available Abstract Successful instruction of a complicated subject as Physical Rehabilitation demands organization. To understand principles and processes of such a field demands a hierarchy of steps to achieve the intended outcome. This paper is intended to be an introduction to a proposed pyramid scheme of general physical rehabilitation principles. The purpose of the pyramid scheme is to allow for a greater understanding for the student and patient. As the respected Food Guide Pyramid accomplishes, the student will further appreciate and apply supported physical rehabilitation principles and the patient will understand that there is a progressive method to their functional healing process.

Annotating pathogenic non-coding variants in genic regions.

Science.gov (United States)

Gelfman, Sahar; Wang, Quanli; McSweeney, K Melodi; Ren, Zhong; La Carpia, Francesca; Halvorsen, Matt; Schoch, Kelly; Ratzon, Fanni; Heinzen, Erin L; Boland, Michael J; Petrovski, Slavé; Goldstein, David B

2017-08-09

Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes.While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

The r-process nucleosynthesis: Nuclear physics challenges

Energy Technology Data Exchange (ETDEWEB)

Goriely, S. [Institut d' Astronomie et d' Astrophysique, Universite Libre de Bruxelles Campus de la Plaine, CP 226, 1050 Brussels (Belgium)

2012-10-20

About half of the nuclei heavier than iron observed in nature are produced by the socalled rapid neutron capture process, or r-process, of nucleosynthesis. The identification of the astrophysics site and the specific conditions in which the r-process takes place remains, however, one of the still-unsolved mysteries of modern astrophysics. Another underlying difficulty associated with our understanding of the r-process concerns the uncertainties in the predictions of nuclear properties for the few thousands exotic neutron-rich nuclei involved and for which essentially no experimental data exist. The present contribution emphasizes some important future challenges faced by nuclear physics in this problem, particularly in the determination of the nuclear structure properties of exotic neutron-rich nuclei as well as their radiative neutron capture rates and their fission probabilities. These quantities are particularly relevant to determine the composition of the matter resulting from the r-process. Their impact on the r-abundance distribution resulting from the decompression of neutron star matter is discussed.

Histone variants and lipid metabolism

NARCIS (Netherlands)

Borghesan, Michela; Mazzoccoli, Gianluigi; Sheedfar, Fareeba; Oben, Jude; Pazienza, Valerio; Vinciguerra, Manlio

2014-01-01

Within nucleosomes, canonical histones package the genome, but they can be opportunely replaced with histone variants. The incorporation of histone variants into the nucleosome is a chief cellular strategy to regulate transcription and cellular metabolism. In pathological terms, cellular steatosis

Revision Vodcast Influence on Assessment Scores and Study Processes in Secondary Physics

Science.gov (United States)

Marencik, Joseph J.

A quasi-experimental switching replications design with matched participants was employed to determine the influence of revision vodcasts, or video podcasts, on students' assessment scores and study processes in secondary physics. This study satisfied a need for quantitative results in the area of vodcast influence on students' learning processes. Thirty-eight physics students in an urban Ohio public high school participated in the study. The students in one Physics class were paired with students in another Physics class through the matching characteristics of current student cumulative test score mean and baseline study process as measured by the Study Process Questionnaire (SPQ). Students in both classes were given identical pedagogic treatment and access to traditional revision tools except for the supplemental revision vodcasts given to the experimental group. After students in the experimental group viewed the revision vodcast for a particular topic, the assessment scores of the students in the experimental group were compared to the assessment scores of the control group through the direct-difference, D, test to determine any difference between the assessment score means of each group. The SPQ was given at the beginning of the experiment and after each physics assessment. The direct-difference method was again used to determine any difference between the SPQ deep approach scores of each group. The SPQ was also used to determine any correlative effects between study process and revision vodcast use on students' assessment scores through descriptive statistics and an analysis of variance (ANOVA) test. Analysis indicated that revision vodcast use significantly increased students' assessment scores (p.05). There were no significant correlative effects of revision vodcast use and study processes on students' assessment scores (p>.05). This study offers educators the empirical support to devote the necessary effort, time, and resources into developing successful

CLEVER: Clique-Enumerating Variant Finder

NARCIS (Netherlands)

Marschall, T.; Costa, I.; Canzar, S.; bauer, m; Klau, G.W.; Schliep, A.; Schönhuth, A.

2012-01-01

Motivation: Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most

Physical activity across the curriculum: year one process evaluation results

Directory of Open Access Journals (Sweden)

Sullivan Debra K

2008-07-01

Full Text Available Abstract Background Physical Activity Across the Curriculum (PAAC is a 3-year elementary school-based intervention to determine if increased amounts of moderate intensity physical activity performed in the classroom will diminish gains in body mass index (BMI. It is a cluster-randomized, controlled trial, involving 4905 children (2505 intervention, 2400 control. Methods We collected both qualitative and quantitative process evaluation data from 24 schools (14 intervention and 10 control, which included tracking teacher training issues, challenges and barriers to effective implementation of PAAC lessons, initial and continual use of program specified activities, and potential competing factors, which might contaminate or lessen program effects. Results Overall teacher attendance at training sessions showed exceptional reach. Teachers incorporated active lessons on most days, resulting in significantly greater student physical activity levels compared to controls (p Conclusion In the first year of the PAAC intervention, process evaluation results were instrumental in identifying successes and challenges faced by teachers when trying to modify existing academic lessons to incorporate physical activity.

a Variant of Lsd-Slam Capable of Processing High-Speed Low-Framerate Monocular Datasets

Science.gov (United States)

Schmid, S.; Fritsch, D.

2017-11-01

We develop a new variant of LSD-SLAM, called C-LSD-SLAM, which is capable of performing monocular tracking and mapping in high-speed low-framerate situations such as those of the KITTI datasets. The methods used here are robust against the influence of erronously triangulated points near the epipolar direction, which otherwise causes tracking divergence.

Word Variant Identification in Old French

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Peter Willett

1997-01-01

Full Text Available Increasing numbers of historical texts are available in machine-readable form, which retain the original spelling, which can be very different from the modern-day equivalents due to the natural evolution of a language, and because the concept of standardisation in spelling is comparatively modern. Among medieval vernacular writers, the same word could be spelled in different ways and the same author (or scribe might even use several alternative spellings in the same passage. Thus, we do not know,a priori, how many variant forms of a particular word there are in such texts, let alone what these variants might be. Searching on the modern equivalent, or even the commonest historical variant, of a particular word may thus fail to retrieve an appreciable number of occurrences unless the searcher already has an extensive knowledge of the language of the documents. Moreover, even specialist scholars may be unaware of some idiosyncratic variants. Here, we consider the use of computer methods to retrieve variant historical spellings.

Physical activity attenuates the influence of FTO variants on obesity risk: a meta-analysis of 218,166 adults and 19,268 children.

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Tuomas O Kilpeläinen

2011-11-01

Full Text Available The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute unambiguously whether PA attenuates the association of FTO with obesity risk, we meta-analyzed data from 45 studies of adults (n = 218,166 and nine studies of children and adolescents (n = 19,268.All studies identified to have data on the FTO rs9939609 variant (or any proxy [r(2>0.8] and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were performed within each study by including the FTO×PA interaction term in an additive model, adjusting for age and sex. Subsequently, random effects meta-analysis was used to pool the interaction terms. In adults, the minor (A- allele of rs9939609 increased the odds of obesity by 1.23-fold/allele (95% CI 1.20-1.26, but PA attenuated this effect (p(interaction  = 0.001. More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio  = 1.22/allele, 95% CI 1.19-1.25 than in the inactive group (odds ratio  = 1.30/allele, 95% CI 1.24-1.36. No such interaction was found in children and adolescents.The association of the FTO risk allele with the odds of obesity is attenuated by 27% in physically active adults, highlighting the importance of PA in particular in those genetically predisposed to obesity.

TREM2 Variants in Alzheimer's Disease

Science.gov (United States)

Guerreiro, Rita; Wojtas, Aleksandra; Bras, Jose; Carrasquillo, Minerva; Rogaeva, Ekaterina; Majounie, Elisa; Cruchaga, Carlos; Sassi, Celeste; Kauwe, John S.K.; Younkin, Steven; Hazrati, Lilinaz; Collinge, John; Pocock, Jennifer; Lashley, Tammaryn; Williams, Julie; Lambert, Jean-Charles; Amouyel, Philippe; Goate, Alison; Rademakers, Rosa; Morgan, Kevin; Powell, John; St. George-Hyslop, Peter; Singleton, Andrew; Hardy, John

2013-01-01

BACKGROUND Homozygous loss-of-function mutations in TREM2, encoding the triggering receptor expressed on myeloid cells 2 protein, have previously been associated with an autosomal recessive form of early-onset dementia. METHODS We used genome, exome, and Sanger sequencing to analyze the genetic variability in TREM2 in a series of 1092 patients with Alzheimer's disease and 1107 controls (the discovery set). We then performed a meta-analysis on imputed data for the TREM2 variant rs75932628 (predicted to cause a R47H substitution) from three genomewide association studies of Alzheimer's disease and tested for the association of the variant with disease. We genotyped the R47H variant in an additional 1887 cases and 4061 controls. We then assayed the expression of TREM2 across different regions of the human brain and identified genes that are differentially expressed in a mouse model of Alzheimer's disease and in control mice. RESULTS We found significantly more variants in exon 2 of TREM2 in patients with Alzheimer's disease than in controls in the discovery set (P = 0.02). There were 22 variant alleles in 1092 patients with Alzheimer's disease and 5 variant alleles in 1107 controls (P<0.001). The most commonly associated variant, rs75932628 (encoding R47H), showed highly significant association with Alzheimer's disease (P<0.001). Meta-analysis of rs75932628 genotypes imputed from genomewide association studies confirmed this association (P = 0.002), as did direct genotyping of an additional series of 1887 patients with Alzheimer's disease and 4061 controls (P<0.001). Trem2 expression differed between control mice and a mouse model of Alzheimer's disease. CONCLUSIONS Heterozygous rare variants in TREM2 are associated with a significant increase in the risk of Alzheimer's disease. (Funded by Alzheimer's Research UK and others.) PMID:23150934

Physics-based signal processing algorithms for micromachined cantilever arrays

Science.gov (United States)

Candy, James V; Clague, David S; Lee, Christopher L; Rudd, Robert E; Burnham, Alan K; Tringe, Joseph W

2013-11-19

A method of using physics-based signal processing algorithms for micromachined cantilever arrays. The methods utilize deflection of a micromachined cantilever that represents the chemical, biological, or physical element being detected. One embodiment of the method comprises the steps of modeling the deflection of the micromachined cantilever producing a deflection model, sensing the deflection of the micromachined cantilever and producing a signal representing the deflection, and comparing the signal representing the deflection with the deflection model.

Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.

Science.gov (United States)

Mitsui, Jun; Fukuda, Yoko; Azuma, Kyo; Tozaki, Hirokazu; Ishiura, Hiroyuki; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

2010-07-01

We have recently found that multiple rare variants of the glucocerebrosidase gene (GBA) confer a robust risk for Parkinson disease, supporting the 'common disease-multiple rare variants' hypothesis. To develop an efficient method of identifying rare variants in a large number of samples, we applied multiplexed resequencing using a next-generation sequencer to identification of rare variants of GBA. Sixteen sets of pooled DNAs from six pooled DNA samples were prepared. Each set of pooled DNAs was subjected to polymerase chain reaction to amplify the target gene (GBA) covering 6.5 kb, pooled into one tube with barcode indexing, and then subjected to extensive sequence analysis using the SOLiD System. Individual samples were also subjected to direct nucleotide sequence analysis. With the optimization of data processing, we were able to extract all the variants from 96 samples with acceptable rates of false-positive single-nucleotide variants.

Study of USH1 splicing variants through minigenes and transcript analysis from nasal epithelial cells.

Directory of Open Access Journals (Sweden)

María José Aparisi

Full Text Available Usher syndrome type I (USH1 is an autosomal recessive disorder characterized by congenital profound deafness, vestibular areflexia and prepubertal retinitis pigmentosa. The first purpose of this study was to determine the pathologic nature of eighteen USH1 putative splicing variants found in our series and their effect in the splicing process by minigene assays. These variants were selected according to bioinformatic analysis. The second aim was to analyze the USH1 transcripts, obtained from nasal epithelial cells samples of our patients, in order to corroborate the observed effect of mutations by minigenes in patient's tissues. The last objective was to evaluate the nasal ciliary beat frequency in patients with USH1 and compare it with control subjects. In silico analysis were performed using four bioinformatic programs: NNSplice, Human Splicing Finder, NetGene2 and Spliceview. Afterward, minigenes based on the pSPL3 vector were used to investigate the implication of selected changes in the mRNA processing. To observe the effect of mutations in the patient's tissues, RNA was extracted from nasal epithelial cells and RT-PCR analyses were performed. Four MYO7A (c.470G>A, c.1342_1343delAG, c.5856G>A and c.3652G>A, three CDH23 (c.2289+1G>A, c.6049G>A and c.8722+1delG and one PCDH15 (c.3717+2dupTT variants were observed to affect the splicing process by minigene assays and/or transcripts analysis obtained from nasal cells. Based on our results, minigenes are a good approach to determine the implication of identified variants in the mRNA processing, and the analysis of RNA obtained from nasal epithelial cells is an alternative method to discriminate neutral Usher variants from those with a pathogenic effect on the splicing process. In addition, we could observe that the nasal ciliated epithelium of USH1 patients shows a lower ciliary beat frequency than control subjects.

Locus Reference Genomic sequences: An improved basis for describing human DNA variants

KAUST Repository

Dalgleish, Raymond; Flicek, Paul; Cunningham, Fiona; Astashyn, Alex; Tully, Raymond E; Proctor, Glenn; Chen, Yuan; McLaren, William M; Larsson, Pontus; Vaughan, Brendan W; Bé roud, Christophe; Dobson, Glen; Lehvä slaiho, Heikki; Taschner, Peter EM; den Dunnen, Johan T; Devereau, Andrew; Birney, Ewan; Brookes, Anthony J; Maglott, Donna R

2010-01-01

As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

Locus Reference Genomic sequences: An improved basis for describing human DNA variants

KAUST Repository

Dalgleish, Raymond

2010-04-15

As our knowledge of the complexity of gene architecture grows, and we increase our understanding of the subtleties of gene expression, the process of accurately describing disease-causing gene variants has become increasingly problematic. In part, this is due to current reference DNA sequence formats that do not fully meet present needs. Here we present the Locus Reference Genomic (LRG) sequence format, which has been designed for the specifi c purpose of gene variant reporting. The format builds on the successful National Center for Biotechnology Information (NCBI) RefSeqGene project and provides a single-fi le record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants. In principle, LRGs can be created for any organism, not just human. In addition, we recognize the need to respect legacy numbering systems for exons and amino acids and the LRG format takes account of these. We hope that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute (EBI) - along with consistent use of the Human Genome Variation Society (HGVS)- approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants aff ecting human health. Further information can be found on the LRG web site (http://www.lrg-sequence.org). 2010 Dalgleish et al.; licensee BioMed Central Ltd.

Research on spatial-variant property of bistatic ISAR imaging plane of space target

International Nuclear Information System (INIS)

Guo Bao-Feng; Wang Jun-Ling; Gao Mei-Guo

2015-01-01

The imaging plane of inverse synthetic aperture radar (ISAR) is the projection plane of the target. When taking an image using the range-Doppler theory, the imaging plane may have a spatial-variant property, which causes the change of scatter’s projection position and results in migration through resolution cells. In this study, we focus on the spatial-variant property of the imaging plane of a three-axis-stabilized space target. The innovative contributions are as follows. 1) The target motion model in orbit is provided based on a two-body model. 2) The instantaneous imaging plane is determined by the method of vector analysis. 3) Three Euler angles are introduced to describe the spatial-variant property of the imaging plane, and the image quality is analyzed. The simulation results confirm the analysis of the spatial-variant property. The research in this study is significant for the selection of the imaging segment, and provides the evidence for the following data processing and compensation algorithm. (paper)

Non-replication of genome-wide based associations between common variants in INSIG2 and PFKP and obesity in studies of 18,014 Danes

DEFF Research Database (Denmark)

Sandholt, Camilla Helene; Mogensen, Mette S; Borch-Johnsen, Knut

2008-01-01

The INSIG2 rs7566605 and PFKP rs6602024 polymorphisms have been identified as obesity gene variants in genome-wide association (GWA) studies. However, replication has been contradictory for both variants. The aims of this study were to validate these obesity-associations through case-control stud......The INSIG2 rs7566605 and PFKP rs6602024 polymorphisms have been identified as obesity gene variants in genome-wide association (GWA) studies. However, replication has been contradictory for both variants. The aims of this study were to validate these obesity-associations through case......-control studies and analyses of obesity-related quantitative traits. Moreover, since environmental and genetic factors may modulate the impact of a genetic variant, we wanted to perform such interaction analyses. We focused on physical activity as an environmental risk factor, and on the GWA identified obesity...

Macro-economic effects of two policy variants to reduce greenhouse gas emission

International Nuclear Information System (INIS)

Vromans, M.W.A.M.

1998-10-01

The macro-economic effects of two variants for reducing CO2-emissions by yearly 2% in the period 2000-2020 have been calculated. Regulations as limiting the maximum speed to 90 km/h on motorways and lowering the standards of energy use of houses form an important part of variant 1. In the second variant the competitive market policy plays a more important role. An increase of the existing small-user energy tax to four times the current level and an introduction of tradeable reduction certificates are among the policy measures. In both variants, but in variant 2 more than in variant 1, backstop-options, e.g. import of biomass and carbon dioxide storage, are added to further reduce the emissions. The effects on energy and the environment and the costs of the policy packages have been calculated by the Netherlands Energy Research Foundation (ECN). Those figures served as input for the CPB-calculations with the multi-sectoral model Athena. In variant 1 the volume of private consumption (an indicator for the material welfare loss) is, in 2020, 1.5% lower in comparison with the baseline scenario. GDP diminishes with 1 % and labour demand is 0.5% lower. As a consequence of the gradually increasing government subsidies to finance the extra costs of environmental investments and backstop-options the negative effects are increasing gradually too. This process will continue also after 2020 because the subsidies will be still growing after the scenario period. The negative effects of variant 2 in 2020 are about 50% higher than the results for variant 1. Private consumption decreases with 2.5%, GDP is 1.75% lower and employment diminishes with 0.75%. More subsidies for backstop-options, a higher increase of the small-user energy tax and a less positive effect because of less environmental investments, particularly less investments in dwellings, account for the more negative picture in comparison with the results for variant 1. The study ends with some points of discussion as

Greenhouse climate : from physical processes to a dynamic model

OpenAIRE

Bot, G.P.A.

1983-01-01

In this thesis greenhouse climate has been studied as the set of environmental conditions in a greenhouse in so far as they affect crop growth and development. In chapter 2 this set has been defined in terms of temperatures and vapour pressures. Moreover we have indicated which physical processes co-operate in the greenhouse. So the dependency of the greenhouse climate on the outside weather, the physical properties of the greenhouse construction and the way ventilation and heating is perform...

Levels of processing and picture memory: the physical superiority effect.

Science.gov (United States)

Intraub, H; Nicklos, S

1985-04-01

Six experiments studied the effect of physical orienting questions (e.g., "Is this angular?") and semantic orienting questions (e.g., "Is this edible?") on memory for unrelated pictures at stimulus durations ranging from 125-2,000 ms. Results ran contrary to the semantic superiority "rule of thumb," which is based primarily on verbal memory experiments. Physical questions were associated with better free recall and cued recall of a diverse set of visual scenes (Experiments 1, 2, and 4). This occurred both when general and highly specific semantic questions were used (Experiments 1 and 2). Similar results were obtained when more simplistic visual stimuli--photographs of single objects--were used (Experiments 5 and 6). As in the case of the semantic superiority effect with words, the physical superiority effect for pictures was eliminated or reversed when the same physical questions were repeated throughout the session (Experiments 4 and 6). Conflicts with results of previous levels of processing experiments with words and nonverbal stimuli (e.g., faces) are explained in terms of the sensory-semantic model (Nelson, Reed, & McEvoy, 1977). Implications for picture memory research and the levels of processing viewpoint are discussed.

Molecular Mechanisms of Disease Pathogenesis Differ in Krabbe Disease Variants

DEFF Research Database (Denmark)

Spratley, Samantha J; Hill, Chris H; Viuff, Agnete H

2016-01-01

different mutations have been identified in GALC that cause Krabbe disease but the mechanisms by which they cause disease remain unclear. We have generated monoclonal antibodies against full-length human GALC and used these to monitor the trafficking and processing of GALC variants in cell-based assays...

Evaluation of the role of SNCA variants in survival without neurological disease.

Directory of Open Access Journals (Sweden)

Michael G Heckman

Full Text Available A variety of definitions of successful aging have been proposed, many of which relate to longevity, freedom from disease and disability, or preservation of high physical and cognitive function. Many behavioral, biomedical, and psychological factors have been linked with these various measures of successful aging, however genetic predictors are less understood. Parkinson's disease (PD is an age-related neurodegenerative disorder, and variants in the α-synuclein gene (SNCA affect susceptibility to PD. This exploratory study examined whether SNCA variants may also promote successful aging as defined by survival without neurological disease.We utilized 769 controls without neurological disease (Mean age: 79 years, Range: 33-99 years and examined the frequency of 20 different SNCA variants across age groups using logistic regression models. We also included 426 PD cases to assess the effect of these variants on PD risk.There was a significant decline in the proportion of carriers of the minor allele of rs10014396 as age increased (P = 0.021, from 30% in controls younger than 60 to 14% in controls 90 years of age or older. Findings were similar for rs3775439, where the proportion of carriers of the minor allele declined from 32% in controls less than 60 years old to 19% in those 90 or older (P = 0.025. A number of SNCA variants, not including rs10014396 or rs3775439, were significantly associated with susceptibility to PD.In addition to its documented roles in PD and α-synucleinopathies, our results suggest that SNCA has a role in survival free of neurological disease. Acknowledging that our findings would not have withstood correction for multiple testing, validation in an independent series of aged neurologically normal controls is needed.

Issues in Process Variants Mining

NARCIS (Netherlands)

Li, C.; Reichert, M.U.; Wombacher, Andreas

In today's dynamic business world economic success of an enterprise increasingly depends on its ability to react to internal and external changes in a quick and flexible way. In response to this need, process-aware information systems (PAIS) emerged, which support the modeling, orchestration and

Stochastic processes in chemical physics

CERN Document Server

Shuler, K E

2009-01-01

The Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.

One Size Does Not Fit All: Face Emotion Processing Impairments in Semantic Dementia, Behavioural-Variant Frontotemporal Dementia and Alzheimer?s Disease Are Mediated by Distinct Cognitive Deficits

OpenAIRE

Miller, Laurie A.; Hsieh, Sharpley; Lah, Suncica; Savage, Sharon; Hodges, John R.; Piguet, Olivier

2011-01-01

Patients with frontotemporal dementia (both behavioural variant [bvFTD] and semantic dementia [SD]) as well as those with Alzheimer's disease (AD) show deficits on tests of face emotion processing, yet the mechanisms underlying these deficits have rarely been explored. We compared groups of patients with bvFTD (n = 17), SD (n = 12) or AD (n = 20) to an age- and education-matched group of healthy control subjects (n = 36) on three face emotion processing tasks (Ekman 60, Emotion Matching and E...

Quantum Processes and Dynamic Networks in Physical and Biological Systems.

Science.gov (United States)

Dudziak, Martin Joseph

Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

Process depending morphology and resulting physical properties of TPU

Energy Technology Data Exchange (ETDEWEB)

Frick, Achim, E-mail: achim.frick@hs-aalen.de; Spadaro, Marcel, E-mail: marcel.spadaro@hs-aalen.de [Institute of Polymer Science and Processing (iPSP), Aalen University (Germany)

2015-12-17

Thermoplastic polyurethane (TPU) is a rubber like material with outstanding properties, e.g. for seal applications. TPU basically provides high strength, low frictional behavior and excellent wear resistance. Though, due to segmented structure of TPU, which is composed of hard segments (HSs) and soft segments (SSs), physical properties depend strongly on the morphological arrangement of the phase separated HSs at a certain ratio of HSs to SSs. It is obvious that the TPU deforms differently depending on its bulk morphology. Basically, the morphology can either consist of HSs segregated into small domains, which are well dispersed in the SS matrix or of few strongly phase separated large size HS domains embedded in the SS matrix. The morphology development is hardly ruled by the melt processing conditions of the TPU. Depending on the morphology, TPU provides quite different physical properties with respect to strength, deformation behavior, thermal stability, creep resistance and tribological performance. The paper deals with the influence of important melt processing parameters, such as temperature, pressure and shear conditions, on the resulting physical properties tested by tensile and relaxation experiments. Furthermore the morphology is studied employing differential scanning calorimeter (DSC), transmission light microscopy (TLM), scanning electron beam microscopy (SEM) and transmission electron beam microscopy (TEM) investigations. Correlations between processing conditions and resulting TPU material properties are elaborated. Flow and shear simulations contribute to the understanding of thermal and flow induced morphology development.

Tech-X Corporation releases simulation code for solving complex problems in plasma physics : VORPAL code provides a robust environment for simulating plasma processes in high-energy physics, IC fabrications and material processing applications

CERN Multimedia

2005-01-01

Tech-X Corporation releases simulation code for solving complex problems in plasma physics : VORPAL code provides a robust environment for simulating plasma processes in high-energy physics, IC fabrications and material processing applications

Combined analyses of 20 common obesity susceptibility variants

DEFF Research Database (Denmark)

Sandholt, Camilla Helene; Sparsø, Thomas; Grarup, Niels

2010-01-01

Genome-wide association studies and linkage studies have identified 20 validated genetic variants associated with obesity and/or related phenotypes. The variants are common, and they individually exhibit small-to-modest effect sizes.......Genome-wide association studies and linkage studies have identified 20 validated genetic variants associated with obesity and/or related phenotypes. The variants are common, and they individually exhibit small-to-modest effect sizes....

Cough Variant Asthma in Medical Outpatient Department of a Tertiary Care Hospital in Bangladesh

Directory of Open Access Journals (Sweden)

Rukhsana Parvin

2013-01-01

Full Text Available Background: Cough variant asthma (CVA is a subset of asthma where the only symptom is chronic persistent cough. Many cases go unrecognized due to lack of proper evaluation. Response to asthma medication with features supportive of airway hypersensitivity helps in management of this disease. Objective: To find out the proportion of cough variant asthma among the patients attending medicine outpatient department of Enam Medical College, Savar, Dhaka. Materials and Methods: This cross sectional study was conducted in Enam Medical College Hospital, Savar, Dhaka over a period of two years from July 2009 to July 2011. Cough variant asthma was diagnosed mainly on clinical ground as chronic cough without wheezing, fever, weight loss, shortness of breath or sputum or any other apparent cause that persisted for more than eight weeks with absolutely normal physical examination of chest, normal chest radiography and blood count except raised eosinophil count and IgE level. Patients who met these criteria were given 2 weeks course of inhaler beclomethasone propionate and were assessed for improvement. Those who improved after steroid inhalation were categorised as having cough variant asthma. Results: Out of purposively selected 148 patients complaining only of chronic dry cough for more than eight weeks, 92 patients met the primary selection criteria for cough variant asthma. These 92 patients were given 2 weeks trial of 250 ìgm beclomethasone inhalation twice daily. Seventy nine patients reported almost complete recovery from chronic cough after 2 weeks and were categorized as having CVA. Thirteen patients did not improve and were not categorized as CVA. Conclusion: These findings suggest that cough variant asthma is the most common among the patients with chronic cough not due to any apparent cause. The efficacy of inhaled corticosteroid suggests that early intervention is effective in the treatment of this disease.

Stochastic processes from physics to finance

CERN Document Server

Paul, Wolfgang

2013-01-01

This book introduces the theory of stochastic processes with applications taken from physics and finance. Fundamental concepts like the random walk or Brownian motion but also Levy-stable distributions are discussed. Applications are selected to show the interdisciplinary character of the concepts and methods. In the second edition of the book a discussion of extreme events ranging from their mathematical definition to their importance for financial crashes was included. The exposition of basic notions of probability theory and the Brownian motion problem as well as the relation between conservative diffusion processes and quantum mechanics is expanded. The second edition also enlarges the treatment of financial markets. Beyond a presentation of geometric Brownian motion and the Black-Scholes approach to option pricing as well as the econophysics analysis of the stylized facts of financial markets, an introduction to agent based modeling approaches is given.

Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana.

Science.gov (United States)

McAllister, Chandra H; Good, Allen G

2015-01-01

Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.

3D physical modeling for patterning process development

Science.gov (United States)

Sarma, Chandra; Abdo, Amr; Bailey, Todd; Conley, Will; Dunn, Derren; Marokkey, Sajan; Talbi, Mohamed

2010-03-01

In this paper we will demonstrate how a 3D physical patterning model can act as a forensic tool for OPC and ground-rule development. We discuss examples where the 2D modeling shows no issues in printing gate lines but 3D modeling shows severe resist loss in the middle. In absence of corrective measure, there is a high likelihood of line discontinuity post etch. Such early insight into process limitations of prospective ground rules can be invaluable for early technology development. We will also demonstrate how the root cause of broken poly-line after etch could be traced to resist necking in the region of STI step with the help of 3D models. We discuss different cases of metal and contact layouts where 3D modeling gives an early insight in to technology limitations. In addition such a 3D physical model could be used for early resist evaluation and selection for required ground-rule challenges, which can substantially reduce the cycle time for process development.

Upper ocean physical processes in the Tropical Indian Ocean

Digital Repository Service at National Institute of Oceanography (India)

Rao, L.V.G.; Ram, P.S.

This monograph is the outcome of an attempt by the authors to present a synthesis of the studies on physical processes in the Tropical Indian Ocean (TIO) in relation to air-sea interaction, monsoon/climate variability and biological productivity...

Signal processing approaches to secure physical layer communications in multi-antenna wireless systems

CERN Document Server

Hong, Y-W Peter; Kuo, C-C Jay

2013-01-01

This book introduces various signal processing approaches to enhance physical layer secrecy in multi-antenna wireless systems. Wireless physical layer secrecy has attracted much attention in recent years due to the broadcast nature of the wireless medium and its inherent vulnerability to eavesdropping. While most articles on physical layer secrecy focus on the information-theoretic aspect, we focus specifically on the signal processing aspects, including beamforming and precoding techniques for data transmission and discriminatory training schemes for channel estimation. The discussions will c

Process Variations and Probabilistic Integrated Circuit Design

CERN Document Server

Haase, Joachim

2012-01-01

Uncertainty in key parameters within a chip and between different chips in the deep sub micron era plays a more and more important role. As a result, manufacturing process spreads need to be considered during the design process.  Quantitative methodology is needed to ensure faultless functionality, despite existing process variations within given bounds, during product development.   This book presents the technological, physical, and mathematical fundamentals for a design paradigm shift, from a deterministic process to a probability-orientated design process for microelectronic circuits.  Readers will learn to evaluate the different sources of variations in the design flow in order to establish different design variants, while applying appropriate methods and tools to evaluate and optimize their design.  Trains IC designers to recognize problems caused by parameter variations during manufacturing and to choose the best methods available to mitigate these issues during the design process; Offers both qual...

Health physics aspects of processing EBR-I coolant

International Nuclear Information System (INIS)

Burke, L.L.; Thalgott, J.O.; Poston, J.W. Jr.

1998-01-01

The sodium-potassium reactor coolant removed from the Experimental Breeder Reactor Number One after a partial reactor core meltdown had been stored at the Idaho National Engineering and Environmental Laboratory for 40 years. The State of Idaho considered this waste the most hazardous waste stored in the state and required its processing. The reactor coolant was processed in three phases. The first phase converted the alkali metal into a liquid sodium-potassium hydroxide. The second phase converted this caustic to a liquid sodium-potassium carbonate. The third phase solidified the sodium-potassium carbonate into a form acceptable for land disposal. Health physics aspects and dose received during each phase of the processing are discussed

Detectors and signal processing for high-energy physics

International Nuclear Information System (INIS)

Rehak, P.

1981-01-01

Basic principles of the particle detection and signal processing for high-energy physics experiments are presented. It is shown that the optimum performance of a properly designed detector system is not limited by incidental imperfections, but solely by more fundamental limitations imposed by the quantum nature and statistical behavior of matter. The noise sources connected with the detection and signal processing are studied. The concepts of optimal filtering and optimal detector/amplifying device matching are introduced. Signal processing for a liquid argon calorimeter is analyzed in some detail. The position detection in gas counters is studied. Resolution in drift chambers for the drift coordinate measurement as well as the second coordinate measurement is discussed

Physical quality of grains subjected to moistening and drying processes for marketing

Directory of Open Access Journals (Sweden)

Paulo C. Coradi

Full Text Available ABSTRACT The aim was to evaluate the physical quality of conventional and transgenic corn grains, through drying and wetting processes for marketing. The experimental design was completely randomized in a factorial scheme (7 x 3 x 2, corresponding to seven drying times (0, 20, 40, 60, 80, 100 and 120 min, three temperatures of the drying air (80, 100 and 120 °C and two hybrids of corn (conventional AG 1051 and transgenic Herculex@ 30S31H. Grain drying was held in convection oven with forced air ventilation while the wetting was done in a B.O.D chamber. The water movement in the grain, the volume and the electrical conductivity were evaluated periodically. The results showed that the transgenic corn grain reduced the negative effects of drying and moistening on the physical quality. The increase in drying air temperature accelerated the physical deterioration of conventional and transgenic corn grains. The increase in water content by the moistening process caused losses in grain physical quality, similar to the drying process, for both the conventional and transgenic corn grains.

Novel atomic force microscopy based biopanning for isolation of morphology specific reagents against TDP-43 variants in amyotrophic lateral sclerosis.

Science.gov (United States)

Williams, Stephanie M; Venkataraman, Lalitha; Tian, Huilai; Khan, Galam; Harris, Brent T; Sierks, Michael R

2015-02-12

Because protein variants play critical roles in many diseases including TDP-43 in Amyotrophic Lateral Sclerosis (ALS), alpha-synuclein in Parkinson's disease and beta-amyloid and tau in Alzheimer's disease, it is critically important to develop morphology specific reagents that can selectively target these disease-specific protein variants to study the role of these variants in disease pathology and for potential diagnostic and therapeutic applications. We have developed novel atomic force microscopy (AFM) based biopanning techniques that enable isolation of reagents that selectively recognize disease-specific protein variants. There are two key phases involved in the process, the negative and positive panning phases. During the negative panning phase, phages that are reactive to off-target antigens are eliminated through multiple rounds of subtractive panning utilizing a series of carefully selected off-target antigens. A key feature in the negative panning phase is utilizing AFM imaging to monitor the process and confirm that all undesired phage particles are removed. For the positive panning phase, the target antigen of interest is fixed on a mica surface and bound phages are eluted and screened to identify phages that selectively bind the target antigen. The target protein variant does not need to be purified providing the appropriate negative panning controls have been used. Even target protein variants that are only present at very low concentrations in complex biological material can be utilized in the positive panning step. Through application of this technology, we acquired antibodies to protein variants of TDP-43 that are selectively found in human ALS brain tissue. We expect that this protocol should be applicable to generating reagents that selectively bind protein variants present in a wide variety of different biological processes and diseases.

Variant Review with the Integrative Genomics Viewer.

Science.gov (United States)

Robinson, James T; Thorvaldsdóttir, Helga; Wenger, Aaron M; Zehir, Ahmet; Mesirov, Jill P

2017-11-01

Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review features for both single-nucleotide variants and structural variants, with examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org Cancer Res; 77(21); e31-34. ©2017 AACR . ©2017 American Association for Cancer Research.

An integrative variant analysis suite for whole exome next-generation sequencing data

Directory of Open Access Journals (Sweden)

Challis Danny

2012-01-01

Full Text Available Abstract Background Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data. Results Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeline optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454. The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%. Conclusion We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for download at http://sourceforge.net/projects/atlas2/. In addition to a command line version, the suite has been integrated into the Genboree Workbench, allowing biomedical scientists with minimal informatics expertise to remotely call, view, and further analyze variants through a simple web interface. The existing genomic databases displayed via the Genboree browser also streamline the process from variant discovery to functional genomics analysis, resulting in an off-the-shelf toolkit for the broader community.

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.

Science.gov (United States)

Quang, Daniel; Chen, Yifei; Xie, Xiaohui

2015-03-01

Annotating genetic variants, especially non-coding variants, for the purpose of identifying pathogenic variants remains a challenge. Combined annotation-dependent depletion (CADD) is an algorithm designed to annotate both coding and non-coding variants, and has been shown to outperform other annotation algorithms. CADD trains a linear kernel support vector machine (SVM) to differentiate evolutionarily derived, likely benign, alleles from simulated, likely deleterious, variants. However, SVMs cannot capture non-linear relationships among the features, which can limit performance. To address this issue, we have developed DANN. DANN uses the same feature set and training data as CADD to train a deep neural network (DNN). DNNs can capture non-linear relationships among features and are better suited than SVMs for problems with a large number of samples and features. We exploit Compute Unified Device Architecture-compatible graphics processing units and deep learning techniques such as dropout and momentum training to accelerate the DNN training. DANN achieves about a 19% relative reduction in the error rate and about a 14% relative increase in the area under the curve (AUC) metric over CADD's SVM methodology. All data and source code are available at https://cbcl.ics.uci.edu/public_data/DANN/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Radiological/Health physics program assessement at Rocky Flats, the process

International Nuclear Information System (INIS)

Psomas, P.O.

1996-01-01

The Department of Energy, Rocky Flats Office, Safety and Health Group, Health Physics Team (HPT) is responsible for oversight of the Radiation Protection and Health Physics Program (RPHP) of the Integrating Management Contractor (IMC), Kaiser-Hill (K-H) operations at the Rocky Flats Environmental Technology Site (RFETS). As of 1 January 1996 the Rocky Flats Plant employed 300 DOE and 4,300 contractor personnel (K-H and their subcontractors). WSI is a subcontractor and provides plant security. To accomplish the RPHP program oversight HPT personnel developed a systematic methodology for performing a functional RPHP Assessment. The initial process included development of a flow diagram identifying all programmatic elements and assessment criteria documents. Formulation of plans for conducting interviews and performance of assessments constituted the second major effort. The generation of assessment reports was the final step, based on the results of this process. This assessment will be a 6 person-year effort, over the next three years. This process is the most comprehensive assessment of any Radiation Protection and Health Physics (RPHP) Program ever performed at Rocky Flats. The results of these efforts will establish a baseline for future RPHP Program assessments at RFETS. This methodology has been well-received by contractor personnel and creates no Privacy Act violations or other misunderstandings

Theoretical and methodological foundation of the process of students’ physical training of higher educational institutions

Directory of Open Access Journals (Sweden)

Pilipej L. P.

2013-02-01

Full Text Available Efficiency of the existent system of physical education is considered in the higher institutes of Ukraine. Information of unsatisfactory level of physical preparedness of university entrants and graduating students of higher institutes is resulted. The lacks of construction of process of physical education are shown on the basis of normatively-command approach. Absence of the programs, which take into account motivation and terms of activity of higher institutes, disparity the requirements of integration in the river-bed of the Bologna Process, is shown. The analysis of publications is resulted in accordance with the modern scientific paradigm of construction of the system of physical education of students on the basis of methodology of synergetics. Information of the questionnaire questioning is utillized in research. Cross-correlation connections are presented between elements of physical education systems, which influence on efficiency of process. The basic requirements of construction of process of physical education of students of institutes of higher are set.

Operative and informative nuclear-physical quality monitoring of technological process

International Nuclear Information System (INIS)

Sattarov, G.S.; Muzafarov, A.M.; Komilov, J.M.; Kadirov, F.; Kist, A.A.

2004-01-01

Full text: In Navoi region more than 40 years extraction of uranium and more than 35 years of gold are conducted. For the element analysis of ores and the technological products containing uranium and gold, various physical and chemical and nuclear-physical methods of the analysis are applied. The last possess a number of advantages, due to their high sensitivity, an opportunity of simultaneous definition elements with automation of process of the analysis and with expressness, necessary at the analysis of elements on short-living radionuclides. In the given work comparative characteristics of the operative control of technological process of extraction of gold, uranium and some rare elements with the help of nuclear-physical methods of the analysis of powder samples, a continuous stream of a pulp and solutions are presented. They are: the control of process of sorption leaching of gold; qualities of ores, gravity and fleet-concentrates methods x-ray spectral, x-ray-energy-disperse, radio display, gamma-absorption and neutron-activation analyses are related to them. Concrete examples of use of the developed techniques for research of geochemical behaviour of the basic and accompanying elements, for the control of technological process of extraction of gold, uranium and some rare and rare-earth elements (V, Sc, Mo, Re) from ores and intermediate products of manufacture are presented; for the analysis of uranium protoxide-oxide, and also for an estimation of a condition of tailing mines of the industrial enterprises

Germline Variants of Prostate Cancer in Japanese Families.

Directory of Open Access Journals (Sweden)

Takahide Hayano

Full Text Available Prostate cancer (PC is the second most common cancer in men. Family history is the major risk factor for PC. Only two susceptibility genes were identified in PC, BRCA2 and HOXB13. A comprehensive search of germline variants for patients with PC has not been reported in Japanese families. In this study, we conducted exome sequencing followed by Sanger sequencing to explore responsible germline variants in 140 Japanese patients with PC from 66 families. In addition to known susceptibility genes, BRCA2 and HOXB13, we identified TRRAP variants in a mutually exclusive manner in seven large PC families (three or four patients per family. We also found shared variants of BRCA2, HOXB13, and TRRAP from 59 additional small PC families (two patients per family. We identified two deleterious HOXB13 variants (F127C and G132E. Further exploration of the shared variants in rest of the families revealed deleterious variants of the so-called cancer genes (ATP1A1, BRIP1, FANCA, FGFR3, FLT3, HOXD11, MUTYH, PDGFRA, SMARCA4, and TCF3. The germline variant profile provides a new insight to clarify the genetic etiology and heterogeneity of PC among Japanese men.

Detecting rare variants in case-parents association studies.

Directory of Open Access Journals (Sweden)

Kuang-Fu Cheng

Full Text Available Despite the success of genome-wide association studies (GWASs in detecting common variants (minor allele frequency ≥0.05 many suggested that rare variants also contribute to the genetic architecture of diseases. Recently, researchers demonstrated that rare variants can show a strong stratification which may not be corrected by using existing methods. In this paper, we focus on a case-parents study and consider methods for testing group-wise association between multiple rare (and common variants in a gene region and a disease. All tests depend on the numbers of transmitted mutant alleles from parents to their diseased children across variants and hence they are robust to the effect of population stratification. We use extensive simulation studies to compare the performance of four competing tests: the largest single-variant transmission disequilibrium test (TDT, multivariable test, combined TDT, and a likelihood ratio test based on a random-effects model. We find that the likelihood ratio test is most powerful in a wide range of settings and there is no negative impact to its power performance when common variants are also included in the analysis. If deleterious and protective variants are simultaneously analyzed, the likelihood ratio test was generally insensitive to the effect directionality, unless the effects are extremely inconsistent in one direction.

Variants of glycoside hydrolases

Science.gov (United States)

Teter, Sarah [Davis, CA; Ward, Connie [Hamilton, MT; Cherry, Joel [Davis, CA; Jones, Aubrey [Davis, CA; Harris, Paul [Carnation, WA; Yi, Jung [Sacramento, CA

2011-04-26

The present invention relates to variants of a parent glycoside hydrolase, comprising a substitution at one or more positions corresponding to positions 21, 94, 157, 205, 206, 247, 337, 350, 373, 383, 438, 455, 467, and 486 of amino acids 1 to 513 of SEQ ID NO: 2, and optionally further comprising a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2 a substitution at one or more positions corresponding to positions 8, 22, 41, 49, 57, 113, 193, 196, 226, 227, 246, 251, 255, 259, 301, 356, 371, 411, and 462 of amino acids 1 to 513 of SEQ ID NO: 2, wherein the variants have glycoside hydrolase activity. The present invention also relates to nucleotide sequences encoding the variant glycoside hydrolases and to nucleic acid constructs, vectors, and host cells comprising the nucleotide sequences.

Physical processes in the Gulf of Kachchh: A review

Digital Repository Service at National Institute of Oceanography (India)

Vethamony, P.; Babu, M.T.

A brief review of various physical processes acting in the Gulf of Kachchh (GoK), which have prominent roles in Gulf dynamics, is presented in this article. The eddies present in the GoK confirm that they are permanent features of the Go...

Multiple lupus-associated ITGAM variants alter Mac-1 functions on neutrophils.

Science.gov (United States)

Zhou, Yebin; Wu, Jianming; Kucik, Dennis F; White, Nathan B; Redden, David T; Szalai, Alexander J; Bullard, Daniel C; Edberg, Jeffrey C

2013-11-01

Multiple studies have demonstrated that single-nucleotide polymorphisms (SNPs) in the ITGAM locus (including the nonsynonymous SNPs rs1143679, rs1143678, and rs1143683) are associated with systemic lupus erythematosus (SLE). ITGAM encodes the protein CD11b, a subunit of the β2 integrin Mac-1. The purpose of this study was to determine the effects of ITGAM genetic variation on the biologic functions of neutrophil Mac-1. Neutrophils from ITGAM-genotyped and -sequenced healthy donors were isolated for functional studies. The phagocytic capacity of neutrophil ITGAM variants was probed with complement-coated erythrocytes, serum-treated zymosan, heat-treated zymosan, and IgG-coated erythrocytes. The adhesion capacity of ITGAM variants, in adhering to either purified intercellular adhesion molecule 1 or tumor necrosis factor α-stimulated endothelial cells, was assessed in a flow chamber. Expression levels of total CD11b and activation of CD11b were assessed by flow cytometry. Mac-1-mediated neutrophil phagocytosis, determined in cultures with 2 different complement-coated particles, was significantly reduced in individuals with nonsynonymous variant alleles of ITGAM. This reduction in phagocytosis was related to variation at either rs1143679 (in the β-propeller region) or rs1143678/rs1143683 (highly linked SNPs in the cytoplasmic/calf-1 regions). Phagocytosis mediated by Fcγ receptors was also significantly reduced in donors with variant ITGAM alleles. Similarly, firm adhesion of neutrophils was significantly reduced in individuals with variant ITGAM alleles. These functional alterations were not attributable to differences in total receptor expression or activation. The nonsynonymous ITGAM variants rs1143679 and rs1143678/rs113683 contribute to altered Mac-1 function on neutrophils. These results underscore the need to consider multiple nonsynonymous SNPs when assessing the functional consequences of ITGAM variation on immune cell processes and the risk of SLE

Local binary patterns new variants and applications

CERN Document Server

Jain, Lakhmi; Nanni, Loris; Lumini, Alessandra

2014-01-01

This book introduces Local Binary Patterns (LBP), arguably one of the most powerful texture descriptors, and LBP variants. This volume provides the latest reviews of the literature and a presentation of some of the best LBP variants by researchers at the forefront of textual analysis research and research on LBP descriptors and variants. The value of LBP variants is illustrated with reported experiments using many databases representing a diversity of computer vision applications in medicine, biometrics, and other areas. There is also a chapter that provides an excellent theoretical foundation for texture analysis and LBP in particular. A special section focuses on LBP and LBP variants in the area of face recognition, including thermal face recognition. This book will be of value to anyone already in the field as well as to those interested in learning more about this powerful family of texture descriptors.

Nuclear Data Processing for Reactor Physics Calculation

International Nuclear Information System (INIS)

Suwoto; Zuhair; Pandiangan, Tumpal

2003-01-01

Nuclear data processing for reactor physics calculation has been done. Raw nuclear data cross-sections on file ENDF should be prepared and processed before it used in neutronic calculation. The processing code system such as NJOY-PC code has been used from linearization of nuclear cross-sections data and background contribution of resonance parameter (MF2) using RECONR module (0K) with energy range from 10 -5 to 10 7 eV. Afterward, the neutron cross-sections data should be processed and broadened to desire temperature (i.e. 293K) by using BROADR module. The Grouper and Therma modules will be applied for multi-groups calculation which suitable for WIMS/D4 (69 groups) and thermalization of nuclear constants. The final stage of processing nuclear cross-sections is updating WIMS/D4 library. The WIMSR module in NJOY-PC and WILLIE code will be applied in this stage. The evaluated nuclear data file, especially for 1 H 1 isotope, was taken from JENDL-3.2 and ENDF/B-VI for preliminary study. The results of nuclear data processing 1 H 1 shows that the old-WIMS (WIMS-lama) library have much discrepancies comparing with JENDL-3.2 or ENDF/B-VI files, especially in energy around 5 keV

Geneva University: Experiments in Physics: Hands-on Creative Processes

CERN Multimedia

Université de Genève

2011-01-01

Geneva University Physics Department 24, quai Ernest-Ansermet CH-1211 Geneva 4 Tel: (022) 379 62 73 Fax: (022) 379 69 92   Lundi 3 octobre 2011, 17h00 Ecole de Physique, Auditoire Stueckelberg «Experiments in Physics : Hands-on Creative Processes» Prof. Manfred Euler Leibniz-Institute for Mathematics and Science Education (IPN) University of Kiel, Deutschland Experiments play a variety of different roles in knowledge generation. The lecture will focus on the function of experiments as engines of intuition that foster insights into complex processes. The experimental presentations consider self-organization phenomena in various domains that range from the nanomechanics of biomolecules to perception and cognition. The inherent universality contributes to elucidating the enigmatic phenomenon of creativity. Une verrée en compagnie du conférencier sera offerte après le colloque.       &...

Determining Purpose of Academic Discipline “Physical Education” for Future Teachers

Directory of Open Access Journals (Sweden)

Ж. О. Цимбалюк

2016-09-01

Full Text Available The research objective is to determine the purpose of physical education in pedagogical higher educational institutions. Materials and methods. The research used: theoretical analysis and collation of scientific literature; study of guidelines and documents regulating the process of organizing and conducting the discipline “Physical Education” in a higher educational institution; questionnaires. The participants of the experiment were 60 first-year students (enrolled in 2015-2016 of the School of Ukrainian Language and Literature of H. S. Skovoroda Kharkiv National Pedagogical University. Research results. The analysis of the questionnaires revealed low rates of motivational variants in the choice of the sports section related to the future profession. The research specified the purpose of the discipline “Physical Education” in a pedagogical higher educational institution, and defined the health-preserving competence. Conclusions. The specific nature of the pedagogical profession requires that future teachers acquire the health-preserving competence within the discipline “Physical Education”, namely, the ability to maintain a general level of physical health needed to conduct social and professional activity.

Variant Creutzfeldt-Jakob Disease (vCJD)

Science.gov (United States)

... Form Controls Cancel Submit Search the CDC Variant Creutzfeldt-Jakob Disease (vCJD) Note: Javascript is disabled or is not ... gov . Recommend on Facebook Tweet Share Compartir Variant Creutzfeldt-Jakob disease (vCJD) is a prion disease that was first ...

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.

Gold processing residue from Jacobina Basin: chemical and physical properties

OpenAIRE

Lima, Luiz Rogério Pinho de Andrade; Bernardez, Letícia Alonso; Barbosa, Luís Alberto Dantas

2007-01-01

p. 848-852 Gold processing residues or tailings are found in several areas in the Itapicuru River region (Bahia, Brazil), and previous studies indicated significant heavy metals content in the river sediments. The present work focused on an artisanal gold processing residue found in a site from this region. Samples were taken from the processing residue heaps and used to perform a physical and chemical characterization study using X-ray diffraction, scanning electron microscopy, neutron...

Optical Properties Of Polymeric Films Of Bacteriorhodopsin And Its Functional Variants: New Materials For Optical Information Processing

Science.gov (United States)

Hampp, Norbert; Braeuchle, Christoph R.; Oesterhelt, Dieter

1990-01-01

Purple membrane (PM) from Halobacterium halobium consists of a two-dimensional crystal of the photochromic retinal protein bacteriorhodopsin (BR). Purple membrane embedded in inert polymer matrices can be used as reversible recording medium in holography. The thermal and photochemical stability (at least 100.000 recording cycles at room temperature), the high quantum yield (70%), the high resolution (~ 5000 lines/mm) and the wide spectral range (400-680 nm) of these films are promising features for any possible technical application. The variability of this material was restricted to chemical modifications of the chromophoric group for a long time. new class of BR based recording media is introduced by the availability of variants of BR with a modified amino acid sequence. After generation of a mutant strain PM variants can be easily produced by the same cultivation and purification procedures as the PM of the wildtype and therefore are available in virtually unlimited amounts, too. As an example the properties of PM-films containing the variant BR-326, which differs from the wildtype by a single amino acid, are reported here. The improved diffraction efficiency (~ 2-fold) and increased sensitivity (~ 50%) of films containing BR-326 give an impression of the new possibilities for optimizing reversible recording media by biochemical and gentechnological methods as an alternative or an addition to conventional chemical methods.

Image processing applications: From particle physics to society

International Nuclear Information System (INIS)

Sotiropoulou, C.-L.; Citraro, S.; Dell'Orso, M.; Luciano, P.; Gkaitatzis, S.; Giannetti, P.

2017-01-01

We present an embedded system for extremely efficient real-time pattern recognition execution, enabling technological advancements with both scientific and social impact. It is a compact, fast, low consumption processing unit (PU) based on a combination of Field Programmable Gate Arrays (FPGAs) and the full custom associative memory chip. The PU has been developed for real time tracking in particle physics experiments, but delivers flexible features for potential application in a wide range of fields. It has been proposed to be used in accelerated pattern matching execution for Magnetic Resonance Fingerprinting (biomedical applications), in real time detection of space debris trails in astronomical images (space applications) and in brain emulation for image processing (cognitive image processing). We illustrate the potentiality of the PU for the new applications.

Formations, anomalies and variants of the mediastinum and the lung roots in children, simulating enlarged intrathoracic lymph nodes

International Nuclear Information System (INIS)

Rabkin, I.Kh.; Borisova, N.K.

1983-01-01

Timely detection of enlarged intrathoracic lymph nodes is of great importance in pediatric practice. Meanwhile there exist various mediastinal and lung root as well as anomalies and variants of their development, which could imitate the mediastinal lymph node hyperplasia. Their diagnosis is individually designed employing a complex of X-ray methods. In recent years the anatomo-physiological development of thoracic organs in children and teenagers has been affected by the acceleration process. Under the latters' impact the phenomenon of an increase in the large pulmonary vessels appeared in children with signs of high physical development, which caused lung root dilatation and produced an impression of the intrathoracic lymph node enlargement. The Valsalva functional tests should be used in combination with X-ray research methods

Digital Signal Processing applied to Physical Signals

CERN Document Server

Alberto, Diego; Musa, L

2011-01-01

It is well known that many of the scientific and technological discoveries of the XXI century will depend on the capability of processing and understanding a huge quantity of data. With the advent of the digital era, a fully digital and automated treatment can be designed and performed. From data mining to data compression, from signal elaboration to noise reduction, a processing is essential to manage and enhance features of interest after every data acquisition (DAQ) session. In the near future, science will go towards interdisciplinary research. In this work there will be given an example of the application of signal processing to different fields of Physics from nuclear particle detectors to biomedical examinations. In Chapter 1 a brief description of the collaborations that allowed this thesis is given, together with a list of the publications co-produced by the author in these three years. The most important notations, definitions and acronyms used in the work are also provided. In Chapter 2, the last r...

Imaging pitfalls, normal anatomy, and anatomical variants that can simulate disease on cardiac imaging as demonstrated on multidetector computed tomography

International Nuclear Information System (INIS)

Terpenning, Silanath; White, Charles S

2015-01-01

Advances in computed tomography have led to continuous improvement in cardiac imaging. Dedicated postprocessing capabilities, faster scan times, and cardiac gating methods reveal details of normal cardiac anatomy and anatomic variants that can mimic pathologic conditions. This article will review normal cardiac anatomy and variants that can mimic disease. Radiologists should be familiar with normal cardiac anatomy and anatomic variants to avoid misinterpretation of normal findings for pathologic processes

System for measurements and data processing in neutron physics researches

International Nuclear Information System (INIS)

Kadashevich, V.I.; Kondurov, I.A.; Nikolaev, S.N.; Ryabov, Yu.F.

1976-01-01

A system of measuring and computing means created for automation of studies in the field of the neutron physics is discussed. Within the framework of this system each experiment is provided with its individual measuring station which consists of a set of analog and digital modules implemented in accordance with the CAMAC standard. On the higher level of this system there are measuring-computing centres (MCC) which simultaneously serve a number of physical installations. These MCCs are based on ''Minsk-22'' computers whose computational facilities are used for the preliminary processing and for creation of temporary data archives. In its turn, all the MCCs are users of the time-sharing system on the basis of the ''Minsk-32'' computers. This system extends possibilities for user's fast data processing, archive creation and provides transfer of required information to the main computing system based on the BESM-6 computer. Transfer of information and preliminary processing are performed by remote terminals with the help of a special directive language

Adaptive, maladaptive, mediational, and bidirectional processes of relational and physical aggression, relational and physical victimization, and peer liking.

Science.gov (United States)

Kawabata, Yoshito; Tseng, Wan-Ling; Crick, Nicki R

2014-01-01

A three-wave longitudinal study among ethnically diverse preadolescents (N = 597 at Time 1, ages 9-11) was conducted to examine adaptive, maladaptive, mediational, and bidirectional processes of relational and physical aggression, victimization, and peer liking indexed by peer acceptance and friendships. A series of nested structural equation models tested the hypothesized links among these peer-domain factors. It was hypothesized that (1) relational aggression trails both adaptive and maladaptive processes, linking to more peer victimization and more peer liking, whereas physical aggression is maladaptive, resulting in more peer victimization and less peer liking; (2) physical and relational victimization is maladaptive, relating to more aggression and less peer liking; (3) peer liking may be the social context that promotes relational aggression (not physical aggression), whereas peer liking may protect against peer victimization, regardless of its type; and (4) peer liking mediates the link between forms of aggression and forms of peer victimization. Results showed that higher levels of peer liking predicted relative increases in relational aggression (not physical aggression), which in turn led to more peer liking. On the other hand, more peer liking was predictive of relative decreases in relational aggression and relational victimization in transition to the next grade (i.e., fifth grade). In addition, relational victimization predicted relative increases in relational aggression and relative decreases in peer liking. Similarly, physical aggression was consistently and concurrently associated more physical victimization and was marginally predictive of relative increases in physical victimization in transition to the next grade. More peer liking predicted relative decreases in physical victimization, which resulted in lower levels of peer liking. The directionality and magnitude of these paths did not differ between boys and girls. © 2013 Wiley

Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia.

Science.gov (United States)

Sivley, R Michael; Sheehan, Jonathan H; Kropski, Jonathan A; Cogan, Joy; Blackwell, Timothy S; Phillips, John A; Bush, William S; Meiler, Jens; Capra, John A

2018-01-23

Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial distribution of missense variants in protein structures contains information about function and pathogenicity that can help prioritize variants of unknown significance (VUS) and elucidate the structural mechanisms leading to disease. To illustrate this approach in a clinical application, we analyzed 13 candidate missense variants in regulator of telomere elongation helicase 1 (RTEL1) identified in patients with Familial Interstitial Pneumonia (FIP). We curated pathogenic and neutral RTEL1 variants from the literature and public databases. We then used homology modeling to construct a 3D structural model of RTEL1 and mapped known variants into this structure. We next developed a pathogenicity prediction algorithm based on proximity to known disease causing and neutral variants and evaluated its performance with leave-one-out cross-validation. We further validated our predictions with segregation analyses, telomere lengths, and mutagenesis data from the homologous XPD protein. Our algorithm for classifying RTEL1 VUS based on spatial proximity to pathogenic and neutral variation accurately distinguished 7 known pathogenic from 29 neutral variants (ROC AUC = 0.85) in the N-terminal domains of RTEL1. Pathogenic proximity scores were also significantly correlated with effects on ATPase activity (Pearson r = -0.65, p = 0.0004) in XPD, a related helicase. Applying the algorithm to 13 VUS identified from sequencing of RTEL1 from patients predicted five out of six disease-segregating VUS to be pathogenic. We provide structural hypotheses regarding how these mutations may disrupt RTEL1 ATPase and helicase function. Spatial analysis of missense variation accurately classified candidate VUS in RTEL1 and suggests how such variants cause disease. Incorporating

Spin physics and inclusive processes at short distances

International Nuclear Information System (INIS)

Craigie, N.S.

1982-10-01

The following aspects of spin physics at short distances are studied: 1. the factorization theorem in perturbative QCD and helicity asymmetries in inclusive processes, 2. the effect of higher order radiative corrections on helicity asymmetries, 3. the higher order power mechanism and spin asymmetries, 4. difficulties in understanding transverse spin in perturbative QCD, 5. helicity asymmetries of short distances as a means of recognizing supersymmetric interactions. Experiments are suggested for the verification of theoretical conclusions. Although spin-physics at short distances is difficult to demonstrate experimentally it may provide a valuable tool to show how perturbative QCD operates in the presence of the non-perturbative hadronic structure. It may also prove valuable to show new interactions which might occur at very short distances

Data-variant kernel analysis

CERN Document Server

Motai, Yuichi

2015-01-01

Describes and discusses the variants of kernel analysis methods for data types that have been intensely studied in recent years This book covers kernel analysis topics ranging from the fundamental theory of kernel functions to its applications. The book surveys the current status, popular trends, and developments in kernel analysis studies. The author discusses multiple kernel learning algorithms and how to choose the appropriate kernels during the learning phase. Data-Variant Kernel Analysis is a new pattern analysis framework for different types of data configurations. The chapters include

An integrated numerical and physical modeling system for an enhanced in situ bioremediation process

International Nuclear Information System (INIS)

Huang, Y.F.; Huang, G.H.; Wang, G.Q.; Lin, Q.G.; Chakma, A.

2006-01-01

Groundwater contamination due to releases of petroleum products is a major environmental concern in many urban districts and industrial zones. Over the past years, a few studies were undertaken to address in situ bioremediation processes coupled with contaminant transport in two- or three-dimensional domains. However, they were concentrated on natural attenuation processes for petroleum contaminants or enhanced in situ bioremediation processes in laboratory columns. In this study, an integrated numerical and physical modeling system is developed for simulating an enhanced in situ biodegradation (EISB) process coupled with three-dimensional multiphase multicomponent flow and transport simulation in a multi-dimensional pilot-scale physical model. The designed pilot-scale physical model is effective in tackling natural attenuation and EISB processes for site remediation. The simulation results demonstrate that the developed system is effective in modeling the EISB process, and can thus be used for investigating the effects of various uncertainties. - An integrated modeling system was developed to enhance in situ bioremediation processes

Modeling of Teaching 5th-7th-Grade Boys Physical Exercises

Directory of Open Access Journals (Sweden)

Т. Г. Абдулхалікова

2017-09-01

Full Text Available The research objective is to determine the effectiveness of orthogonal variants of teaching 5th-7th graders physical exercises. Materials and methods. The participants in the research were boys of the 5th grade (n = 32, 6th grade (n = 40, 7th grade (n = 52. To achieve the tasks set, the research used the following methods: analysis of scientific and methodological literature; pedagogical testing, pedagogical observation, timing of educational tasks; pedagogical experiment, medical and biological research methods; methods of mathematical statistics, methods of mathematical experiment planning. In order to achieve the objective set, the research has studied the effect of different variants of the educational process structure, namely: the number of repetitions (х1 and rest intervals (х2 when learning the technique of performing physical exercises. The research has conducted a complete factor experiment of type 22. According to the experiment plan, the 5th-7th graders were divided into training groups. In total, there were 12 experimental groups organized. Research results. The analysis of the regression equations shows that the teaching of physical exercises to the 5th-7th-grade boys is mostly influenced by rest intervals between repetitions (х2. The number of repetitions (х1 has somewhat less influence. The interaction of these factors is insignificant when teaching physical exercises and becomes much more influential only when teaching a switch leg pull-over exercise (х1х2. Conclusions. To increase the effectiveness of teaching 5th-7th graders physical exercises, it is necessary to shorten rest intervals between repetition to 60 s and to reduce the number of repetitions to six. When teaching boys the switch leg pull-over exercise, rest intervals should be increased to 120 s and the number of repetitions — to twelve.

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

Directory of Open Access Journals (Sweden)

Raunaq Malhotra

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

A de novo variant in the ASPRV1 gene in a dog with ichthyosis.

Science.gov (United States)

Bauer, Anina; Waluk, Dominik P; Galichet, Arnaud; Timm, Katrin; Jagannathan, Vidhya; Sayar, Beyza S; Wiener, Dominique J; Dietschi, Elisabeth; Müller, Eliane J; Roosje, Petra; Welle, Monika M; Leeb, Tosso

2017-03-01

Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin, scaling and/or hyperkeratosis. Ichthyosis vulgaris is the most common form of ichthyosis in humans and caused by genetic variants in the FLG gene encoding filaggrin. Filaggrin is a key player in the formation of the stratum corneum, the uppermost layer of the epidermis and therefore crucial for barrier function. During terminal differentiation of keratinocytes, the precursor profilaggrin is cleaved by several proteases into filaggrin monomers and eventually processed into free amino acids contributing to the hydration of the cornified layer. We studied a German Shepherd dog with a novel form of ichthyosis. Comparing the genome sequence of the affected dog with 288 genomes from genetically diverse non-affected dogs we identified a private heterozygous variant in the ASPRV1 gene encoding "aspartic peptidase, retroviral-like 1", which is also known as skin aspartic protease (SASPase). The variant was absent in both parents and therefore due to a de novo mutation event. It was a missense variant, c.1052T>C, affecting a conserved residue close to an autoprocessing cleavage site, p.(Leu351Pro). ASPRV1 encodes a retroviral-like protease involved in profilaggrin-to-filaggrin processing. By immunofluorescence staining we showed that the filaggrin expression pattern was altered in the affected dog. Thus, our findings provide strong evidence that the identified de novo variant is causative for the ichthyosis in the affected dog and that ASPRV1 plays an essential role in skin barrier formation. ASPRV1 is thus a novel candidate gene for unexplained human forms of ichthyoses.

A de novo variant in the ASPRV1 gene in a dog with ichthyosis.

Directory of Open Access Journals (Sweden)

Anina Bauer

2017-03-01

Full Text Available Ichthyoses are a heterogeneous group of inherited cornification disorders characterized by generalized dry skin, scaling and/or hyperkeratosis. Ichthyosis vulgaris is the most common form of ichthyosis in humans and caused by genetic variants in the FLG gene encoding filaggrin. Filaggrin is a key player in the formation of the stratum corneum, the uppermost layer of the epidermis and therefore crucial for barrier function. During terminal differentiation of keratinocytes, the precursor profilaggrin is cleaved by several proteases into filaggrin monomers and eventually processed into free amino acids contributing to the hydration of the cornified layer. We studied a German Shepherd dog with a novel form of ichthyosis. Comparing the genome sequence of the affected dog with 288 genomes from genetically diverse non-affected dogs we identified a private heterozygous variant in the ASPRV1 gene encoding "aspartic peptidase, retroviral-like 1", which is also known as skin aspartic protease (SASPase. The variant was absent in both parents and therefore due to a de novo mutation event. It was a missense variant, c.1052T>C, affecting a conserved residue close to an autoprocessing cleavage site, p.(Leu351Pro. ASPRV1 encodes a retroviral-like protease involved in profilaggrin-to-filaggrin processing. By immunofluorescence staining we showed that the filaggrin expression pattern was altered in the affected dog. Thus, our findings provide strong evidence that the identified de novo variant is causative for the ichthyosis in the affected dog and that ASPRV1 plays an essential role in skin barrier formation. ASPRV1 is thus a novel candidate gene for unexplained human forms of ichthyoses.

Brownian Motion as a Limit to Physical Measuring Processes

DEFF Research Database (Denmark)

Niss, Martin

2016-01-01

In this paper, we examine the history of the idea that noise presents a fundamental limit to physical measuring processes. This idea had its origins in research aimed at improving the accuracy of instruments for electrical measurements. Out of these endeavors, the Swedish physicist Gustaf A. Ising...

Multiscale physical processes of fine sediment in an estuary

NARCIS (Netherlands)

Wan, Y.

2015-01-01

This study presented in this book investigates micro- and macro- scale physical processes of a large-scale fine sediment estuarine system with a moderate tidal range as well as a highly seasonal-varying freshwater inflow. Based on a series measured, experimented and modeled results, the research

Workshop on Processing Physic-Chemistry Advanced – WPPCA

International Nuclear Information System (INIS)

2016-01-01

In the present volume of Journal of Physics: Conference Series we publish the proceedings of the “2nd Workshop on Processing Physic-Chemistry advanced (WPPCA)”, that was held from, April 4-8, 2016, at the Universidad Industrial de Santander (UIS), Bucaramanga, Colombia. The proceedings consist of 17 contributions that were presented as plenary talks at the event. The abstracts of all participants contributions were published in the Abstract Book with ISSN 2500-8420. The scientific program of the 2nd WPPCA consisted of 12 Magisterial Conferences, 28 Poster Presentations and 2 Courses with the participation of undergraduate and graduate students, professors, researchers and entrepreneurs from Colombia, Spain, Unite States of America, Mexico and Chile. Moreover, the 2nd WPPCA allowed to establish a shared culture of the research and innovation that enriches the area of the processing physical-chemistry of the materials and the industrial applications. All papers in these Proceedings refer to one from the following topics: Semiconductors, Superconductivity, Nanostructure Materials and Modelling, Simulation and Diagnostics. The editor hopes that those interested in the area of the science of materials can to enjoy this reading, that reflects a wide variety of current issues. On behalf of the organizing committee of the 2nd WPPCA, we are extremely thankful to all authors for providing their valuable contributions for these Proceedings as well as the reviewers for their constructive recommendations and criticism aiding to improve the presented articles. Besides, especially we appreciate the great support provided by the Sponsors and Partners. (paper)

Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

Science.gov (United States)

Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

2016-07-01

Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

Physical masking process for integrating micro metallic structures on polymer substrate

DEFF Research Database (Denmark)

Islam, Mohammad Aminul; Hansen, Hans Nørgaard

2009-01-01

plasmon devices need micro metallic structures on a polymer substrate with an uniform metal layer thickness in the nanometer range. A well known fabrication process to achieve such metallic surface pattern on polymer substrate is photolithography which involves an expensive mask and toxic chemicals......Integration of micro metallic structures in polymer devices is a broad multi-disciplinary research field, consisting of various combinations of mechanical, chemical and physical fabrication methods. Each of the methods has its specific advantages and disadvantages. Some applications like surface....... The current study shows a novel approach for fabricating thin micro metallic structures on polymer substrates using a simple physical mask and a PVD equipment. The new process involves fewer process steps, it is cost effective and suitable for high volume industrial production. Current study suggests...

SPG7 Variant Escapes Phosphorylation-Regulated Processing by AFG3L2, Elevates Mitochondrial ROS, and Is Associated with Multiple Clinical Phenotypes

Directory of Open Access Journals (Sweden)

Naif A.M. Almontashiri

2014-05-01

Full Text Available Mitochondrial production of reactive oxygen species (ROS affects many processes in health and disease. SPG7 assembles with AFG3L2 into the mAAA protease at the inner membrane of mitochondria, degrades damaged proteins, and regulates the synthesis of mitochondrial ribosomes. SPG7 is cleaved and activated by AFG3L2 upon assembly. A variant in SPG7 that replaces arginine 688 with glutamine (Q688 is associated with several phenotypes, including toxicity of chemotherapeutic agents, type 2 diabetes mellitus, and (as reported here coronary artery disease. We demonstrate that SPG7 processing is regulated by tyrosine phosphorylation of AFG3L2. Carriers of Q688 bypass this regulation and constitutively process and activate SPG7 mAAA protease. Cells expressing Q688 produce higher ATP levels and ROS, promoting cell proliferation. Our results thus reveal an unexpected link between the phosphorylation-dependent regulation of the mitochondria mAAA protease affecting ROS production and several clinical phenotypes.

Combinations of Genetic Variants Occurring Exclusively in Patients

Directory of Open Access Journals (Sweden)

Erling Mellerup

Full Text Available In studies of polygenic disorders, scanning the genetic variants can be used to identify variant combinations. Combinations that are exclusively found in patients can be separated from those combinations occurring in control persons. Statistical analyses can be performed to determine whether the combinations that occur exclusively among patients are significantly associated with the investigated disorder. This research strategy has been applied in materials from various polygenic disorders, identifying clusters of patient-specific genetic variant combinations that are significant associated with the investigated disorders. Combinations from these clusters are found in the genomes of up to 55% of investigated patients, and are not present in the genomes of any control persons. Keywords: Genetic variants, Polygenic disorder, Combinations of genetic variants, Patient-specific combinations

ToTem: a tool for variant calling pipeline optimization.

Science.gov (United States)

Tom, Nikola; Tom, Ondrej; Malcikova, Jitka; Pavlova, Sarka; Kubesova, Blanka; Rausch, Tobias; Kolarik, Miroslav; Benes, Vladimir; Bystry, Vojtech; Pospisilova, Sarka

2018-06-26

High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. ToTem is a tool for automated pipeline optimization which is freely available as a web application at  https://totem.software .

Connections between physical, optical and biogeochemical processes in the Pacific Ocean

Science.gov (United States)

Xiu, Peng; Chai, Fei

2014-03-01

A new biogeochemical model has been developed and coupled to a three-dimensional physical model in the Pacific Ocean. With the explicitly represented dissolved organic pools, this new model is able to link key biogeochemical processes with optical processes. Model validation against satellite and in situ data indicates the model is robust in reproducing general biogeochemical and optical features. Colored dissolved organic matter (CDOM) has been suggested to play an important role in regulating underwater light field. With the coupled model, physical and biological regulations of CDOM in the euphotic zone are analyzed. Model results indicate seasonal variability of CDOM is mostly determined by biological processes, while the importance of physical regulation manifests in the annual mean terms. Without CDOM attenuating light, modeled depth-integrated primary production is about 10% higher than the control run when averaged over the entire basin, while this discrepancy is highly variable in space with magnitudes reaching higher than 100% in some locations. With CDOM dynamics integrated in physical-biological interactions, a new mechanism by which physical processes affect biological processes is suggested, namely, physical transport of CDOM changes water optical properties, which can further modify underwater light field and subsequently affect the distribution of phytoplankton chlorophyll. This mechanism tends to occur in the entire Pacific basin but with strong spatial variability, implying the importance of including optical processes in the coupled physical-biogeochemical model. If ammonium uptake is sufficient to permit utilization of DOM, that is, UB∗⩾-U{U}/{U}-{(1-r_b)}/{RB}, then bacteria uptake of DOM has the form of FB=(1-r_b){U}/{RB}, bacteria respiration, SB=r_b×U, remineralization by bacteria, EB=UC{UN}/{UC}-{(1-r_b)}/{RB}. If EB > 0, then UB = 0; otherwise, UB = -EB. If there is insufficient ammonium, that is, UB∗CO2 is calculated using the

Black rings and the physical process version of the first law of thermodynamics

International Nuclear Information System (INIS)

Rogatko, Marek

2005-01-01

We consider the problem of the physical process version of the first law of black ring thermodynamics in n-dimensional Einstein gravity with additional (p+1)-form field strength and dilaton fields. The first order variations of mass, angular momentum and local charge for black ring are derived. From them we prove the physical process version of the first law of thermodynamic for stationary black rings

Physical health of the student as the main value of pedagogical process

Directory of Open Access Journals (Sweden)

Deminskaya L.A.

2012-07-01

Full Text Available The features of physical health of students are considered. Factors which influence on the physical health of children of school age are rotined. Methodical experience of teachers of physical education is presented. It is determined maintenance of concept «Physical health». The methods of estimation of the functional state of organism of schoolboys are selected. It is set that the axiological going near the health of students requires knowledge of methods of control after the functional state of organism and methods of development of physical health. It is marked that the modern teacher of physical education can not execute the educational, educate and health tasks of pedagogical process without knowledge of level of development of physical health and physical preparedness of students. It is marked that the modern teacher of physical education must know and able to estimate the indexes of physical health and physical preparedness of organism of children level.

Greenhouse climate : from physical processes to a dynamic model

NARCIS (Netherlands)

Bot, G.P.A.

1983-01-01

In this thesis greenhouse climate has been studied as the set of environmental conditions in a greenhouse in so far as they affect crop growth and development. In chapter 2 this set has been defined in terms of temperatures and vapour pressures. Moreover we have indicated which physical processes

Search for exotic physics with ATLAS

CERN Document Server

Delsart, Pierre-Antoine

2006-01-01

At the LHC, the program of research in particle physics beyond the Standard Model is extremely rich. With the ATLAS detector, besides SUSY mainstream studies, many exotic theoretical models will be investigated. They range from compositeness of fundamental fermions to extra dimension scenarii through GUT models and include many variants. I shall review some selected typical studies by the ATLAS collaboration on exotic physics, highlighting the discovery prospects and the recent analyses using the latest full detector simulations.

Normal variants and artifacts in bone scan: potential for errors in interpretation

International Nuclear Information System (INIS)

Sohn, Myung Hee

2004-01-01

Bone scan is one of the most frequently performed studies in nuclear medicine. In bone scan, the amount of radioisotope taken up by lesion depends primarily on the local rate of bone turnover rather than on the bone mass. Bone scan is extremely sensitive for detecting bony abnormalities. However, abnormalities that appear on bone scan may not always represent disease. The normal scan appearances may be affected not only by skeletal physiology and anatomy but also by a variety of technical factors which can influence image quality. Many normal variants and artifacts may appear on bone scan. They could simulate a pathologic process and could mislead into the wrong diagnostic interpretation. Therefore, their recognition is necessary to avoid misdiagnosis. A nuclear medicine physician should be aware of variable appearance of the normal variants and artifacts on bone scan. In this article, a variety of normal variants and artifacts mimicking real pathologic lesion in bone scan interpretation are discussed and illustrated

NMNAT1 variants cause cone and cone-rod dystrophy.

Science.gov (United States)

Nash, Benjamin M; Symes, Richard; Goel, Himanshu; Dinger, Marcel E; Bennetts, Bruce; Grigg, John R; Jamieson, Robyn V

2018-03-01

Cone and cone-rod dystrophies (CD and CRD, respectively) are degenerative retinal diseases that predominantly affect the cone photoreceptors. The underlying disease gene is not known in approximately 75% of autosomal recessive cases. Variants in NMNAT1 cause a severe, early-onset retinal dystrophy called Leber congenital amaurosis (LCA). We report two patients where clinical phenotyping indicated diagnoses of CD and CRD, respectively. NMNAT1 variants were identified, with Case 1 showing an extremely rare homozygous variant c.[271G > A] p.(Glu91Lys) and Case 2 compound heterozygous variants c.[53 A > G];[769G > A] p.(Asn18Ser);(Glu257Lys). The detailed variant analysis, in combination with the observation of an associated macular atrophy phenotype, indicated that these variants were disease-causing. This report demonstrates that the variants in NMNAT1 may cause CD or CRD associated with macular atrophy. Genetic investigations of the patients with CD or CRD should include NMNAT1 in the genes examined.

Analysis of the MTHFR C677T variant with migraine phenotypes

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Haupt Larisa M

2010-07-01

Full Text Available Abstract Background The methylenetetrahydrofolate reductase (MTHFR gene variant C677T has been implicated as a genetic risk factor in migraine susceptibility, particularly in Migraine with Aura. Migraine, with and without aura (MA and MO have many diagnostic characteristics in common. It is postulated that migraine symptomatic characteristics might themselves be influenced by MTHFR. Here we analysed the clinical profile, migraine symptoms, triggers and treatments of 267 migraineurs previously genotyped for the MTHFR C677T variant. The chi-square test was used to analyse all potential relationships between genotype and migraine clinical variables. Regression analyses were performed to assess the association of C677T with all migraine clinical variables after adjusting for gender. Findings The homozygous TT genotype was significantly associated with MA (P P = 0.002. While the CT genotype was significantly associated with physical activity discomfort (P P = 0.002. Females with the TT genotype were significantly associated with unilateral head pain (P P P = 0.002, and the use of natural remedy for migraine treatment (P = 0.003. Conversely, male migraineurs with the TT genotype experienced higher incidences of bilateral head pain (63% vs 34% and were less likely to use a natural remedy as a migraine treatment compared to female migraineurs (5% vs 20%. Conclusions MTHFR genotype is associated with specific clinical variables of migraine including unilateral head pain, physical activity discomfort and stress.

Bayesian detection of causal rare variants under posterior consistency.

KAUST Repository

Liang, Faming

2013-07-26

Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD), to tackle this problem. The new method simultaneously addresses two issues: (i) (Global association test) Are there any of the variants associated with the disease, and (ii) (Causal variant detection) Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI) Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

Bayesian detection of causal rare variants under posterior consistency.

Directory of Open Access Journals (Sweden)

Faming Liang

Full Text Available Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD, to tackle this problem. The new method simultaneously addresses two issues: (i (Global association test Are there any of the variants associated with the disease, and (ii (Causal variant detection Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

Bayesian detection of causal rare variants under posterior consistency.

KAUST Repository

Liang, Faming; Xiong, Momiao

2013-01-01

Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD), to tackle this problem. The new method simultaneously addresses two issues: (i) (Global association test) Are there any of the variants associated with the disease, and (ii) (Causal variant detection) Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI) Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

Placenta-specific novel splice variants of Rho GDP dissociation inhibitor β are highly expressed in cancerous cells

Directory of Open Access Journals (Sweden)

Hatakeyama Keiichi

2012-12-01

Full Text Available Abstract Background Alternative splicing of pre-mRNA transcripts not only plays a role in normal molecular processes but is also associated with cancer development. While normal transcripts are ubiquitously expressed in normal tissues, splice variants created through abnormal alternative splicing events are often expressed in cancer cells. Although the Rho GDP dissociation inhibitor β (ARHGDIB gene has been found to be ubiquitously expressed in normal tissues and involved in cancer development, the presence of splice variants of ARHGDIB has not yet been investigated. Results Validation analysis for the presence of and exon structures of splice variants of ARHGDIB, performed using reverse-transcriptase polymerase chain reaction and DNA sequencing, successfully identified novel splice variants of ARHGDIB, that is, 6a, 6b, and 6c, in colon, pancreas, stomach, and breast cancer cell lines. Quantitative real-time polymerase chain reaction analysis showed that these variants were also highly expressed in normal placental tissue but not in other types of normal tissue. Conclusions Expression of ARHGDIB variants 6a, 6b, and 6c appears to be restricted to cancer cells and normal placental tissue, suggesting that these variants possess cancer-specific functions and, as such, are potential cancer-related biomarkers.

Discovering Process Reference Models from Process Variants Using Clustering Techniques

NARCIS (Netherlands)

Li, C.; Reichert, M.U.; Wombacher, Andreas

2008-01-01

In today's dynamic business world, success of an enterprise increasingly depends on its ability to react to changes in a quick and flexible way. In response to this need, process-aware information systems (PAIS) emerged, which support the modeling, orchestration and monitoring of business processes

Influence of HFE variants and cellular iron on monocyte chemoattractant protein-1

Directory of Open Access Journals (Sweden)

Simmons Zachary

2009-02-01

Full Text Available Abstract Background Polymorphisms in the MHC class 1-like gene known as HFE have been proposed as genetic modifiers of neurodegenerative diseases that include neuroinflammation as part of the disease process. Variants of HFE are relatively common in the general population and are most commonly associated with iron overload, but can promote subclinical cellular iron loading even in the absence of clinically identified disease. The effects of the variants as well as the resulting cellular iron dyshomeostasis potentially impact a number of disease-associated pathways. We tested the hypothesis that the two most common HFE variants, H63D and C282Y, would affect cellular secretion of cytokines and trophic factors. Methods We screened a panel of cytokines and trophic factors using a multiplexed immunoassay in human neuroblastoma SH-SY5Y cells expressing different variants of HFE. The influence of cellular iron secretion on the potent chemokine monocyte chemoattractant protein-1 (MCP-1 was assessed using ferric ammonium citrate and the iron chelator, desferroxamine. Additionally, an antioxidant, Trolox, and an anti-inflammatory, minocycline, were tested for their effects on MCP-1 secretion in the presence of HFE variants. Results Expression of the HFE variants altered the labile iron pool in SH-SY5Y cells. Of the panel of cytokines and trophic factors analyzed, only the release of MCP-1 was affected by the HFE variants. We further examined the relationship between iron and MCP-1 and found MCP-1 secretion tightly associated with intracellular iron status. A potential direct effect of HFE is considered because, despite having similar levels of intracellular iron, the association between HFE genotype and MCP-1 expression was different for the H63D and C282Y HFE variants. Moreover, HFE genotype was a factor in the effect of minocycline, a multifaceted antibiotic used in treating a number of neurologic conditions associated with inflammation, on MCP-1

Electrophoretic variants of blood proteins in japanese, 5

International Nuclear Information System (INIS)

Fujita, Mikio; Satoh, Chiyoko; Asakawa, Jun-ichi; Nagahata, Yuko; Tanaka, Yoshiko; Hazama, Ryuji; Goriki, Kazuaki.

1985-08-01

The plasma ceruloplasmin (CP) of 22,367 children of atomic bomb survivors in Hiroshima and Nagasaki was examined for variants by electrophoresis. The sample was composed of 14,964 unrelated children and 7,403 siblings of the unrelated persons. A total of seven types of electrophoretic variants were detected; four migrating anodally and three cathodally to the normal B band. We have reported two of these variants, CP A sub(NG1) and CP C sub(NG1), previously but the other five, CP A sub(NG2), CP A sub(HR1), CP A sub(HR2), CP C sub(HR1), and CP C sub(HR2), are newly identified. The allelic frequency of CP*CNG1 was 0.00916, so that the variant is considered to be a polymorphic allele. Homozygosity for the CP*CNG1 allele was detected in five individuals. This is the first report of a homozygous phenotype for a CP variant in a Japanese population. Family study of the new five variants all demonstrated patterns of codominant inheritance. (author)

Depth-variant blind restoration with pupil-phase constraints for 3D confocal microscopy

International Nuclear Information System (INIS)

Hadj, Saima Ben; Blanc-Féraud, Laure; Engler, Gilbert

2013-01-01

Three-dimensional images of confocal laser scanning microscopy suffer from a depth-variant blur, due to refractive index mismatch between the different mediums composing the system as well as the specimen, leading to optical aberrations. Our goal is to develop an image restoration method for 3D confocal microscopy taking into account the blur variation with depth. The difficulty is that optical aberrations depend on the refractive index of the biological specimen. The depth-variant blur function or the Point Spread Function (PSF) is thus different for each observation. A blind or semi-blind restoration method needs to be developed for this system. For that purpose, we use a previously developed algorithm for the joint estimation of the specimen function (original image) and the 3D PSF, the continuously depth-variant PSF is approximated by a convex combination of a set of space-invariant PSFs taken at different depths. We propose to add to that algorithm a pupil-phase constraint for the PSF estimation, given by the the optical instrument geometry. We thus define a blind estimation algorithm by minimizing a regularized criterion in which we integrate the Gerchberg-Saxton algorithm allowing to include these physical constraints. We show the efficiency of this method relying on some numerical tests

Explorations of the viability of ARM and Xeon Phi for physics processing

International Nuclear Information System (INIS)

Abdurachmanov, David; Arya, Kapil; Cooperman, Gene; Bendavid, Josh; Boccali, Tommaso; Dotti, Andrea; Elmer, Peter; Eulisse, Giulio; Jones, Christopher D; Muzaffar, Shahzad; Giacomini, Francesco; Manzali, Matteo

2014-01-01

We report on our investigations into the viability of the ARM processor and the Intel Xeon Phi co-processor for scientific computing. We describe our experience porting software to these processors and running benchmarks using real physics applications to explore the potential of these processors for production physics processing.

Explorations of the Viability of ARM and Xeon Phi for Physics Processing

CERN Document Server

Abdurachmanov, David; Bendavid, Josh; Boccali, Tommaso; Cooperman, Gene; Dotti, Andrea; Elmer, Peter; Eulisse, Giulio; Giacomini, Francesco; Jones, Christopher D.; Manzali, Matteo; Muzaffar, Shahzad

2014-01-01

We report on our investigations into the viability of the ARM processor and the Intel Xeon Phi co-processor for scientific computing. We describe our experience porting software to these processors and running benchmarks using real physics applications to explore the potential of these processors for production physics processing.

Identification of genomic variants putatively targeted by selection during dog domestication.

Science.gov (United States)

Cagan, Alex; Blass, Torsten

2016-01-12

around non-synonymous variants. Strong selection in the initial stages of dog domestication appears to have occurred on multiple genes involved in the fight-or-flight response, particularly in the catecholamine synthesis pathway. Different alleles in some of these genes have been associated with behavioral differences between modern dog breeds, suggesting an important role for this pathway at multiple stages in the domestication process.

MR imaging of acute disseminated encephalomyelitis, cerebellitis and myelitis in infancy: likely topographic variant of a single process; Imagen en RM de encefalomielitis aguda diseminada, cerebelitis y mielitis en la infancia: probables variantes topograficas de un mismo proceso

Energy Technology Data Exchange (ETDEWEB)

Fortuno, J. R.; Menor, F.; Esteban, M. J.; Pamies, J. [Hospital Universitario Infantil La Fe (Spain); Gomez-Gosalvez, F. A. [Hospital Verge dels Liris de Alcoi (Spain); Jover, J. [Hospital General de Elda (Spain)

2003-07-01

To describe MR images of acute disseminated encephalomyelitis (ADE) in a paediatric group, particularly focused on its likely topographic variants, cerebellitis and myelitis, its evolution, and the differential diagnosis between it an an initial outbreak of multiple sclerosis. Initial and follow-up cranial MR images were retrospectively reviewed for 14 paediatric patients diagnosed with either ADE, cerebellitis or myelitis. In 9 patients, a spinal cord monitoring was included. Three topographic variants have been considered: ADE (7 patients). In the case of ADE, the supratentorial white matter was always affected, the brain stem in five (71%) and the cerebellum in two (28,5%). Basal ganglionic lesions were detected in 5 patients (71%) and cortical lesions in one (14%). Associated spinal cord abnormality was found in five of the six cases in which this study was included (83%). ADE lesions tended to be nodular and poorly differentiated whereas in cerebellitis and myelitis the predominant pattern was one of diffuse damage. Evolution of the lesions was toward reduction/resolution. Follow-up using MR in the medium-term in 6 patients (four ADE and two cerebellitis) did not detect any new lesions. Clinical follow-up of the patients did not show any neurological recurrences in any of them. ADE, cerebillits and myelitis could be topographic variants of a single process with a common pathogeny. As the spinal cord often seems to play a role in ADE, spinal cord monitoring would be recommended, even in the absence of the above-mentioned symptoms. This spinal cord abnormality, which is usually diffuse, plus deep gray matter damage, as well as the disease of monophase course, corroborated by a sequential MR follow-up, is all helpful in the differential diagnosis with multiple sclerosis. Nonetheless, the differential diagnosis between a recurring form of ADE and an encephalomyelitis is practically impossible to make. (Author) 33 refs.

Gauge-fixing parameter dependence of two-point gauge-variant correlation functions

International Nuclear Information System (INIS)

Zhai, C.

1996-01-01

The gauge-fixing parameter ξ dependence of two-point gauge-variant correlation functions is studied for QED and QCD. We show that, in three Euclidean dimensions, or for four-dimensional thermal gauge theories, the usual procedure of getting a general covariant gauge-fixing term by averaging over a class of covariant gauge-fixing conditions leads to a nontrivial gauge-fixing parameter dependence in gauge-variant two-point correlation functions (e.g., fermion propagators). This nontrivial gauge-fixing parameter dependence modifies the large-distance behavior of the two-point correlation functions by introducing additional exponentially decaying factors. These factors are the origin of the gauge dependence encountered in some perturbative evaluations of the damping rates and the static chromoelectric screening length in a general covariant gauge. To avoid this modification of the long-distance behavior introduced by performing the average over a class of covariant gauge-fixing conditions, one can either choose a vanishing gauge-fixing parameter or apply an unphysical infrared cutoff. copyright 1996 The American Physical Society

Cigarette brand variant portfolio strategy and the use of colour in a darkening market.

Science.gov (United States)

Greenland, Steven J

2015-03-01

To evaluate cigarette branding strategies used to segment a market with some of the toughest tobacco controls. To document brand variant and packaging portfolios and assess the role played by colour before plain packaging, as well as consider the threat that recently implemented legislation poses for tobacco manufacturers. Brand variant and packaging details were extracted from manufacturer ingredient reports, as well as a retail audit of Australian supermarkets. Details were also collected for other product categories to provide perspective on cigarette portfolios. Secondary and primary data sources were analysed to evaluate variant and packaging portfolio strategy. In Australia, 12 leading cigarette brands supported 120 brand variants. Of these 61 had names with a specific colour and a further 26 had names with colour connotation. There were 338 corresponding packaging configurations, with most variants available in the primary cigarette distribution channel in four pack size options. Tobacco companies microsegment Australian consumers with highly differentiated product offerings and a family branding strategy that helps ameliorate the effects of marketing restrictions. To date, tobacco controls have had little negative impact upon variant and packaging portfolios, which have continued to expand. Colour has become a key visual signifier differentiating one variant from the next, and colour names are used to extend brand lines. However, the role of colour, as a heuristic to simplify consumer decision-making processes, becomes largely redundant with plain packaging. Plain packaging's impact upon manufacturers' branding strategies is therefore likely to be significant. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Purification of human growth hormone. Isolation of the 22k variant. Assays of biological and radioimmunological activities

International Nuclear Information System (INIS)

Camillo, M.A.P.

1985-01-01

An extraction method for hGH from frozen human pituitaries with high yield: 8,7 mg per processed gland, is described. Isoelectric focusing studies made it possible to isolate and integral variant of the total preparation of hGH. After liophylization the protein was analysed in polyacrylamide gel electrophoresis showing only one protein band that corresponds to the 22K variant. (M.A.C.) [pt

Association analysis identifies ZNF750 regulatory variants in psoriasis

Directory of Open Access Journals (Sweden)

Birnbaum Ramon Y

2011-12-01

Full Text Available Abstract Background Mutations in the ZNF750 promoter and coding regions have been previously associated with Mendelian forms of psoriasis and psoriasiform dermatitis. ZNF750 encodes a putative zinc finger transcription factor that is highly expressed in keratinocytes and represents a candidate psoriasis gene. Methods We examined whether ZNF750 variants were associated with psoriasis in a large case-control population. We sequenced the promoter and exon regions of ZNF750 in 716 Caucasian psoriasis cases and 397 Caucasian controls. Results We identified a total of 47 variants, including 38 rare variants of which 35 were novel. Association testing identified two ZNF750 haplotypes associated with psoriasis (p ZNF750 promoter and 5' UTR variants displayed a 35-55% reduction of ZNF750 promoter activity, consistent with the promoter activity reduction seen in a Mendelian psoriasis family with a ZNF750 promoter variant. However, the rare promoter and 5' UTR variants identified in this study did not strictly segregate with the psoriasis phenotype within families. Conclusions Two haplotypes of ZNF750 and rare 5' regulatory variants of ZNF750 were found to be associated with psoriasis. These rare 5' regulatory variants, though not causal, might serve as a genetic modifier of psoriasis.

[Clinico-pathogenetic variants of chronic gastritis].

Science.gov (United States)

Chernin, V V; Dzhulaĭ, G S

2004-01-01

To evaluate specific features of the course of chronic gastritis (CG), morphofunctional condition of gastric mucosa, vegetative regulation, adrenergic and cholinergic shifts, histamine metabolism and effects of exogenic and endogenic risk factors in CG patients; to study clinicopathogenetic variants of CG. A total of 311 CG patients aged from 16 to 72 years were studied. They were divided into three groups by their gastric mucosa condition. The control group consisted of 30 healthy donors. The following parameters were studied: visual and histological condition of gastric mucosa, total acidity, the levels of free hydrochloric acid, pepsin, bioelectric gastric activity, general autonomic tonicity, cholinesterase activity. Three clinicopathogenetic variants of the disease have been identified. Variant 1 was characterized by a recurrent course, subjective manifestation of the disease only in exacerbation, surface (primarily antral) mucosal affection, normal or enhanced secretory and motor functions of the stomach, adequate reaction of acid production to caffeine and histamine stimulation, parasympathicotonia, absolute hyperhistaminemia, relative hypoacetylcholinemia, subnormal urinary excretion of adrenalin. Variant 2 manifested with rare recurrences, longer and more severe exacerbations, frequent spontaneous and provoked aggravations, moderate focal atrophy of the mucosa, secretory insufficiency with adequate reaction to histamine and minor to caffeine stimuli, hypomotor gastric dyskinesia, vegetative eutonia, normohistaminemia, absolute hypoacetylcholinemia, subnormal urinary excretion of noradrenaline. Variant 3 runs without definite remissions and exacerbations, with continuous abdominal pain and dyspepsia, frequent spontaneous aggravations, marked extended mucosal atrophy with secretory insufficiency up to achlorhydria, no stimulation of acid production in response to caffeine and histamine, gastric hypomotility, sympathicotonia, absolute hypohistaminemia

Transforming the Learning Environment of Undergraduate Physics Laboratories to Enhance Physics Inquiry Processes

Directory of Open Access Journals (Sweden)

Gregory P. Thomas

2017-04-01

Full Text Available Concerns persist regarding the lack of promotion of students’ scientific inquiry processes in undergraduate physics laboratories. The consensus in the literature is that, especially in the early years of undergraduate physics programs, students’ laboratory work is characterized by recipe type, step-by-step instructions for activities where the aim is often confirmation of an already well-established physics principle or concept. In response to evidence reflecting these concerns at their university, the authors successfully secured funding for this study. A mixed-method design was employed. In the 2011/2012 academic year baseline data were collected. A quantitative survey, the Undergraduate Physics Laboratory Learning Environment Scale (UPLLES was developed, validated, and used to explore students’ perceptions of their physics laboratory environments. Analysis of data from the UPLLES and from interviews confirmed the concerns evident in the literature and in a previous evaluation of laboratories undertaken in 2002. To address these concerns the activities that students were to perform in the laboratory section of the course/s were re/designed to engage students in more inquiry oriented thinking and activity. In Fall 2012, the newly developed laboratory activities and tutorials, were implemented for the first time in PHYS124; a first year course. These changes were accompanied by structured training of teaching assistants and changes to the structure of the evaluation of students’ laboratory performance. At the end of that term the UPLLES was administered (n = 266 and interviews with students conducted (n = 16 to explore their perceptions of their laboratory environments. Statistically significant differences (p<.001 between the students in the PHYS 124 classes of 2011/2012 and 2012/2013 across all dimensions were found. Effect sizes of 0.82 to 1.3, between the views of students in the first semester physics classes of 2011/2012 and 2012

Analysis of the energy development variants

International Nuclear Information System (INIS)

Tsvetanov, P.

1990-01-01

Analysis of the variants of energy development is made as the third stage of a procedure of energy-economy interrelations dynamics study, the other two stages being the scenarios description and the formulation of the variants. This stage includes a research on the dimensions and the dynamics of the resources demands, the general features and the trends of the national energy development. There is a presentation of a comparative analysis of the variants in terms of economic indices and energy values, computed by the model IMPACT-B. A resource evaluation of the development variants is given in terms of investments, requirements (direct, indirect and total) and limited national resources demands of the energy system. The trends of the national energy development discussed are: trends characterizing the changes in the structure of the energy consumption, resulting from changes in the economy; trends of the energy system impact on the productivity of labor; general trends of the proportionality in the industrial, the household and services sector development. 16 refs., 16 figs., 4 tabs. (R.Ts.)

Physical Activity Attenuates the Influence of FTO Variants on Obesity Risk

DEFF Research Database (Denmark)

Oskari Kilpeläinen, Tuomas; Qi, Lu; Brage, Soren

2011-01-01

Background The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA) may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute......>0.8]) and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active) in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were.......20–1.26), but PA attenuated this effect (pinteraction = 0.001). More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio = 1.22/allele, 95% CI 1.19–1.25) than in the inactive group (odds ratio = 1.30/allele, 95% CI 1...

BPFlexTemplate: A Business Process template generation tool based on similarity and flexibility

Directory of Open Access Journals (Sweden)

Latifa Ilahi

2017-01-01

Full Text Available In large organizations with multiple organizational units, process variants emerge due to many aspects, including local management policies, resources or socio-technical limitations. Organizations then struggle to improve a business process which has no longer a single process model to redesign, implement and adjust. In this paper, we propose an approach to tackle these two challenges: decrease the proliferation of process variants in these organizations, and foresee, at the same time, the need of having flexible business processes that allow for a certain degree of adjustment. To validate our approach, we first conducted case studies where we collected six real-world business process variants from two organizational units of the same healthcare organization. We then proposed an algorithm to derive a template process model from all the variants, which includes common and flexible process elements. We implemented our approach in a software tool called BPFlexTemplate, and tested it with the elicited variants.

Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

Science.gov (United States)

Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

2017-01-03

Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

Impact of physical permafrost processes on hydrological change

Science.gov (United States)

Hagemann, Stefan; Blome, Tanja; Beer, Christian; Ekici, Altug

2015-04-01

Permafrost or perennially frozen ground is an important part of the terrestrial cryosphere; roughly one quarter of Earth's land surface is underlain by permafrost. As it is a thermal phenomenon, its characteristics are highly dependent on climatic factors. The impact of the currently observed warming, which is projected to persist during the coming decades due to anthropogenic CO2 input, certainly has effects for the vast permafrost areas of the high northern latitudes. The quantification of these effects, however, is scientifically still an open question. This is partly due to the complexity of the system, where several feedbacks are interacting between land and atmosphere, sometimes counterbalancing each other. Moreover, until recently, many global circulation models (GCMs) and Earth system models (ESMs) lacked the sufficient representation of permafrost physics in their land surface schemes. Within the European Union FP7 project PAGE21, the land surface scheme JSBACH of the Max-Planck-Institute for Meteorology ESM (MPI-ESM) has been equipped with the representation of relevant physical processes for permafrost studies. These processes include the effects of freezing and thawing of soil water for both energy and water cycles, thermal properties depending on soil water and ice contents, and soil moisture movement being influenced by the presence of soil ice. In the present study, it will be analysed how these permafrost relevant processes impact projected hydrological changes over northern hemisphere high latitude land areas. For this analysis, the atmosphere-land part of MPI-ESM, ECHAM6-JSBACH, is driven by prescribed SST and sea ice in an AMIP2-type setup with and without the newly implemented permafrost processes. Observed SST and sea ice for 1979-1999 are used to consider induced changes in the simulated hydrological cycle. In addition, simulated SST and sea ice are taken from a MPI-ESM simulation conducted for CMIP5 following the RCP8.5 scenario. The

Identifying structural variants using linked-read sequencing data.

Science.gov (United States)

Elyanow, Rebecca; Wu, Hsin-Ta; Raphael, Benjamin J

2017-11-03

Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification - including two recent methods that also analyze linked-reads - on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Software is available at compbio.cs.brown.edu/software. braphael@princeton.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Physical Properties for Lipids Based Process and Product Design

DEFF Research Database (Denmark)

Ana Perederic, Olivia; Kalakul, Sawitree; Sarup, Bent

Lipid processing covers several oil and fats technologies such as: edible oil production, biodieselproduction, oleochemicals (e.g.: food additives, detergents) and pharmaceutical product manufacturing. New demands regarding design and development of better products and more sustainable processes...... related to lipids technology, emerge according to consumers demanding improved product manufacturing from sustainable resources and new legislation regarding environmental safety [1]. Physical and thermodynamic property data and models for prediction of pure compound properties and mixtures properties...... involving lipids represent the basic and most important requirements for process product design, simulation and optimization. Experimentally measured values of involved compounds are desirable, but in most of the cases these are not available for all the compounds and properties needed. The lack...

REGULATED VESICULAR TRAFFICKING OF SPECIFIC PCDH15 AND VLGR1 VARIANTS IN AUDITORY HAIR CELLS

Science.gov (United States)

Zallocchi, Marisa; Delimont, Duane; Meehan, Daniel T.; Cosgrove, Dominic

2012-01-01

Usher syndrome is a genetically heterogeneous disorder characterized by hearing and balance dysfunction and progressive retinitis pigmentosa. Mouse models carrying mutations for the nine Usher-associated genes have splayed stereocilia and some show delayed maturation of ribbon synapses suggesting these proteins may play different roles in terminal differentiation of auditory hair cells. The presence of the Usher proteins at the basal and apical aspects of the neurosensory epithelia suggests the existence of regulated trafficking through specific transport proteins and routes. Immature mouse cochleae and UB/OC-1 cells were used in this work to address whether specific variants of PCDH15 and VLGR1 are being selectively transported to opposite poles of the hair cells. Confocal co-localization studies between apical and basal vesicular markers and the different PCDH15 and VLGR1 variants along with sucrose density gradients and the use of vesicle trafficking inhibitors show the existence of Usher protein complexes in at least two vesicular sub-pools. The apically trafficked pool co-localized with the early endosomal vesicle marker, rab5, while the basally trafficked pool associates with membrane microdomains and SNAP25. Moreover, co-immunoprecipitation experiments between SNAP25 and VLGR1 show a physical interaction of these two proteins in organ of Corti and brain. Collectively, these findings establish the existence of a differential vesicular trafficking mechanism for specific Usher protein variants in mouse cochlear hair cells, with the apical variants playing a potential role in endosomal recycling and stereocilia development/maintenance and the basolateral variants involved in vesicle docking and/or fusion through SNAP25-mediated interactions. PMID:23035094

Physical processes and the maintenance of nutrient-rich euphotic zones

International Nuclear Information System (INIS)

Gargett, A.E.

1991-01-01

Oceanic euphotic zones characterized by high macronutrients but low primary productivity are found in the upwelling gyres of the world ocean. This paper reviews the physical processes which interact to maintain high nutrient concentrations in the near-surface ocean in such regions, illustrating the range of relevant forcing functions with regional examples. Predictions of the direction of change of the physical systems in these areas under increasing greenhouse gas concentrations can be based on the present generation of coupled ocean-atmosphere global circulation models, but these results have significant uncertainty

Identification of variant-specific surface proteins in Giardia muris trophozoites.

Science.gov (United States)

Ropolo, Andrea S; Saura, Alicia; Carranza, Pedro G; Lujan, Hugo D

2005-08-01

Giardia lamblia undergoes antigenic variation, a process that might allow the parasite to evade the host's immune response and adapt to different environments. Here we show that Giardia muris, a related species that naturally infects rodents, possesses multiple variant-specific surface proteins (VSPs) and expresses VSPs on its surface, suggesting that it undergoes antigenic variation similar to that of G. lamblia.

Identification of Variant-Specific Surface Proteins in Giardia muris Trophozoites

OpenAIRE

Ropolo, Andrea S.; Saura, Alicia; Carranza, Pedro G.; Lujan, Hugo D.

2005-01-01

Giardia lamblia undergoes antigenic variation, a process that might allow the parasite to evade the host's immune response and adapt to different environments. Here we show that Giardia muris, a related species that naturally infects rodents, possesses multiple variant-specific surface proteins (VSPs) and expresses VSPs on its surface, suggesting that it undergoes antigenic variation similar to that of G. lamblia.

Physical characteristics of welding arc ignition process

Science.gov (United States)

Shi, Linan; Song, Yonglun; Xiao, Tianjiao; Ran, Guowei

2012-07-01

The existing research of welding arc mainly focuses on the stable combustion state and the research on the mechanism of welding arc ignition process is quite lack. The tungsten inert gas(TIG) touch arc ignition process is observed via a high speed camera and the high time resolution spectral diagnosis system. The changing phenomenon of main ionized element provided the electrons in the arc ignition is found. The metallic element is the main contributor to provide the electrons at the beginning of the discharging, and then the excitated shielding gas element replaces the function of the metallic element. The electron density during the period of the arc ignition is calculated by the Stark-broadened lines of Hα. Through the discussion with the repeatability in relaxation phenomenon, the statistical regularity in the arc ignition process is analyzed. The similar rules as above are observed through the comparison with the laser-assisted arc ignition experiments and the metal inert gas(MIG) arc ignition experiments. This research is helpful to further understanding on the generation mechanism of welding arc ignition and also has a certain academic and practical significance on enriching the welding physical theoretical foundation and improving the precise monitoring on automatic arc welding process.

Residence time and physical processes in lakes

Directory of Open Access Journals (Sweden)

Nicoletta SALA

2003-09-01

Full Text Available The residence time of a lake is highly dependent on internal physical processes in the water mass conditioning its hydrodynamics; early attempts to evaluate this physical parameter emphasize the complexity of the problem, which depends on very different natural phenomena with widespread synergies. The aim of this study is to analyse the agents involved in these processes and arrive at a more realistic definition of water residence time which takes account of these agents, and how they influence internal hydrodynamics. With particular reference to temperate lakes, the following characteristics are analysed: 1 the set of the lake's caloric components which, along with summer heating, determine the stabilizing effect of the surface layers, and the consequent thermal stratification, as well as the winter destabilizing effect; 2 the wind force, which transfers part of its momentum to the water mass, generating a complex of movements (turbulence, waves, currents with the production of active kinetic energy; 3 the water flowing into the lake from the tributaries, and flowing out through the outflow, from the standpoint of hydrology and of the kinetic effect generated by the introduction of these water masses into the lake. These factors were studied in the context of the general geographical properties of the lake basin and the watershed (latitude, longitude, morphology, also taking account of the local and regional climatic situation. Also analysed is the impact of ongoing climatic change on the renewal of the lake water, which is currently changing the equilibrium between lake and atmosphere, river and lake, and relationships

Persistent trigeminal artery/persistent trigeminal artery variant and coexisting variants of the head and neck vessels diagnosed using 3 T MRA

International Nuclear Information System (INIS)

Bai, M.; Guo, Q.; Li, S.

2013-01-01

Aim: To report the prevalence and characteristic features of persistent trigeminal artery (PTA), PTA variant (PTAV), and other variants of the head and neck vessels, identified using magnetic resonance angiography (MRA). Materials and methods: The three-dimensional (3D) time of flight (TOF) MRA and 3D contrast-enhanced (CE) MRA images of 6095 consecutive patients who underwent 3 T MRA at Liaocheng People's Hospital from 1 September 2008 through 31 May 2012 were retrospectively reviewed and analysed. Thirty-two patients were excluded because of suboptimal image quality or internal carotid artery (ICA) occlusion. Results: The prevalence of both PTA and PTAV was 0.63% (PTA, 26 cases; PTAV, 12 cases). The prevalence of coexisting variants of the head and neck vessels in cases of PTA/PTAV was 52.6% (20 of 38 cases). The vascular variants that coexisted with cases of PTA/PTAV were as follows: the intracranial arteries varied in 10 cases, the origin of the supra-aortic arteries varied in nine cases, the vertebral artery (VA) varied in 14 cases, and six cases displayed fenestrations. Fifteen of the 20 cases contained more than two types of variants. Conclusion: The prevalence of both PTA and PTAV was 0.63%. Although PTA and PTAV are rare vascular variants, they frequently coexist with other variants of the head and neck vessels. Multiple vascular variations can coexist in a single patient. Recognizing PTA, PTAV, and other variants of the head and neck vessels is crucial when planning a neuroradiological intervention or surgery. Recognizing the medial PTA is very important in clinical practice when performing trans-sphenoidal surgery on the pituitary as failure to do so could result in massive haemorrhage

Cold comfort at the Magh Mela: social identity processes and physical hardship.

Science.gov (United States)

Pandey, Kavita; Stevenson, Clifford; Shankar, Shail; Hopkins, Nicholas P; Reicher, Stephen D

2014-12-01

Humans inhabit environments that are both social and physical, and in this article we investigate if and how social identity processes shape the experience and negotiation of physically demanding environmental conditions. Specifically, we consider how severe cold can be interpreted and experienced in relation to group members' social identity. Our data comprise ethnographic observation and semi-structured interviews with pilgrims attending a month-long winter Hindu religious festival that is characterized by near-freezing conditions. The analysis explores (1) how pilgrims appraised the cold and how these appraisals were shaped by their identity as pilgrims; (2) how shared identity with other pilgrims led to forms of mutual support that made it easier to cope with the cold. Our findings therefore extend theorizing on social identity processes to highlight their relevance to physical as well as social conditions. © 2013 The British Psychological Society.

Developing consistent pronunciation models for phonemic variants

CSIR Research Space (South Africa)

Davel, M

2006-09-01

Full Text Available Pronunciation lexicons often contain pronunciation variants. This can create two problems: It can be difficult to define these variants in an internally consistent way and it can also be difficult to extract generalised grapheme-to-phoneme rule sets...

Comparison of the BioRad Variant and Primus Ultra2 high-pressure liquid chromatography (HPLC) instruments for the detection of variant hemoglobins.

Science.gov (United States)

Gosselin, R C; Carlin, A C; Dwyre, D M

2011-04-01

Hemoglobin variants are a result of genetic changes resulting in abnormal or dys-synchronous hemoglobin chain production (thalassemia) or the generation of hemoglobin chain variants such as hemoglobin S. Automated high-pressure liquid chromatography (HPLC) systems have become the method of choice for the evaluation of patients suspected with hemoglobinopathies. In this study, we evaluated the performance of two HPLC methods used in the detection of common hemoglobin variants: Variant and Ultra2. There were 377 samples tested, 26% (99/377) with HbS, 8.5% (32/377) with HbC, 20.7% (78/377) with other hemoglobin variant or thalassemia, and 2.9% with increased hemoglobin A(1) c. The interpretations of each chromatograph were compared. There were no differences noted for hemoglobins A(0), S, or C. There were significant differences between HPLC methods for hemoglobins F, A(2), and A(1) c. However, there was good concordance between normal and abnormal interpretations (97.9% and 96.2%, respectively). Both Variant and Ultra2 HPLC methods were able to detect most common hemoglobin variants. There was better discrimination for fast hemoglobins, between hemoglobins E and A(2), and between hemoglobins S and F using the Ultra2 HPLC method. © 2010 Blackwell Publishing Ltd.

Exposure of the Plasmodium falciparum clonally variant STEVOR proteins on the merozoite surface

Directory of Open Access Journals (Sweden)

Meri Seppo

2011-03-01

Full Text Available Abstract Background Plasmodium falciparum merozoites are free invasive forms that invade host erythrocytes in iterative cycles in the presence of different arms of the immune system. Variant antigens are known to play a role in immune evasion and several gene families coding for variant antigens have been identified in P. falciparum. However, none of them have been reported to be expressed on the surface of merozoites. Methods Flow cytometry, immunofluorescence microscopy, and immunoblotting assays were performed to assess surface exposure, membrane association and stage specific expression of the STEVOR family of variants proteins, respectively. Results Using a polyclonal antibody (anti-PFL2610w with a broad specificity towards different STEVOR variants, the STEVOR proteins were identified on the surface of non-permeabilized/non-fixed merozoites in flow cytometry assays. Anti-PFL2610w antibody showed that several STEVORs were expressed in the trophozoite stage of the parasite but only one variant was integrated into the merozoite membrane. Moreover, this antibody failed to identify STEVORs on the surface of the parent schizont infected erythrocytes (IE although they were readily identified when schizont IE were permeabilized. Conclusions These data suggest for a role for STEVOR in immune evasion by P. falciparum merozoites to allow successful invasion of erythrocytes. Additionally, the expression of STEVORs in the schizont stage may only represent a step in the biogenesis process of the merozoite surface coat.

Variants of PLCXD3 are not associated with variant or sporadic Creutzfeldt-Jakob disease in a large international study.

Science.gov (United States)

Balendra, Rubika; Uphill, James; Collinson, Claire; Druyeh, Ronald; Adamson, Gary; Hummerich, Holger; Zerr, Inga; Gambetti, Pierluigi; Collinge, John; Mead, Simon

2016-04-07

Human prion diseases are relentlessly progressive neurodegenerative disorders which include sporadic Creutzfeldt-Jakob disease (sCJD) and variant CJD (vCJD). Aside from variants of the prion protein gene (PRNP) replicated association at genome-wide levels of significance has proven elusive. A recent association study identified variants in or near to the PLCXD3 gene locus as strong disease risk factors in multiple human prion diseases. This study claimed the first non-PRNP locus to be highly significantly associated with prion disease in genomic studies. A sub-study of a genome-wide association study with imputation aiming to replicate the finding at PLCXD3 including 129 vCJD and 2500 sCJD samples. Whole exome sequencing to identify rare coding variants of PLCXD3. Imputation of relevant polymorphisms was accurate based on wet genotyping of a sample. We found no supportive evidence that PLCXD3 variants are associated with disease. The marked discordance in vCJD genotype frequencies between studies, despite extensive overlap in vCJD cases, and the finding of Hardy-Weinberg disequilibrium in the original study, suggests possible reasons for the discrepancies between studies.

A genetic electrophoretic variant of high-sulfur hair proteins for forensic hair comparisons. I. Characterization of variant high-sulfur proteins of human hair.

Science.gov (United States)

Miyake, B

1989-02-01

In a survey of the proteins from human hair, a genetic electrophoretic variant has been observed in the high-sulfur protein region. S-carboxymethylated proteins were examined by 15% polyacrylamide gel electrophoresis at pH 8.9. Out of 150 unrelated samples of Japanese head hairs analyzed, 107 showed 6 major high-sulfur protein bands (normal) and the remaining 43 samples showed an additional high-sulfur protein band (variant). Of 21 Caucasian samples analyzed only one variant sample was found. Characterization of the proteins by two-dimensional electrophoresis evidenced a variant protein spot which showed an apparent molecular weight of 30 k Da. Isoelectric points of the high-sulfur proteins ranged from 3.25-3.55 and that of variant protein band from 3.3-3.4. Family studies of 21 matings resulting in 49 children indicated that this variant was inherited in an autosomal fashion.

[The phonological variant of primary progressive aphasia, a single case study].

Science.gov (United States)

Diesfeldt, H F A

2011-04-01

Primary progressive aphasia (PPA) is a neurodegenerative syndrome characterized by an insidious onset and gradual progression of deficits that can involve any aspect of language, including word finding, object naming, fluency, syntax, phonology and word comprehension. The initial symptoms occur in the absence of major deficits in other cognitive domains, including episodic memory, visuospatial abilities and visuoconstruction. According to recent diagnostic guidelines, PPA is typically divided into three variants: nonfluent variant PPA (also termed progressive nonfluent aphasia), semantic variant PPA (also termed semantic dementia) and logopenic/phonological variant PPA (also termed logopenic progressive aphasia). The paper describes a 79-yr old man, who presented with normal motor speech and production rate, impaired single word retrieval and phonemic errors in spontaneous speech and confrontational naming. Confrontation naming was strongly affected by lexical frequency. He was impaired on repetition of sentences and phrases. Reading was intact for regularly spelled words but not for irregular words (surface dyslexia). Comprehension was spared at the single word level, but impaired for complex sentences. He performed within the normal range on the Dutch equivalent of the Pyramids and Palm Trees (PPT) Pictures Test, indicating that semantic processing was preserved. There was, however, a slight deficiency on the PPT Words Test, which appeals to semantic knowledge of verbal associations. His core deficit was interpreted as an inability to retrieve stored lexical-phonological information for spoken word production in spontaneous speech, confrontation naming, repetition and reading aloud.

ABCA7 rare variants and Alzheimer disease risk.

Science.gov (United States)

Le Guennec, Kilan; Nicolas, Gaël; Quenez, Olivier; Charbonnier, Camille; Wallon, David; Bellenguez, Céline; Grenier-Boley, Benjamin; Rousseau, Stéphane; Richard, Anne-Claire; Rovelet-Lecrux, Anne; Bacq, Delphine; Garnier, Jean-Guillaume; Olaso, Robert; Boland, Anne; Meyer, Vincent; Deleuze, Jean-François; Amouyel, Philippe; Munter, Hans Markus; Bourque, Guillaume; Lathrop, Mark; Frebourg, Thierry; Redon, Richard; Letenneur, Luc; Dartigues, Jean-François; Pasquier, Florence; Rollin-Sillaire, Adeline; Génin, Emmanuelle; Lambert, Jean-Charles; Hannequin, Didier; Campion, Dominique

2016-06-07

To study the association between ABCA7 rare coding variants and Alzheimer disease (AD) in a case-control setting. We conducted a whole exome analysis among 484 French patients with early-onset AD and 590 ethnically matched controls. After collapsing rare variants (minor allele frequency ≤1%), we detected an enrichment of ABCA7 loss of function (LOF) and predicted damaging missense variants in cases (odds ratio [OR] 3.40, 95% confidence interval [CI] 1.68-7.35, p = 0.0002). Performing a meta-analysis with previously published data, we found that in a combined sample of 1,256 patients and 1,347 controls from France and Belgium, the OR was 2.81 (95% CI 1.89-4.20, p = 3.60 × 10(-7)). These results confirm that ABCA7 LOF variants are enriched in patients with AD and extend this finding to predicted damaging missense variants. © 2016 American Academy of Neurology.

Electrophoretic variants of blood proteins in Japanese, 7

International Nuclear Information System (INIS)

Satoh, Chiyoko; Takahashi, Norio; Kimura, Yasukazu; Miura, Akiko; Kaneko, Junko; Fujita, Mikio; Toyama, Kyoko.

1986-11-01

A total of 16,835 children, of whom 11,737 are unrelated, from Hiroshima and Nagasaki were examined for erythrocyte cytoplasmic glutamate-oxaloacetate transaminase (GOT1) by starch gel electrophoresis. A variant allele named GOT1*2HR1 which seems to be identical with GOT1*2 was encountered in polymorphic frequency. Five kinds of rare variants, 3NG1, 4NG1, 5NG1, 6HR1, and 7NG1 were encountered in a total of 109 children. Except for 7NG1 for which complete family study was unable, family studies confirmed the genetic nature of these rare variants, since for all instances in which both parents could be examined, one of the parents exhibited the same variant as that of their child. Thermostability profiles of these six variants were normal. The enzyme activities of five were decreased, while the value of one was normal compared to that of GOT1 1. (author)

Using Noble Gas Measurements to Derive Air-Sea Process Information and Predict Physical Gas Saturations

Science.gov (United States)

Hamme, Roberta C.; Emerson, Steven R.; Severinghaus, Jeffrey P.; Long, Matthew C.; Yashayaev, Igor

2017-10-01

Dissolved gas distributions are important because they influence oceanic habitats and Earth's climate, yet competing controls by biology and physics make gas distributions challenging to predict. Bubble-mediated gas exchange, temperature change, and varying atmospheric pressure all push gases away from equilibrium. Here we use new noble gas measurements from the Labrador Sea to demonstrate a technique to quantify physical processes. Our analysis shows that water-mass formation can be represented by a quasi steady state in which bubble fluxes and cooling push gases away from equilibrium balanced by diffusive gas exchange forcing gases toward equilibrium. We quantify the rates of these physical processes from our measurements, allowing direct comparison to gas exchange parameterizations, and predict the physically driven saturation of other gases. This technique produces predictions that reasonably match N2/Ar observations and demonstrates that physical processes should force SF6 to be ˜6% more supersaturated than CFC-11 and CFC-12, impacting ventilation age calculations.

Identifying noncoding risk variants using disease-relevant gene regulatory networks.

Science.gov (United States)

Gao, Long; Uzun, Yasin; Gao, Peng; He, Bing; Ma, Xiaoke; Wang, Jiahui; Han, Shizhong; Tan, Kai

2018-02-16

Identifying noncoding risk variants remains a challenging task. Because noncoding variants exert their effects in the context of a gene regulatory network (GRN), we hypothesize that explicit use of disease-relevant GRNs can significantly improve the inference accuracy of noncoding risk variants. We describe Annotation of Regulatory Variants using Integrated Networks (ARVIN), a general computational framework for predicting causal noncoding variants. It employs a set of novel regulatory network-based features, combined with sequence-based features to infer noncoding risk variants. Using known causal variants in gene promoters and enhancers in a number of diseases, we show ARVIN outperforms state-of-the-art methods that use sequence-based features alone. Additional experimental validation using reporter assay further demonstrates the accuracy of ARVIN. Application of ARVIN to seven autoimmune diseases provides a holistic view of the gene subnetwork perturbed by the combinatorial action of the entire set of risk noncoding mutations.

Effects of Physical Exercise on Autism Spectrum Disorders: A Meta-Analysis

Science.gov (United States)

Sowa, Michelle; Meulenbroek, Ruud

2012-01-01

It is generally agreed that regular physical exercise promotes physical and mental health, but what are the benefits in people with Autism Spectrum Disorders (ASD)? This meta-analysis evaluates 16 behavioural studies reporting on a total of 133 children and adults with various variants of the syndrome who were offered structured physical…

Common variants of the genes encoding erythropoietin and its receptor modulate cognitive performance in schizophrenia

DEFF Research Database (Denmark)

Kästner, Anne; Grube, Sabrina; El-Kordi, Ahmed

2012-01-01

-term memory readouts, with one particular combination of genotypes superior to all others (p 800), these associations were confirmed. A matching preclinical study with mice demonstrated cognitive processing speed and memory enhanced upon transgenic......Erythropoietin (EPO) improves cognitive performance in clinical studies and rodent experiments. We hypothesized that an intrinsic role of EPO for cognition exists, with particular relevance in situations of cognitive decline, which is reflected by associations of EPO and EPO receptor (EPOR......) genotypes with cognitive functions. To prove this hypothesis, schizophrenic patients (N > 1000) were genotyped for 5' upstream-located gene variants, EPO SNP rs1617640 (T/G) and EPORSTR(GA)(n). Associations of these variants were obtained for cognitive processing speed, fine motor skills and short...

Golden Rule of Morphology and Variants of Word forms

Directory of Open Access Journals (Sweden)

Hlaváčová Jaroslava

2017-12-01

Full Text Available In many languages, some words can be written in several ways. We call them variants. Values of all their morphological categories are identical, which leads to an identical morphological tag. Together with the identical lemma, we have two or more wordforms with the same morphological description. This ambiguity may cause problems in various NLP applications. There are two types of variants – those affecting the whole paradigm (global variants and those affecting only wordforms sharing some combinations of morphological values (inflectional variants. In the paper, we propose means how to tag all wordforms, including their variants, unambiguously. We call this requirement “Golden rule of morphology”. The paper deals mainly with Czech, but the ideas can be applied to other languages as well.

Teaching Information Systems Development via Process Variants

Science.gov (United States)

Tan, Wee-Kek; Tan, Chuan-Hoo

2010-01-01

Acquiring the knowledge to assemble an integrated Information System (IS) development process that is tailored to the specific needs of a project has become increasingly important. It is therefore necessary for educators to impart to students this crucial skill. However, Situational Method Engineering (SME) is an inherently complex process that…

Self-efficacy mediates the relationship between behavioral processes of change and physical activity in older breast cancer survivors.

Science.gov (United States)

Loprinzi, Paul D; Cardinal, Bradley J

2013-01-01

The degree to which breast cancer survivors use behavioral processes of change has not been investigated. Additionally, the relationship between behavioral processes and other theory-based mediators of adult physical activity behavior has not been extensively studied among breast cancer survivors. The objectives of this study were to: (1) determine the extent to which breast cancer survivors use behavioral processes associated with physical activity behavior change, and (2) examine the inter-relationships between behavioral processes, self-efficacy, and physical activity behavior among breast cancer survivors. Sixty-nine breast cancer survivors completed surveys examining behavioral processes and exercise-specific self-efficacy. Six months later they completed a self-report physical activity questionnaire. Findings showed the majority of breast cancer survivors did not use approximately half of the behavioral processes on a regular basis, and self-efficacy completely mediated the relationship between behavioral processes and physical activity. Health care professionals may help enhance self-efficacy and ultimately increase physical activity behavior in breast cancer survivors by teaching behavior skills such as enlisting social support.

N-terminal nesprin-2 variants regulate β-catenin signalling

Energy Technology Data Exchange (ETDEWEB)

Zhang, Qiuping; Minaisah, Rose-Marie; Ferraro, Elisa; Li, Chen; Porter, Lauren J.; Zhou, Can; Gao, Fang; Zhang, Junyi; Rajgor, Dipen; Autore, Flavia; Shanahan, Catherine M.; Warren, Derek T., E-mail: derek.warren@kcl.ac.uk

2016-07-15

The spatial compartmentalisation of biochemical signalling pathways is essential for cell function. Nesprins are a multi-isomeric family of proteins that have emerged as signalling scaffolds, herein, we investigate the localisation and function of novel nesprin-2 N-terminal variants. We show that these nesprin-2 variants display cell specific distribution and reside in both the cytoplasm and nucleus. Immunofluorescence microscopy revealed that nesprin-2 N-terminal variants colocalised with β-catenin at cell-cell junctions in U2OS cells. Calcium switch assays demonstrated that nesprin-2 and β-catenin are lost from cell-cell junctions in low calcium conditions whereas emerin localisation at the NE remained unaltered, furthermore, an N-terminal fragment of nesprin-2 was sufficient for cell-cell junction localisation and interacted with β-catenin. Disruption of these N-terminal nesprin-2 variants, using siRNA depletion resulted in loss of β-catenin from cell-cell junctions, nuclear accumulation of active β-catenin and augmented β-catenin transcriptional activity. Importantly, we show that U2OS cells lack nesprin-2 giant, suggesting that the N-terminal nesprin-2 variants regulate β-catenin signalling independently of the NE. Together, these data identify N-terminal nesprin-2 variants as novel regulators of β-catenin signalling that tether β-catenin to cell-cell contacts to inhibit β-catenin transcriptional activity. - Highlights: • N-terminal nesprin-2 variants display cell specific expression patterns. • N-terminal spectrin repeats of nesprin-2 interact with β-catenin. • N-terminal nesprin-2 variants scaffold β-catenin at cell-cell junctions.. • Nesprin-2 variants play multiple roles in β-catenin signalling.

Fundamental Characteristics of Industrial Variant Specification Systems

DEFF Research Database (Denmark)

Hansen, Benjamin Loer; Hvam, Lars

2004-01-01

fundamental concepts related to this task, which are relevant to understand for academia and practitioners working with the subject. This is done through a description of variant specification tasks and typical aspects of system solutions. To support the description of variant specification tasks and systems...

Xeroderma pigmentosum variants have a slow recovery of DNA synthesis after irradiation with ultraviolet light

International Nuclear Information System (INIS)

Cleaver, J.E.; Thomas, G.H.; Park, S.D.

1979-01-01

Human cells (normal and xeroderma pigmentosum variant) irradiated with ultraviolet light and pulse-labelled with [ 3 H]thymidine underwent transient decline and recovery of molecular weights of newly synthesized DNA and rates of [ 3 H]thymidine incorporation. The ability of synthesize normal-sized DNA recovered more rapidly in both cell types than thymidine incorporation. During recovery cells steadily increased in their ability to replicate normalsized DNA on damaged templates. The molecular weight versus time curves fitted exponential functions with similar rate constants in normal and heterozygous xeroderma pigmentosum cells, but with a slower rate in two xeroderma pigmentosum variant cell lines. Caffeine added during the post-irradiation period eliminated the recovery of molecular weights in xeroderma pigmentsoum variant but not in normal cells. The recovery of the ability to synthesize normal-sized DNA represents a combination of a number of cellular regulatory processes, some of which are constitutive, and one of which is altered in the xeroderma pigmentosum variant such that recovery becomes slow and caffeine sensitive. (Auth.)

Physically based modelling and optimal operation for product drying during post-harvest processing.

NARCIS (Netherlands)

Boxtel, van A.J.B.; Lukasse, L.; Farkas, I.; Rendik, Z.

1996-01-01

The development of new procedures for crop production and post-harvest processing requires models. Models based on physical backgrounds are most useful for this purpose because of their extrapolation potential. An optimal procedure is developed for alfalfa drying using a physical model. The model

Microsatellite Instability Use in Mismatch Repair Gene Sequence Variant Classification

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Bryony A. Thompson

2015-03-01

Full Text Available Inherited mutations in the DNA mismatch repair genes (MMR can cause MMR deficiency and increased susceptibility to colorectal and endometrial cancer. Microsatellite instability (MSI is the defining molecular signature of MMR deficiency. The clinical classification of identified MMR gene sequence variants has a direct impact on the management of patients and their families. For a significant proportion of cases sequence variants of uncertain clinical significance (also known as unclassified variants are identified, constituting a challenge for genetic counselling and clinical management of families. The effect on protein function of these variants is difficult to interpret. The presence or absence of MSI in tumours can aid in determining the pathogenicity of associated unclassified MMR gene variants. However, there are some considerations that need to be taken into account when using MSI for variant interpretation. The use of MSI and other tumour characteristics in MMR gene sequence variant classification will be explored in this review.

ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants.

Science.gov (United States)

Patel, Ronak Y; Shah, Neethu; Jackson, Andrew R; Ghosh, Rajarshi; Pawliczek, Piotr; Paithankar, Sameer; Baker, Aaron; Riehle, Kevin; Chen, Hailin; Milosavljevic, Sofia; Bizon, Chris; Rynearson, Shawn; Nelson, Tristan; Jarvik, Gail P; Rehm, Heidi L; Harrison, Steven M; Azzariti, Danielle; Powell, Bradford; Babb, Larry; Plon, Sharon E; Milosavljevic, Aleksandar

2017-01-12

The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through practice guidelines, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have published standards and guidelines for the interpretation of sequence variants. However, manual application of the guidelines is tedious and prone to human error. Web-based tools and software systems may not only address this problem but also document reasoning and supporting evidence, thus enabling transparency of evidence-based reasoning and resolution of discordant interpretations. In this report, we describe the design, implementation, and initial testing of the Clinical Genome Resource (ClinGen) Pathogenicity Calculator, a configurable system and web service for the assessment of pathogenicity of Mendelian germline sequence variants. The system allows users to enter the applicable ACMG/AMP-style evidence tags for a specific allele with links to supporting data for each tag and generate guideline-based pathogenicity assessment for the allele. Through automation and comprehensive documentation of evidence codes, the system facilitates more accurate application of the ACMG/AMP guidelines, improves standardization in variant classification, and facilitates collaborative resolution of discordances. The rules of reasoning are configurable with gene-specific or disease-specific guideline variations (e.g. cardiomyopathy-specific frequency thresholds and functional assays). The software is modular, equipped with robust application program interfaces (APIs), and available under a free open source license and as a cloud-hosted web service, thus facilitating both stand-alone use and integration with existing variant curation and interpretation systems. The Pathogenicity Calculator is accessible at http

Characterization of mussel H2A.Z.2: a new H2A.Z variant preferentially expressed in germinal tissues from Mytilus.

Science.gov (United States)

Rivera-Casas, Ciro; González-Romero, Rodrigo; Vizoso-Vazquez, Ángel; Cheema, Manjinder S; Cerdán, M Esperanza; Méndez, Josefina; Ausió, Juan; Eirin-Lopez, Jose M

2016-10-01

Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin. In the present work we describe, for the first time, the presence of a second H2A.Z variant (H2A.Z.2) in the genome of a non-vertebrate animal, the mussel Mytilus. The molecular and evolutionary characterization of mussel H2A.Z.1 and H2A.Z.2 histones is consistent with their functional specialization, supported on sequence divergence at promoter and coding regions as well as on varying gene expression patterns. More precisely, the expression of H2A.Z.2 transcripts in gonadal tissue and its potential upregulation in response to genotoxic stress might be mirroring the specialization of this variant in DNA repair. Overall, the findings presented in this work complement recent reports describing the widespread presence of other histone variants across eukaryotes, supporting an ancestral origin and conserved role for histone variants in chromatin.

HFE gene variants affect iron in the brain.

Science.gov (United States)

Nandar, Wint; Connor, James R

2011-04-01

Iron accumulation in the brain and increased oxidative stress are consistent observations in many neurodegenerative diseases. Thus, we have begun examination into gene mutations or allelic variants that could be associated with loss of iron homeostasis. One of the mechanisms leading to iron overload is a mutation in the HFE gene, which is involved in iron metabolism. The 2 most common HFE gene variants are C282Y (1.9%) and H63D (8.9%). The C282Y HFE variant is more commonly associated with hereditary hemochromatosis, which is an autosomal recessive disorder, characterized by iron overload in a number of systemic organs. The H63D HFE variant appears less frequently associated with hemochromatosis, but its role in the neurodegenerative diseases has received more attention. At the cellular level, the HFE mutant protein resulting from the H63D HFE gene variant is associated with iron dyshomeostasis, increased oxidative stress, glutamate release, tau phosphorylation, and alteration in inflammatory response, each of which is under investigation as a contributing factor to neurodegenerative diseases. Therefore, the HFE gene variants are proposed to be genetic modifiers or a risk factor for neurodegenerative diseases by establishing an enabling milieu for pathogenic agents. This review will discuss the current knowledge of the association of the HFE gene variants with neurodegenerative diseases: amyotrophic lateral sclerosis, Alzheimer's disease, Parkinson's disease, and ischemic stroke. Importantly, the data herein also begin to dispel the long-held view that the brain is protected from iron accumulation associated with the HFE mutations.

Genotype–phenotype correlations in individuals with pathogenic RERE variants

Science.gov (United States)

Jordan, Valerie K.; Fregeau, Brieana; Ge, Xiaoyan; Giordano, Jessica; Wapner, Ronald J.; Balci, Tugce B.; Carter, Melissa T.; Bernat, John A.; Moccia, Amanda N.; Srivastava, Anshika; Martin, Donna M.; Bielas, Stephanie L.; Pappas, John; Svoboda, Melissa D.; Rio, Marlène; Boddaert, Nathalie; Cantagrel, Vincent; Lewis, Andrea M.; Scaglia, Fernando; Kohler, Jennefer N.; Bernstein, Jonathan A.; Dries, Annika M.; Rosenfeld, Jill A.; DeFilippo, Colette; Thorson, Willa; Yang, Yaping; Sherr, Elliott H.; Bi, Weimin; Scott, Daryl A.

2018-01-01

Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype–phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7. PMID:29330883

Molecular models of NS3 protease variants of the Hepatitis C virus

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Mello Isabel MVGC

2005-01-01

Full Text Available Abstract Background Hepatitis C virus (HCV currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed. Results The atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures. Conclusions This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure

Real-Time Joint Streaming Data Processing from Social and Physical Sensors

Science.gov (United States)

Kropivnitskaya, Y. Y.; Qin, J.; Tiampo, K. F.; Bauer, M.

2014-12-01

The results of the technological breakthroughs in computing that have taken place over the last few decades makes it possible to achieve emergency management objectives that focus on saving human lives and decreasing economic effects. In particular, the integration of a wide variety of information sources, including observations from spatially-referenced physical sensors and new social media sources, enables better real-time seismic hazard analysis through distributed computing networks. The main goal of this work is to utilize innovative computational algorithms for better real-time seismic risk analysis by integrating different data sources and processing tools into streaming and cloud computing applications. The Geological Survey of Canada operates the Canadian National Seismograph Network (CNSN) with over 100 high-gain instruments and 60 low-gain or strong motion seismographs. The processing of the continuous data streams from each station of the CNSN provides the opportunity to detect possible earthquakes in near real-time. The information from physical sources is combined to calculate a location and magnitude for an earthquake. The automatically calculated results are not always sufficiently precise and prompt that can significantly reduce the response time to a felt or damaging earthquake. Social sensors, here represented as Twitter users, can provide information earlier to the general public and more rapidly to the emergency planning and disaster relief agencies. We introduce joint streaming data processing from social and physical sensors in real-time based on the idea that social media observations serve as proxies for physical sensors. By using the streams of data in the form of Twitter messages, each of which has an associated time and location, we can extract information related to a target event and perform enhanced analysis by combining it with physical sensor data. Results of this work suggest that the use of data from social media, in conjunction

Poisson Approximation-Based Score Test for Detecting Association of Rare Variants.

Science.gov (United States)

Fang, Hongyan; Zhang, Hong; Yang, Yaning

2016-07-01

Genome-wide association study (GWAS) has achieved great success in identifying genetic variants, but the nature of GWAS has determined its inherent limitations. Under the common disease rare variants (CDRV) hypothesis, the traditional association analysis methods commonly used in GWAS for common variants do not have enough power for detecting rare variants with a limited sample size. As a solution to this problem, pooling rare variants by their functions provides an efficient way for identifying susceptible genes. Rare variant typically have low frequencies of minor alleles, and the distribution of the total number of minor alleles of the rare variants can be approximated by a Poisson distribution. Based on this fact, we propose a new test method, the Poisson Approximation-based Score Test (PAST), for association analysis of rare variants. Two testing methods, namely, ePAST and mPAST, are proposed based on different strategies of pooling rare variants. Simulation results and application to the CRESCENDO cohort data show that our methods are more powerful than the existing methods. © 2016 John Wiley & Sons Ltd/University College London.

Cellulase variants with improved expression, activity and stability, and use thereof

Science.gov (United States)

Aehle, Wolfgang; Bott, Richard R; Bower, Benjamin; Caspi, Jonathan; Estell, David A; Goedegebuur, Frits; Hommes, Ronaldus W.J.; Kaper, Thijs; Kelemen, Bradley; Kralj, Slavko; Van Lieshout, Johan; Nikolaev, Igor; Van Stigt Thans, Sander; Wallace, Louise; Vogtentanz, Gudrun; Sandgren, Mats

2014-03-25

The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having improved expression, activity and/or stability. Also described are nucleic acids encoding the cellulase variants, compositions comprising the cellulase variants, and methods of use thereof.

Cellulase variants with improved expression, activity and stability, and use thereof

Energy Technology Data Exchange (ETDEWEB)

Aehle, Wolfgang; Bott, Richard R.; Bower, Benjamin S.; Caspi, Jonathan; Goedegebuur, Frits; Hommes, Ronaldus Wilhelmus Joannes; Kaper, Thijs; Kelemen, Bradley R.; Kralj, Slavko; Van Lieshout, Johannes Franciscus Thomas; Nikolaev, Igor; Wallace, Louise; Van Stigt Thans, Sander; Vogtentanz, Gudrun; Sandgren, Mats

2016-12-20

The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having improved expression, activity and/or stability. Also described are nucleic acids encoding the cellulase variants, compositions comprising the cellulase variants, and methods of use thereof.

Genetic variants of ghrelin in metabolic disorders.

Science.gov (United States)

Ukkola, Olavi

2011-11-01

An increasing understanding of the role of genes in the development of obesity may reveal genetic variants that, in combination with conventional risk factors, may help to predict an individual's risk for developing metabolic disorders. Accumulating evidence indicates that ghrelin plays a role in regulating food intake and energy homeostasis and it is a reasonable candidate gene for obesity-related co-morbidities. In cross-sectional studies low total ghrelin concentrations and some genetic polymorphisms of ghrelin have been associated with obesity-associated diseases. The present review highlights many of the important problems in association studies of genetic variants and complex diseases. It is known that population-specific differences in reported associations exist. We therefore conclude that more studies on variants of ghrelin gene are needed to perform in different populations to get deeper understanding on the relationship of ghrelin gene and its variants to obesity. Copyright © 2011 Elsevier Inc. All rights reserved.

Isolation of a variant of Candida albicans.

Science.gov (United States)

Buckley, H R; Price, M R; Daneo-Moore, L

1982-01-01

During the course of Candida albicans antigen production, a variant of this organism was encountered which did not produce hyphae at 37 degrees C. Presented here are some of the characteristics of this variant. It produces hyphae at 25 degrees C on cornmeal agar and synthetic medium plus N-acetylglucosamine and Tween 80. At 37 degrees C, it does not produce hyphae on these media, although C. albicans normally does produce hyphae under these circumstances. In liquid synthetic medium, this variant does not produce hyphae at 37 degrees C. The variant strain was analyzed for DNA, RNA, protein content, and particle size. After 50 to 70 h in balanced exponential-phase growth, particle size distribution was narrow, and there were no differences in the DNA, RNA, or protein content per particle in the two strains. When balanced exponential-phase cultures were brought into stationary phase, both strains contained the same amount of DNA per cell. Images PMID:6752021

Isolation of a variant of Candida albicans.

Science.gov (United States)

Buckley, H R; Price, M R; Daneo-Moore, L

1982-09-01

During the course of Candida albicans antigen production, a variant of this organism was encountered which did not produce hyphae at 37 degrees C. Presented here are some of the characteristics of this variant. It produces hyphae at 25 degrees C on cornmeal agar and synthetic medium plus N-acetylglucosamine and Tween 80. At 37 degrees C, it does not produce hyphae on these media, although C. albicans normally does produce hyphae under these circumstances. In liquid synthetic medium, this variant does not produce hyphae at 37 degrees C. The variant strain was analyzed for DNA, RNA, protein content, and particle size. After 50 to 70 h in balanced exponential-phase growth, particle size distribution was narrow, and there were no differences in the DNA, RNA, or protein content per particle in the two strains. When balanced exponential-phase cultures were brought into stationary phase, both strains contained the same amount of DNA per cell.

Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in a Thai Family with Autism Spectrum Disorder

Directory of Open Access Journals (Sweden)

Chuphong Thongnak

2018-01-01

Full Text Available Autism spectrum disorder (ASD has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants. Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing. This study identified a possible causative variant for ASD, c.2951G>A, in the FGD6 gene. We demonstrated the potential for ASD genetic variants associated with ASD using whole-exome sequencing and a bioinformatics filtering procedure. These techniques could be useful in identifying possible causative ASD variants, especially in cases in which variants cannot be identified by other techniques.

Modeling and Validation of the Ecological Behavior of Wild-Type Listeria monocytogenes and Stress-Resistant Variants.

Science.gov (United States)

Metselaar, Karin I; Abee, Tjakko; Zwietering, Marcel H; den Besten, Heidy M W

2016-09-01

Listeria monocytogenes exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress-resistant variants. This study aimed to evaluate the impact of the presence of stress-resistant variants of Listeria monocytogenes and their corresponding trade-offs on population composition under different environmental conditions. A set of stress robustness and growth parameters of the wild type (WT) and an rpsU deletion variant was obtained and used to model their growth behavior under combined mild stress conditions and to model their kinetics under single- and mixed-strain conditions in a simulated food chain. Growth predictions for the WT and the rpsU deletion variant matched the experimental data generally well, although some deviations from the predictions were observed. The data highlighted the influence of the environmental conditions on the ratio between the WT and variant. Prediction of performance in the simulated food chain proved to be challenging. The trend of faster growth and lower stress robustness for the WT than for the rpsU variant in the different steps of the chain was confirmed, but especially for the inactivation steps and the time needed to resume growth after an inactivation step, the experimental data deviated from the model predictions. This report provides insights into the conditions which can select for stress-resistant variants in industrial settings and discusses their potential persistence in food processing environments. Listeria monocytogenes exhibits a heterogeneous stress response which can partially be attributed to the presence of genetic variants. These stress-resistant variants survive better under severe conditions but have, on the other hand, a reduced growth rate. To date, the ecological behavior and potential impact of the presence of stress-resistant variants is not fully understood. In this study, we quantitatively assessed growth and inactivation behavior of wild-type L

Dataset of mitochondrial genome variants in oncocytic tumors

Directory of Open Access Journals (Sweden)

Lihua Lyu

2018-04-01

Full Text Available This dataset presents the mitochondrial genome variants associated with oncocytic tumors. These data were obtained by Sanger sequencing of the whole mitochondrial genomes of oncocytic tumors and the adjacent normal tissues from 32 patients. The mtDNA variants are identified after compared with the revised Cambridge sequence, excluding those defining haplogroups of our patients. The pathogenic prediction for the novel missense variants found in this study was performed with the Mitimpact 2 program.

Biochemical characteristics of glucose-6-phosphate dehydrogenase variants among the Malays of Singapore with report of a new non-deficient (GdSingapore) and three deficient variants.

Science.gov (United States)

Saha, N; Hong, S H; Wong, H A; Jeyaseelan, K; Tay, J S

1991-12-01

Biochemical characteristics of one non-deficient fast G6PD variant (GdSingapore) and six different deficient variants (three new, two Mahidol, one each of Indonesian and Mediterranean) were studied among the Malays of Singapore. The GdSingapore variant had normal enzyme activity (82%) and fast electrophoretic mobilities (140% in TEB buffer, 160% in phosphate and 140% in Tris-HCl buffer systems respectively). This variant is further characterized by normal Km for G6P; utilization of analogues (Gal6P, 2dG6P; dAmNADP), heat stability and pH optimum. The other six deficient G6PD variants had normal electrophoretic mobility in TEB buffer with enzyme activities ranging from 1 to 12% of GdB+. The biochemical characteristics identity them to be 2 Mahidol, 1 Indonesian and 1 Mediterranean variants and three new deficient variants.

Characterization of form variants of Xenorhabdus luminescens.

NARCIS (Netherlands)

Gerritsen, L.J.M.; Raay, de G.; Smits, P.H.

1992-01-01

From Xenorhabdus luminescens XE-87.3 four variants were isolated. One, which produced a red pigment and antibiotics, was luminescent, and could take up dye from culture media, was considered the primary form (XE-red). A pink-pigmented variant (XE-pink) differed from the primary form only in

Overland erosion of uranium-mill-tailings impoundments: physical processes and computational methods

International Nuclear Information System (INIS)

Walters, M.H.

1983-03-01

The surface runoff and erosional processes of watersheds caused by rainfall-runoff are reviewed. Soil properties, topography, and rainstorm distribution are discussed with respect to their effects on soil erosion. The effects of climate and vegetation are briefly presented. Regression models and physical process simulation models are reviewed

A STUDY OF NUCLEAR PHYSICS PROCESSES AT MIDDLE SCHOOL

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Mykola I. Sadovyi

2011-02-01

Full Text Available The article discloses the problem of new technology usage for the physics’ experiment in the quantum physics modeling. Currency of investigation consists in the need of physics experiment organization and realization in high energy physics with the consistent usage of activity method in middle education institutions. This kind of method considerably stirs up the process of model usage and modeling, abstracting, idealization and analogy. Idealized objects’ creation, elementary part transmutation, in particular, that does not exist in the objective reality, but possesses definite prototypes in the real world that help in their first approximation to the truth. The program Macromedia Flesh has been used in the article. This program has a range of advantages comparing to other possible software according to their possibilities and usage simplicity. The program uses all kinds of computer graph (raster, vectorial, which gives great opportunities for graphic objects’ creation, and prepared files take minimum of the constant memory. A part of developed experiments of the modeling character is given in the article. Demonstrations are done in dynamic rate.

Alternative Processes for Water Reclamation and Solid Waste Processing in a Physical/chemical Bioregenerative Life Support System

Science.gov (United States)

Rogers, Tom D.

1990-01-01

Viewgraphs on alternative processes for water reclamation and solid waste processing in a physical/chemical-bioregenerative life support system are presented. The main objective is to focus attention on emerging influences of secondary factors (i.e., waste composition, type and level of chemical contaminants, and effects of microorganisms, primarily bacteria) and to constructively address these issues by discussing approaches which attack them in a direct manner.

Identificação de variantes de hemoglobina em doadores de sangue Identification of hemoglobin variants in blood donor

Directory of Open Access Journals (Sweden)

Ana C. Bonini-Domingos

2004-03-01

Full Text Available Hemoglobinopathies are the most common genetic diseases and affect a great number of individuals in the world, with diverse clinical complications ranging from the almost unnoticeable to lethal consequences. In Brazil the occurrence of hemoglobinopathies is very frequent and influenced by the ethnical groups that are the basis of populations in different regions. The phenotype may be influenced by environmental and genetic factors and by migration. An understanding of these genetic diseases is important for the health and quality of life of the population. In this work we assessed the presence of Hb variants in blood donors from São José do Rio Preto and region, and we observed the occurrence of variants including Hb S and Hb C but in particular the so-called "S-Like" variants. Good determination of the forms of variant hemoglobins is very important to give better guidance to blood donors and their families, and to improve the quality of blood transfusion.

Mouse ribosomal RNA genes contain multiple differentially regulated variants.

Directory of Open Access Journals (Sweden)

Hung Tseng

2008-03-01

Full Text Available Previous cytogenetic studies suggest that various rDNA chromosomal loci are not equally active in different cell types. Consistent with this variability, rDNA polymorphism is well documented in human and mouse. However, attempts to identify molecularly rDNA variant types, which are regulated individually (i.e., independent of other rDNA variants and tissue-specifically, have not been successful. We report here the molecular cloning and characterization of seven mouse rDNA variants (v-rDNA. The identification of these v-rDNAs was based on restriction fragment length polymorphisms (RFLPs, which are conserved among individuals and mouse strains. The total copy number of the identified variants is less than 100 and the copy number of each individual variant ranges from 4 to 15. Sequence analysis of the cloned v-rDNA identified variant-specific single nucleotide polymorphisms (SNPs in the transcribed region. These SNPs were used to develop a set of variant-specific PCR assays, which permitted analysis of the v-rDNAs' expression profiles in various tissues. These profiles show that three v-rDNAs are expressed in all tissues (constitutively active, two are expressed in some tissues (selectively active, and two are not expressed (silent. These expression profiles were observed in six individuals from three mouse strains, suggesting the pattern is not randomly determined. Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA.

Autism as an adaptive common variant pathway for human brain development

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Mark H. Johnson

2017-06-01

Full Text Available While research on focal perinatal lesions has provided evidence for recovery of function, much less is known about processes of brain adaptation resulting from mild but widespread disturbances to neural processing over the early years (such as alterations in synaptic efficiency. Rather than being viewed as a direct behavioral consequence of life-long neural dysfunction, I propose that autism is best viewed as the end result of engaging adaptive processes during a sensitive period. From this perspective, autism is not appropriately described as a disorder of neurodevelopment, but rather as an adaptive common variant pathway of human functional brain development.

Thermal physics of gas-thermal coatings formation processes. State of investigations

International Nuclear Information System (INIS)

Fialko, N.M.; Prokopov, V.G.; Meranova, N.O.; Borisov, Yu.S.; Korzhik, V.N.; Sherenkovskaya, G.P.; AN Ukrainskoj SSR, Kiev

1993-01-01

The analysis of state of investigations of gas-thermal coatings formation processes in presented. Classification of approaches to mathematical simulation of thermal phenomena studies is offered. The general characteristics of three main approaches to the analysis of heat transport processes is given. Some problems of mathematical simulation of single particle thermal interaction with solid surface are considered in details. The main physical assumptions are analysed

Development of a testlet generator in re-engineering the Indonesian physics national-exams

Science.gov (United States)

Mindyarto, Budi Naini; Mardapi, Djemari; Bastari

2017-08-01

The Indonesian Physics national-exams are end-of-course summative assessments that could be utilized to support the assessment for learning in physics educations. This paper discusses the development and evaluation of a testlet generator based on a re-engineering of Indonesian physics national exams. The exam problems were dissected and decomposed into testlets revealing the deeper understanding of the underlying physical concepts by inserting a qualitative question and its scientific reasoning question. A template-based generator was built to facilitate teachers in generating testlet variants that would be more conform to students' scientific attitude development than their original simple multiple-choice formats. The testlet generator was built using open source software technologies and was evaluated focusing on the black-box testing by exploring the generator's execution, inputs and outputs. The results showed the correctly-performed functionalities of the developed testlet generator in validating inputs, generating testlet variants, and accommodating polytomous item characteristics.

Ultrasonographic imaging of papillary thyroid carcinoma variants

Energy Technology Data Exchange (ETDEWEB)

Shin, Jung Hee [Dept. of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

2017-04-15

Ultrasonography (US) is routinely used to evaluate thyroid nodules. The US features of papillary thyroid carcinoma (PTC), the most common thyroid malignancy, include hypoechogenicity, spiculated/microlobulated margins, microcalcifications, and a nonparallel orientation. However, many PTC variants have been identified, some of which differ from the classic type of PTC in terms of biological behavior and clinical outcomes. This review describes the US features and clinical implications of the variants of PTC. With the introduction of active surveillance replacing immediate biopsy or surgical treatment of indolent, small PTCs, an understanding of the US characteristics of PTC variants will facilitate the individualized management of patients with PTC.

Treatment of spelling variants in Setswana monolingual dictionaries

African Journals Online (AJOL)

user

. ..... Table 8: Variants of Names of persons and places. Setswana variants. English. Aforika, Aferika. Africa. Baebele, Babele, Beibele. Bible. Ennyelane, Engelane ..... MWEs. As in variation amongst individual words, the MWEs such as idioms.

Human papillomavirus variants among Inuit women in northern Quebec, Canada.

Science.gov (United States)

Gauthier, Barbara; Coutlée, Francois; Franco, Eduardo L; Brassard, Paul

2015-01-01

Inuit communities in northern Quebec have high rates of human papillomavirus (HPV) infection, cervical cancer and cervical cancer-related mortality as compared to the Canadian population. HPV types can be further classified as intratypic variants based on the extent of homology in their nucleotide sequences. There is limited information on the distribution of intratypic variants in circumpolar areas. Our goal was to describe the HPV intratypic variants and associated baseline characteristics. We collected cervical cell samples in 2002-2006 from 676 Inuit women between the ages of 15 and 69 years in Nunavik. DNA isolates from high-risk HPVs were sequenced to determine the intratypic variant. There were 149 women that were positive for HPVs 16, 18, 31, 33, 35, 45, 52, 56 or 58 during follow-up. There were 5 different HPV16 variants, all of European lineage, among the 57 women positive for this type. There were 8 different variants of HPV18 present and all were of European lineage (n=21). The majority of samples of HPV31 (n=52) were of lineage B. The number of isolates and diversity of the other HPV types was low. Age was the only covariate associated with HPV16 variant category. These frequencies are similar to what was seen in another circumpolar region of Canada, although there appears to be less diversity as only European variants were detected. This study shows that most variants were clustered in one lineage for each HPV type.

De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive.

Science.gov (United States)

Tokita, Mari J; Braxton, Alicia A; Shao, Yunru; Lewis, Andrea M; Vincent, Marie; Küry, Sébastien; Besnard, Thomas; Isidor, Bertrand; Latypova, Xénia; Bézieau, Stéphane; Liu, Pengfei; Motter, Connie S; Melver, Catherine Ward; Robin, Nathaniel H; Infante, Elena M; McGuire, Marianne; El-Gharbawy, Areeg; Littlejohn, Rebecca O; McLean, Scott D; Bi, Weimin; Bacino, Carlos A; Lalani, Seema R; Scott, Daryl A; Eng, Christine M; Yang, Yaping; Schaaf, Christian P; Walkiewicz, Magdalena A

2016-09-01

SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

The revised APTA code of ethics for the physical therapist and standards of ethical conduct for the physical therapist assistant: theory, purpose, process, and significance.

Science.gov (United States)

Swisher, Laura Lee; Hiller, Peggy

2010-05-01

In June 2009, the House of Delegates (HOD) of the American Physical Therapy Association (APTA) passed a major revision of the APTA Code of Ethics for physical therapists and the Standards of Ethical Conduct for the Physical Therapist Assistant. The revised documents will be effective July 1, 2010. The purposes of this article are: (1) to provide a historical, professional, and theoretical context for this important revision; (2) to describe the 4-year revision process; (3) to examine major features of the documents; and (4) to discuss the significance of the revisions from the perspective of the maturation of physical therapy as a doctoring profession. PROCESS OF REVISION: The process for revision is delineated within the context of history and the Bylaws of APTA. FORMAT, STRUCTURE, AND CONTENT OF REVISED CORE ETHICS DOCUMENTS: The revised documents represent a significant change in format, level of detail, and scope of application. Previous APTA Codes of Ethics and Standards of Ethical Conduct for the Physical Therapist Assistant have delineated very broad general principles, with specific obligations spelled out in the Ethics and Judicial Committee's Guide for Professional Conduct and Guide for Conduct of the Physical Therapist Assistant. In contrast to the current documents, the revised documents address all 5 roles of the physical therapist, delineate ethical obligations in organizational and business contexts, and align with the tenets of Vision 2020. The significance of this revision is discussed within historical parameters, the implications for physical therapists and physical therapist assistants, the maturation of the profession, societal accountability and moral community, potential regulatory implications, and the inclusive and deliberative process of moral dialogue by which changes were developed, revised, and approved.

FTO variant rs9939609 is associated with body mass index and waist circumference, but not with energy intake or physical activity in European- and African-American youth

NARCIS (Netherlands)

Liu, Gaifen; Zhu, Haidong; Lagou, Vasiliki; Gutin, Bernard; Stallmann-Jorgensen, Inger S.; Treiber, Frank A.; Dong, Yanbin; Snieder, Harold

2010-01-01

Background: Genome-wide association studies found common variants in the fat mass and obesity-associated (FTO) gene associated with adiposity in Caucasians and Asians but the association was not confirmed in African populations. Association of FTO variants with insulin resistance and energy intake

Physical processes in relativistic plasmas

International Nuclear Information System (INIS)

Svensson, R.

1984-01-01

The continuum emission in many active galactic nuclei (AGNs) extend to 100 keV and beyond (e.g. Rothschild et al. 1983). In thermal models of the continuum emission this implies temperatures above 10 9 K or kT of order mc 2 . In such a plasma the electrons are at least mildly relativistic and furthermore the particles and the photons are energetic enough to produce electron-positron pairs. The physics of such hot plasmas has only recently been studied in any detail and here we review the results of those studies. Significant electron-positron pair production may also occur in non-thermal models of the continuum emission if the optical depth to photon-photon pair production is greater than unity. We review the few results obtained regarding this interesting but not very well studied possibility. First, however, we briefly discuss the processes taking place in relativistic plasmas and the standard models for the continuum emission from AGNs. We then summarize the effects pair production have on these models and the observational implications of the presence of electron-positron pairs. (orig./WL)

Mission Concept to Connect Magnetospheric Physical Processes to Ionospheric Phenomena

Science.gov (United States)

Dors, E. E.; MacDonald, E.; Kepko, L.; Borovsky, J.; Reeves, G. D.; Delzanno, G. L.; Thomsen, M. F.; Sanchez, E. R.; Henderson, M. G.; Nguyen, D. C.; Vaith, H.; Gilchrist, B. E.; Spanswick, E.; Marshall, R. A.; Donovan, E.; Neilson, J.; Carlsten, B. E.

2017-12-01

On the Earth's nightside the magnetic connections between the ionosphere and the dynamic magnetosphere have a great deal of uncertainty: this uncertainty prevents us from scientifically understanding what physical processes in the magnetosphere are driving the various phenomena in the ionosphere. Since the 1990s, the space plasma physics group at Los Alamos National Laboratory has been working on a concept to connect magnetospheric physical processes to auroral phenomena in the ionosphere by firing an electron beam from a magnetospheric spacecraft and optically imaging the beam spot in the ionosphere. The magnetospheric spacecraft will carry a steerable electron accelerator, a power-storage system, a plasma contactor, and instruments to measure magnetic and electric fields, plasma, and energetic particles. The spacecraft orbit will be coordinated with a ground-based network of cameras to (a) locate the electron beam spot in the upper atmosphere and (b) monitor the aurora. An overview of the mission concept will be presented, including recent enabling advancements based on (1) a new understanding of the dynamic spacecraft charging of the accelerator and plasma-contactor system in the tenuous magnetosphere based on ion emission rather than electron collection, (2) a new understanding of the propagation properties of pulsed MeV-class beams in the magnetosphere, and (3) the design of a compact high-power 1-MeV electron accelerator and power-storage system. This strategy to (a) determine the magnetosphere-to-ionosphere connections and (b) reduce accelerator- platform charging responds to one of the six emerging-technology needs called out in the most-recent National Academies Decadal Survey for Solar and Space Physics. [LA-UR-17-23614

Genetic variants influencing phenotypic variance heterogeneity.

Science.gov (United States)

Ek, Weronica E; Rask-Andersen, Mathias; Karlsson, Torgny; Enroth, Stefan; Gyllensten, Ulf; Johansson, Åsa

2018-03-01

Most genetic studies identify genetic variants associated with disease risk or with the mean value of a quantitative trait. More rarely, genetic variants associated with variance heterogeneity are considered. In this study, we have identified such variance single-nucleotide polymorphisms (vSNPs) and examined if these represent biological gene × gene or gene × environment interactions or statistical artifacts caused by multiple linked genetic variants influencing the same phenotype. We have performed a genome-wide study, to identify vSNPs associated with variance heterogeneity in DNA methylation levels. Genotype data from over 10 million single-nucleotide polymorphisms (SNPs), and DNA methylation levels at over 430 000 CpG sites, were analyzed in 729 individuals. We identified vSNPs for 7195 CpG sites (P mean DNA methylation levels. We further showed that variance heterogeneity between genotypes mainly represents additional, often rare, SNPs in linkage disequilibrium (LD) with the respective vSNP and for some vSNPs, multiple low frequency variants co-segregating with one of the vSNP alleles. Therefore, our results suggest that variance heterogeneity of DNA methylation mainly represents phenotypic effects by multiple SNPs, rather than biological interactions. Such effects may also be important for interpreting variance heterogeneity of more complex clinical phenotypes.

Method of generating ploynucleotides encoding enhanced folding variants

Energy Technology Data Exchange (ETDEWEB)

Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

2017-05-02

The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

Influenza A (H3N2) Variant Virus

Science.gov (United States)

... Swine Variant Pandemic Other Influenza A (H3N2) Variant Virus Language: English (US) Español Recommend on Facebook Tweet Share Compartir Influenza viruses that normally circulate in pigs are called “variant” ...

CLARA: A Contemporary Approach to Physics Data Processing

Energy Technology Data Exchange (ETDEWEB)

V Gyurjyan, D Abbott, J Carbonneau, G Gilfoyle, D Heddle, G Heyes, S Paul, C Timmer, D Weygand, E Wolin

2011-12-01

In traditional physics data processing (PDP) systems, data location is static and is accessed by analysis applications. In comparison, CLARA (CLAS12 Reconstruction and Analysis framework) is an environment where data processing algorithms filter continuously flowing data. In CLARA's domain of loosely coupled services, data is not stored, but rather flows from one service to another, mutating constantly along the way. Agents, performing event processing, can then subscribe to particular data/events at any stage of the data transformation, and make intricate decisions (e.g. particle ID) by correlating events from multiple, parallel data streams and/or services. This paper presents a PDP application development framework based on service oriented and event driven architectures. This system allows users to design (Java, C++, and Python languages are supported) and deploy data processing services, as well as dynamically compose PDP applications using available services. The PDP service bus provides a layer on top of a distributed pub-sub middleware implementation, which allows complex service composition and integration without writing code. Examples of service creation and deployment, along with the CLAS12 track reconstruction application design will be presented.

Being qua becoming: Aristotle's "Metaphysics", quantum physics, and Process Philosophy

Science.gov (United States)

Johnson, David Kelley

In Aristotle's First Philosophy, science and philosophy were partners, but with the rise of empiricism, went their separate ways. Metaphysics combined the rational and irrational (i.e. final cause/unmoved mover) elements of existence to equate being with substance, postulating prime matter as pure potential that was actuated by form to create everything. Modern science reveres pure reason and postulates its theory of being by a rigorous scientific methodology. The Standard Model defines matter as energy formed into fundamental particles via forces contained in fields. Science has proved Aristotle's universe wrong in many ways, but as physics delves deeper into the quantum world, empiricism is reaching its limits concerning fundamental questions of existence. To achieve its avowed mission of explaining existence completely, physics must reunite with philosophy in a metascience modeled on the First Philosophy of Aristotle. One theory of being that integrates quantum physics and metaphysics is Process Philosophy.

Ankle fracture spur sign is pathognomonic for a variant ankle fracture.

Science.gov (United States)

Hinds, Richard M; Garner, Matthew R; Lazaro, Lionel E; Warner, Stephen J; Loftus, Michael L; Birnbaum, Jacqueline F; Burket, Jayme C; Lorich, Dean G

2015-02-01

The hyperplantarflexion variant ankle fracture is composed of a posterior tibial lip fracture with posterolateral and posteromedial fracture fragments separated by a vertical fracture line. This infrequently reported injury pattern often includes an associated "spur sign" or double cortical density at the inferomedial tibial metaphysis. The objective of this study was to quantitatively establish the association of the ankle fracture spur sign with the hyperplantarflexion variant ankle fracture. Our clinical database of operative ankle fractures was retrospectively reviewed for the incidence of hyperplantarflexion variant and nonvariant ankle fractures as determined by assessment of injury radiographs, preoperative advanced imaging, and intraoperative observation. Injury radiographs were then evaluated for the presence of the spur sign, and association between the spur sign and variant fractures was analyzed. The incidence of the hyperplantarflexion variant fracture among all ankle fractures was 6.7% (43/640). The spur sign was present in 79% (34/43) of variant fractures and absent in all nonvariant fractures, conferring a specificity of 100% in identifying variant fractures. Positive predictive value and negative predictive value were 100% and 99%, respectively. The ankle fracture spur sign was pathognomonic for the hyperplantarflexion variant ankle fracture. It is important to identify variant fractures preoperatively as patient positioning, operative approach, and fixation construct of variant fractures often differ from those employed for osteosynthesis of nonvariant fractures. Identification of the spur sign should prompt acquisition of advanced imaging to formulate an appropriate operative plan to address the variant fracture pattern. Level III, retrospective comparative study. © The Author(s) 2014.

Variant proteins stimulate more IgM+ GC B-cells revealing a mechanism of cross-reactive recognition by antibody memory.

Science.gov (United States)

Burton, Bronwen R; Tennant, Richard K; Love, John; Titball, Richard W; Wraith, David C; White, Harry N

2018-05-01

Vaccines induce memory B-cells that provide high affinity secondary antibody responses to identical antigens. Memory B-cells can also re-instigate affinity maturation, but how this happens against antigenic variants is poorly understood despite its potential impact on driving broadly protective immunity against pathogens such as Influenza and Dengue. We immunised mice sequentially with identical or variant Dengue-virus envelope proteins and analysed antibody and germinal-centre (GC) responses. Variant protein boosts induced GC with higher proportions of IgM+ B-cells. The most variant protein re-stimulated GCs with the highest proportion of IgM+ cells with the most diverse, least mutated V-genes and with a slower but efficient serum antibody response. Recombinant antibodies from GC B-cells showed a higher affinity for the variant antigen than antibodies from a primary response, confirming a memory origin. This reveals a new process of antibody memory, that IgM memory cells with fewer mutations participate in secondary responses to variant antigens, demonstrating how the hierarchical structure of B-cell memory is used and indicating the potential and limits of cross-reactive antibody based immunity. © 2018, Burton et al.

Does physics instruction foster university students' cognitive processes?: A descriptive study of teacher activities

Science.gov (United States)

Ferguson-Hessler, Monica G. M.; de Jong, Ton

This study aims at giving a systematic description of the cognitive activities involved in teaching physics. Such a description of instruction in physics requires a basis in two models, that is, the cognitive activities involved in learning physics and the knowledge base that is the foundation of expertise in that subject. These models have been provided by earlier research. The model of instruction distinguishes three main categories of instruction process: presenting new information, integrating (i.e., bringing structure into) new knowledge, and connecting elements of new knowledge to prior knowledge. Each of the main categories has been divided into a number of specific instruction processes. Hereby any limited and specific cognitive teacher activity can be described along the two dimensions of process and type of knowledge. The model was validated by application to lectures and problem-solving classes of first year university courses. These were recorded and analyzed as to instruction process and type of knowledge. Results indicate that teachers are indeed involved in the various types of instruction processes defined. The importance of this study lies in the creation of a terminology that makes it possible to discuss instruction in an explicit and specific way.

Methodology and results of investigations of physical parameters of high-temperature reactors

International Nuclear Information System (INIS)

Cherepnin, Yu.S.; Chertkov, Yu.B.

1995-01-01

A physical investigations of reactors of stand complexes Baikal-1 and IGR have been carrying out more 30 years. Measuring methods of the physical investigations were divided into 2 groups: 1) methods for measuring of reactivity effects; 2) methods for measuring relative and absolute values of neutron flux and power release. The physical investigations on the reactors IVG-1 and IGR were carryied out under following conditions: during physical starts-up of regular variants of reactor cores; during energy starts-up of the reactors; before beginning of new loop chanel tests of the reactors; during research hot starts-up of the reactors the physical parameters were controled. The most full and authentic information about studied reactor have been providing by physical investigations. In 1984 physical investigations were carryied out on the IGR reactor and then the hot start-up of the mostest power and mostest large on fuel loading loop chanel was carryied out. This chanel contained 6 fuel assemblies with the summary fuel loading 3,06 kilogrammes of uranium and it was calculated for power equal to 20 MW. In 1988 the physical investigations for selection of project process chanels destined for new water cooled reactor core were carryied out. In 1993 the neutron-physical calculation on possibility of tests for the rector Nerva fuel element was carryied out. 9 refs., 4 figs

Holoprosencephaly Variant

Directory of Open Access Journals (Sweden)

J Gordon Millichap

2003-01-01

Full Text Available The clinical manifestations in 15 patients (6 boys and 9 girls with middle interhemispheric variant (MIH of holoprosencephaly (HPE were compared with classic subtypes (alobar, semilobar, and lobar of HPE in a multicenter study at Stanford University School of Medicine and Lucile Packard Children’s Hospital; Children’s Hospital of Philadelphia; University of California at San Francisco; Texas Scottish Rite Hospital, Dallas; and Kennedy Krieger Institute, Baltimore, MD.

Accumulation of distinct prelamin A variants in human diploid fibroblasts differentially affects cell homeostasis

International Nuclear Information System (INIS)

Candelario, Jose; Borrego, Stacey; Reddy, Sita; Comai, Lucio

2011-01-01

Lamin A is a component of the nuclear lamina that plays a major role in the structural organization and function of the nucleus. Lamin A is synthesized as a prelamin A precursor which undergoes four sequential post-translational modifications to generate mature lamin A. Significantly, a large number of point mutations in the LMNA gene cause a range of distinct human disorders collectively known as laminopathies. The mechanisms by which mutations in lamin A affect cell function and cause disease are unclear. Interestingly, recent studies have suggested that alterations in the normal lamin A pathway can contribute to cellular dysfunction. Specifically, we and others have shown, at the cellular level, that in the absence of mutations or altered splicing events, increased expression of wild-type prelamin A results in a growth defective phenotype that resembles that of cells expressing the mutant form of lamin A, termed progerin, associated with Hutchinson-Gilford Progeria syndrome (HGPS). Remarkably, the phenotypes of cells expressing elevated levels of wild-type prelamin A can be reversed by either treatment with farnesyltransferase inhibitors or overexpression of ZMPSTE24, a critical prelamin A processing enzyme, suggesting that minor increases in the steady-state levels of one or more prelamin A intermediates is sufficient to induce cellular toxicity. Here, to investigate the molecular basis of the lamin A pathway toxicity, we characterized the phenotypic changes occurring in cells expressing distinct prelamin A variants mimicking specific prelamin A processing intermediates. This analysis demonstrates that distinct prelamin A variants differentially affect cell growth, nuclear membrane morphology, nuclear distribution of lamin A and the fundamental process of transcription. Expression of prelamin A variants that are constitutively farnesylated induced the formation of lamin A aggregates and dramatic changes in nuclear membrane morphology, which led to reduced

A Model of the Creative Process Based on Quantum Physics and Vedic Science.

Science.gov (United States)

Rose, Laura Hall

1988-01-01

Using tenets from Vedic science and quantum physics, this model of the creative process suggests that the unified field of creation is pure consciousness, and that the development of the creative process within individuals mirrors the creative process within the universe. Rational and supra-rational creative thinking techniques are also described.…

Investigation of the role of TCF4 rare sequence variants in schizophrenia.

Science.gov (United States)

Basmanav, F Buket; Forstner, Andreas J; Fier, Heide; Herms, Stefan; Meier, Sandra; Degenhardt, Franziska; Hoffmann, Per; Barth, Sandra; Fricker, Nadine; Strohmaier, Jana; Witt, Stephanie H; Ludwig, Michael; Schmael, Christine; Moebus, Susanne; Maier, Wolfgang; Mössner, Rainald; Rujescu, Dan; Rietschel, Marcella; Lange, Christoph; Nöthen, Markus M; Cichon, Sven

2015-07-01

Transcription factor 4 (TCF4) is one of the most robust of all reported schizophrenia risk loci and is supported by several genetic and functional lines of evidence. While numerous studies have implicated common genetic variation at TCF4 in schizophrenia risk, the role of rare, small-sized variants at this locus-such as single nucleotide variants and short indels which are below the resolution of chip-based arrays requires further exploration. The aim of the present study was to investigate the association between rare TCF4 sequence variants and schizophrenia. Exon-targeted resequencing was performed in 190 German schizophrenia patients. Six rare variants at the coding exons and flanking sequences of the TCF4 gene were identified, including two missense variants and one splice site variant. These six variants were then pooled with nine additional rare variants identified in 379 European participants of the 1000 Genomes Project, and all 15 variants were genotyped in an independent German sample (n = 1,808 patients; n = 2,261 controls). These data were then analyzed using six statistical methods developed for the association analysis of rare variants. No significant association (P power analyses suggest that further research into the possible involvement of rare TCF4 sequence variants in schizophrenia risk is warranted by the assessment of larger cohorts with higher statistical power to identify rare variant associations. © 2015 Wiley Periodicals, Inc.

Identification of hemoglobin variants by top-down mass spectrometry using selected diagnostic product ions.

Science.gov (United States)

Coelho Graça, Didia; Hartmer, Ralf; Jabs, Wolfgang; Beris, Photis; Clerici, Lorella; Stoermer, Carsten; Samii, Kaveh; Hochstrasser, Denis; Tsybin, Yury O; Scherl, Alexander; Lescuyer, Pierre

2015-04-01

Hemoglobin disorder diagnosis is a complex procedure combining several analytical steps. Due to the lack of specificity of the currently used protein analysis methods, the identification of uncommon hemoglobin variants (proteoforms) can become a hard task to accomplish. The aim of this work was to develop a mass spectrometry-based approach to quickly identify mutated protein sequences within globin chain variants. To reach this goal, a top-down electron transfer dissociation mass spectrometry method was developed for hemoglobin β chain analysis. A diagnostic product ion list was established with a color code strategy allowing to quickly and specifically localize a mutation in the hemoglobin β chain sequence. The method was applied to the analysis of rare hemoglobin β chain variants and an (A)γ-β fusion protein. The results showed that the developed data analysis process allows fast and reliable interpretation of top-down electron transfer dissociation mass spectra by nonexpert users in the clinical area.

Physical Analysis of Cross-Wedge Rolling Process of a Stepped Shaft

Directory of Open Access Journals (Sweden)

Łukasz Wójcik

2017-12-01

Full Text Available The paper presents experimental- model research results on the process of cross-wedge rolling of an axially-symmetrical element (stepped shaft. During research was used plastic mass on the basis of waxes in black and white colour. The aim of this experimental research was to determine the best option of forming in terms of values obtained and the course of forces. Physical examination was carried out using specialist machines, that is model and laboratory cross-wedge rolling mill. Experimental analysis was carried out using billets with the temperature of 15°C, whereas the actual process was carried out for billet from C45 carbon steel of temperature 1150°C. The study compared the dimensions of the components obtained during rolling tests and forming forces obtained in the result of physical modeling with forces obtained during real tests.

A Nonsense Variant in the ACADVL Gene in German Hunting Terriers with Exercise Induced Metabolic Myopathy.

Science.gov (United States)

Lepori, Vincent; Mühlhause, Franziska; Sewell, Adrian C; Jagannathan, Vidhya; Janzen, Nils; Rosati, Marco; Alves de Sousa, Filipe Miguel Maximiano; Tschopp, Aurélie; Schüpbach, Gertraud; Matiasek, Kaspar; Tipold, Andrea; Leeb, Tosso; Kornberg, Marion

2018-05-04

Several enzymes are involved in fatty acid oxidation, which is a key process in mitochondrial energy production. Inherited defects affecting any step of fatty acid oxidation can result in clinical disease. We present here an extended family of German Hunting Terriers with 10 dogs affected by clinical signs of exercise induced weakness, muscle pain, and suspected rhabdomyolysis. The combination of clinical signs, muscle histopathology and acylcarnitine analysis with an elevated tetradecenoylcarnitine (C14:1) peak suggested a possible diagnosis of acyl-CoA dehydrogenase very long chain deficiency (ACADVLD). Whole genome sequence analysis of one affected dog and 191 controls revealed a nonsense variant in the ACADVL gene encoding acyl-CoA dehydrogenase very long chain, c.1728C>A or p.(Tyr576*). The variant showed perfect association with the phenotype in the 10 affected and more than 500 control dogs of various breeds. Pathogenic variants in the ACADVL gene have been reported in humans with similar myopathic phenotypes. We therefore considered the detected variant to be the most likely candidate causative variant for the observed exercise induced myopathy. To our knowledge, this is the first description of this disease in dogs, which we propose to name exercise induced metabolic myopathy (EIMM), and the identification of the first canine pathogenic ACADVL variant. Our findings provide a large animal model for a known human disease and will enable genetic testing to avoid the unintentional breeding of affected offspring. Copyright © 2018 Lepori et al.

A Nonsense Variant in the ACADVL Gene in German Hunting Terriers with Exercise Induced Metabolic Myopathy

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Vincent Lepori

2018-05-01

Full Text Available Several enzymes are involved in fatty acid oxidation, which is a key process in mitochondrial energy production. Inherited defects affecting any step of fatty acid oxidation can result in clinical disease. We present here an extended family of German Hunting Terriers with 10 dogs affected by clinical signs of exercise induced weakness, muscle pain, and suspected rhabdomyolysis. The combination of clinical signs, muscle histopathology and acylcarnitine analysis with an elevated tetradecenoylcarnitine (C14:1 peak suggested a possible diagnosis of acyl-CoA dehydrogenase very long chain deficiency (ACADVLD. Whole genome sequence analysis of one affected dog and 191 controls revealed a nonsense variant in the ACADVL gene encoding acyl-CoA dehydrogenase very long chain, c.1728C>A or p.(Tyr576*. The variant showed perfect association with the phenotype in the 10 affected and more than 500 control dogs of various breeds. Pathogenic variants in the ACADVL gene have been reported in humans with similar myopathic phenotypes. We therefore considered the detected variant to be the most likely candidate causative variant for the observed exercise induced myopathy. To our knowledge, this is the first description of this disease in dogs, which we propose to name exercise induced metabolic myopathy (EIMM, and the identification of the first canine pathogenic ACADVL variant. Our findings provide a large animal model for a known human disease and will enable genetic testing to avoid the unintentional breeding of affected offspring.

SDS, a structural disruption score for assessment of missense variant deleteriousness

Directory of Open Access Journals (Sweden)

Thanawadee ePreeprem

2014-04-01

Full Text Available We have developed a novel structure-based evaluation for missense variants that explicitly models protein structure and amino acid properties to predict the likelihood that a variant disrupts protein function. A structural disruption score (SDS is introduced as a measure to depict the likelihood that a case variant is functional. The score is constructed using characteristics that distinguish between causal and neutral variants within a group of proteins. The SDS score is correlated with standard sequence-based deleteriousness, but shows promise for improving discrimination between neutral and causal variants at less conserved sites.The prediction was performed on 3-dimentional structures of 57 gene products whose homozygous SNPs were identified as case-exclusive variants in an exome sequencing study of epilepsy disorders. We contrasted the candidate epilepsy variants with scores for likely benign variants found in the EVS database, and for positive control variants in the same genes that are suspected to promote a range of diseases. To derive a characteristic profile of damaging SNPs, we transformed continuous scores into categorical variables based on the score distribution of each measurement, collected from all possible SNPs in this protein set, where extreme measures were assumed to be deleterious. A second epilepsy dataset was used to replicate the findings. Causal variants tend to receive higher sequence-based deleterious scores, induce larger physico-chemical changes between amino acid pairs, locate in protein domains, buried sites or on conserved protein surface clusters, and cause protein destabilization, relative to negative controls. These measures were agglomerated for each variant. A list of nine high-priority putative functional variants for epilepsy was generated. Our newly developed SDS protocol facilitates SNP prioritization for experimental validation.

Comprehensive genotyping in dyslipidemia: mendelian dyslipidemias caused by rare variants and Mendelian randomization studies using common variants.

Science.gov (United States)

Tada, Hayato; Kawashiri, Masa-Aki; Yamagishi, Masakazu

2017-04-01

Dyslipidemias, especially hyper-low-density lipoprotein cholesterolemia and hypertriglyceridemia, are important causal risk factors for coronary artery disease. Comprehensive genotyping using the 'next-generation sequencing' technique has facilitated the investigation of Mendelian dyslipidemias, in addition to Mendelian randomization studies using common genetic variants associated with plasma lipids and coronary artery disease. The beneficial effects of low-density lipoprotein cholesterol-lowering therapies on coronary artery disease have been verified by many randomized controlled trials over the years, and subsequent genetic studies have supported these findings. More recently, Mendelian randomization studies have preceded randomized controlled trials. When the on-target/off-target effects of rare variants and common variants exhibit the same direction, novel drugs targeting molecules identified by investigations of rare Mendelian lipid disorders could be promising. Such a strategy could aid in the search for drug discovery seeds other than those for dyslipidemias.

A variational Bayes discrete mixture test for rare variant association.

Science.gov (United States)

Logsdon, Benjamin A; Dai, James Y; Auer, Paul L; Johnsen, Jill M; Ganesh, Santhi K; Smith, Nicholas L; Wilson, James G; Tracy, Russell P; Lange, Leslie A; Jiao, Shuo; Rich, Stephen S; Lettre, Guillaume; Carlson, Christopher S; Jackson, Rebecca D; O'Donnell, Christopher J; Wurfel, Mark M; Nickerson, Deborah A; Tang, Hua; Reiner, Alexander P; Kooperberg, Charles

2014-01-01

Recently, many statistical methods have been proposed to test for associations between rare genetic variants and complex traits. Most of these methods test for association by aggregating genetic variations within a predefined region, such as a gene. Although there is evidence that "aggregate" tests are more powerful than the single marker test, these tests generally ignore neutral variants and therefore are unable to identify specific variants driving the association with phenotype. We propose a novel aggregate rare-variant test that explicitly models a fraction of variants as neutral, tests associations at the gene-level, and infers the rare-variants driving the association. Simulations show that in the practical scenario where there are many variants within a given region of the genome with only a fraction causal our approach has greater power compared to other popular tests such as the Sequence Kernel Association Test (SKAT), the Weighted Sum Statistic (WSS), and the collapsing method of Morris and Zeggini (MZ). Our algorithm leverages a fast variational Bayes approximate inference methodology to scale to exome-wide analyses, a significant computational advantage over exact inference model selection methodologies. To demonstrate the efficacy of our methodology we test for associations between von Willebrand Factor (VWF) levels and VWF missense rare-variants imputed from the National Heart, Lung, and Blood Institute's Exome Sequencing project into 2,487 African Americans within the VWF gene. Our method suggests that a relatively small fraction (~10%) of the imputed rare missense variants within VWF are strongly associated with lower VWF levels in African Americans.

Physical exercise, inflammatory process and adaptive condition: an overview

OpenAIRE

Silva, Fernando Oliveira Catanho da; Macedo, Denise Vaz

2011-01-01

Physical exercise induces inflammation, a physiological response that is part of immune system activity and promotes tissue remodeling after exercise overload. The activation of the inflammatory process is local and systemic and is mediated by different cells and secreted compounds. The objective is to reestablish organ homeostasis after a single bout of exercise or after several exercise sessions. The acute-phase response involves the combined actions of activated leukocytes, cytokines, acut...

Glucose 6-phosphate dehydrogenase variants in Japan.

Science.gov (United States)

Miwa, S

1980-01-01

Fifty-four cases of glucose 6-phosphate dehydrogenase (G6PD) deficiency have so far been reported in Japan. Among them, 21 G6PD variants have been characterized. Nineteen out of the 21 variants were characterized in our laboratory and G6PD Heian and "Kyoto" by others. G6PD Tokyo, Tokushima, Ogikubo, Kurume, Fukushima, Yokohama, Yamaguchi, Wakayama, Akita, Heian and "Kyoto" were classified as Class 1, because all these cases showed chronic hemolytic anemia and severe enzyme deficiency. All these variants showed thermal instability. G6PD Mediterranean-like, Ogori, Gifu and Fukuoka were classified as Class 2, whereas G6PD Hofu, B(-) Chinese, Ube, Konan, Kamiube and Kiwa belonged to Class 3. All the 6 Class 3 variants were found as the results of the screening tests. The incidence of the deficiency in Japanese seems to be 0.1-0.5% but that of the cases which may slow drug-induced hemolysis would be much less. G6PD Ube and Konan appear to be relatively common in Japan.

Dandy-Walker variant in Coffin-Siris syndrome.

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Imai, T; Hattori, H; Miyazaki, M; Higuchi, Y; Adachi, S; Nakahata, T

2001-04-22

We describe a five-month-old male infant with Coffin-Siris syndrome, the so-called Dandy-Walker variant (hypoplasia of the cerebellar vermis with cystic dilatation of the fourth ventricle, but without enlargement of the posterior fossa), and partial agenesis of the corpus callosum. Dandy-Walker malformation and mega cisterna magna, but not Dandy-Walker variant, have been reported in Coffin-Siris syndrome. The presence of Dandy-Walker variant in the infant we described confirms that the full continuum of the Dandy-Walker complex can occur in Coffin-Siris syndrome. The yet unidentified gene(s) for the syndrome may be related to the development of the hindbrain. Copyright 2001 Wiley-Liss, Inc.

A population-specific uncommon variant in GRIN3A associated with schizophrenia.

Science.gov (United States)

Takata, Atsushi; Iwayama, Yoshimi; Fukuo, Yasuhisa; Ikeda, Masashi; Okochi, Tomo; Maekawa, Motoko; Toyota, Tomoko; Yamada, Kazuo; Hattori, Eiji; Ohnishi, Tetsuo; Toyoshima, Manabu; Ujike, Hiroshi; Inada, Toshiya; Kunugi, Hiroshi; Ozaki, Norio; Nanko, Shinichiro; Nakamura, Kazuhiko; Mori, Norio; Kanba, Shigenobu; Iwata, Nakao; Kato, Tadafumi; Yoshikawa, Takeo

2013-03-15

Genome-wide association studies have successfully identified several common variants showing robust association with schizophrenia. However, individually, these variants only produce a weak effect. To identify genetic variants with larger effect sizes, increasing attention is now being paid to uncommon and rare variants. From the 1000 Genomes Project data, we selected 47 candidate single nucleotide variants (SNVs), which were: 1) uncommon (minor allele frequency way to discover risk variants with larger effects. Copyright © 2013 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity

DEFF Research Database (Denmark)

Dimas, Antigone S; Lagou, Vasiliki; Barker, Adam

2013-01-01

Patients with established type 2 diabetes display both beta-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci and indices of proinsulin pr...

CDKL5 variants: Improving our understanding of a rare neurologic disorder.

Science.gov (United States)

Hector, Ralph D; Kalscheuer, Vera M; Hennig, Friederike; Leonard, Helen; Downs, Jenny; Clarke, Angus; Benke, Tim A; Armstrong, Judith; Pineda, Mercedes; Bailey, Mark E S; Cobb, Stuart R

2017-12-01

To provide new insights into the interpretation of genetic variants in a rare neurologic disorder, CDKL5 deficiency, in the contexts of population sequencing data and an updated characterization of the CDKL5 gene. We analyzed all known potentially pathogenic CDKL5 variants by combining data from large-scale population sequencing studies with CDKL5 variants from new and all available clinical cohorts and combined this with computational methods to predict pathogenicity. The study has identified several variants that can be reclassified as benign or likely benign. With the addition of novel CDKL5 variants, we confirm that pathogenic missense variants cluster in the catalytic domain of CDKL5 and reclassify a purported missense variant as having a splicing consequence. We provide further evidence that missense variants in the final 3 exons are likely to be benign and not important to disease pathology. We also describe benign splicing and nonsense variants within these exons, suggesting that isoform hCDKL5_5 is likely to have little or no neurologic significance. We also use the available data to make a preliminary estimate of minimum incidence of CDKL5 deficiency. These findings have implications for genetic diagnosis, providing evidence for the reclassification of specific variants previously thought to result in CDKL5 deficiency. Together, these analyses support the view that the predominant brain isoform in humans (hCDKL5_1) is crucial for normal neurodevelopment and that the catalytic domain is the primary functional domain.

Variant of Rett syndrome and CDKL5 gene

DEFF Research Database (Denmark)

Pini, Giorgio; Bigoni, Stefania; Engerström, Ingegerd Witt

2012-01-01

UNLABELLED: Rett syndrome (RTT) is a severe neurodevelopmental disorder affecting almost exclusively females. The Hanefeld variant, or early-onset seizure variant, has been associated with mutations in CDKL5 gene. AIMS: In recent years more than 60 patients with mutations in the CDKL5 gene have...... been described in the literature, but the cardiorespiratory phenotype has not been reported. Our aim is to describe clinical and autonomic features of these girls. METHODS: 10 girls with CDKL5 mutations and a diagnosis of Hanefeld variant have been evaluated on axiological and clinical aspects. In all...

Gain-of-function HCN2 variants in genetic epilepsy.

Science.gov (United States)

Li, Melody; Maljevic, Snezana; Phillips, A Marie; Petrovski, Slave; Hildebrand, Michael S; Burgess, Rosemary; Mount, Therese; Zara, Federico; Striano, Pasquale; Schubert, Julian; Thiele, Holger; Nürnberg, Peter; Wong, Michael; Weisenberg, Judith L; Thio, Liu Lin; Lerche, Holger; Scheffer, Ingrid E; Berkovic, Samuel F; Petrou, Steven; Reid, Christopher A

2018-02-01

Genetic generalized epilepsy (GGE) is a common epilepsy syndrome that encompasses seizure disorders characterized by spike-and-wave discharges (SWDs). Pacemaker hyperpolarization-activated cyclic nucleotide-gated channels (HCN) are considered integral to SWD genesis, making them an ideal gene candidate for GGE. We identified HCN2 missense variants from a large cohort of 585 GGE patients, recruited by the Epilepsy Phenome-Genome Project (EPGP), and performed functional analysis using two-electrode voltage clamp recordings from Xenopus oocytes. The p.S632W variant was identified in a patient with idiopathic photosensitive occipital epilepsy and segregated in the family. This variant was also independently identified in an unrelated patient with childhood absence seizures from a European cohort of 238 familial GGE cases. The p.V246M variant was identified in a patient with photo-sensitive GGE and his father diagnosed with juvenile myoclonic epilepsy. Functional studies revealed that both p.S632W and p.V246M had an identical functional impact including a depolarizing shift in the voltage dependence of activation that is consistent with a gain-of-function. In contrast, no biophysical changes resulted from the introduction of common population variants, p.E280K and p.A705T, and the p.R756C variant from EPGP that did not segregate with disease. Our data suggest that HCN2 variants can confer susceptibility to GGE via a gain-of-function mechanism. © 2017 Wiley Periodicals, Inc.

Variant patterns of Subject-Verb agreement in Portuguese: morphological and phonological issues

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Maria Antónia Mota

2013-12-01

Full Text Available In this paper, we start from a basic assumption: agreement is a most relevant operation for the Portuguese language speakers as a whole. The data from different varieties of Portuguese support this view, both in the Subject-Verb domain and within the NP, as well as the fact that speakers don’t prefer the simplest solutions: the most productive plural agreement forms are the most complex ones, morphologically and phonologically. We focus the discussion on the interplay between different linguistic factors intervening in and promoting variant overt and covert patterns of agreement (the existence of agreement and the presence of visible marks, as expected in standard canonical schemes, constitute two separate questions. More specifically, we claim that it is worth to take into account the matching between the morphological and the phonological properties and features of the verb cells, in order to fully understand the attested variant outputs and the variant patterns of subject-verb agreement. We assume that the 3rdplural person-number marker has to be described in morphophonological terms, and we conclude that agreement is a morpho-phono-syntactic process, sensitive to the lexical-semantic features and discourse properties of the controller.

Effects of common hemoglobin variants on HbA1c measurements in China: results for α- and β-globin variants measured by six methods.

Science.gov (United States)

Xu, Anping; Chen, Weidong; Xia, Yong; Zhou, Yu; Ji, Ling

2018-04-07

HbA1c is a widely used biomarker for diabetes mellitus management. Here, we evaluated the accuracy of six methods for determining HbA1c values in Chinese patients with common α- and β-globin chains variants in China. Blood samples from normal subjects and individuals exhibiting hemoglobin variants were analyzed for HbA1c, using Sebia Capillarys 2 Flex Piercing (C2FP), Bio-Rad Variant II Turbo 2.0, Tosoh HLC-723 G8 (ver. 5.24), Arkray ADAMS A1c HA-8180V fast mode, Cobas c501 and Trinity Ultra2 systems. DNA sequencing revealed five common β-globin chain variants and three common α-globin chain variants. The most common variant was Hb E, followed by Hb New York, Hb J-Bangkok, Hb G-Coushatta, Hb Q-Thailand, Hb G-Honolulu, Hb Ube-2 and Hb G-Taipei. Variant II Turbo 2.0, Ultra2 and Cobas c501 showed good agreement with C2FP for most samples with variants. HLC-723 G8 yielded no HbA1c values for Hb J-Bangkok, Hb Q-Thailand and Hb G-Honolulu. Samples with Hb E, Hb G-Coushatta, Hb G-Taipei and Hb Ube-2 produced significant negative biases for HLC-723 G8. HA-8180V showed statistically significant differences for Hb E, Hb G-Coushatta, Hb G-Taipei, Hb Q-Thailand and Hb G-Honolulu. HA-8180V yielded no HbA1c values for Hb J-Bangkok. All methods showed good agreement for samples with Hb New York. Some common hemoglobin variants can interfere with HbA1c determination by the most popular methods in China.

Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification

Science.gov (United States)

Faye, Laura L.; Machiela, Mitchell J.; Kraft, Peter; Bull, Shelley B.; Sun, Lei

2013-01-01

Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations. Yet, identification of causal variants within an established region of association remains a challenge. Counter-intuitively, certain factors that increase power to detect an associated region can decrease power to localize the causal variant. First, combining GWAS with imputation or low coverage sequencing to achieve the large sample sizes required for high power can have the unintended effect of producing differential genotyping error among SNPs. This tends to bias the relative evidence for association toward better genotyped SNPs. Second, re-use of GWAS data for fine-mapping exploits previous findings to ensure genome-wide significance in GWAS-associated regions. However, using GWAS findings to inform fine-mapping analysis can bias evidence away from the causal SNP toward the tag SNP and SNPs in high LD with the tag. Together these factors can reduce power to localize the causal SNP by more than half. Other strategies commonly employed to increase power to detect association, namely increasing sample size and using higher density genotyping arrays, can, in certain common scenarios, actually exacerbate these effects and further decrease power to localize causal variants. We develop a re-ranking procedure that accounts for these adverse effects and substantially improves the accuracy of causal SNP identification, often doubling the probability that the causal SNP is top-ranked. Application to the NCI BPC3 aggressive prostate cancer GWAS with imputation meta-analysis identified a new top SNP at 2 of 3 associated loci and several additional possible causal SNPs at these loci that may have otherwise been overlooked. This method is simple to implement using R scripts provided on the author's website. PMID:23950724

The Inclusion of Science Process Skills in Yemeni Secondary School Physics Textbooks

Science.gov (United States)

Aziz, Majed S.; Zain, Ahmad Nurulazam Md

2010-01-01

The aim of this study is to compare and contrast the science process skills (SPS) included in the 10th-12th grade physics textbooks content utilized in Yemeni schools. The study revealed weaknesses and strengths in the textbooks' content. For instance, a number of science process skills (SPS), such as measuring, predicting and hypothesizing, have…

Height-reducing variants and selection for short stature in Sardinia

NARCIS (Netherlands)

Zoledziewska, Magdalena; Sidore, Carlo; Chiang, Charleston W K; Sanna, Serena; Mulas, Antonella; Steri, Maristella; Busonero, Fabio; Marcus, Joseph H; Marongiu, Michele; Maschio, Andrea; Ortega Del Vecchyo, Diego; Floris, Matteo; Meloni, Antonella; Delitala, Alessandro; Concas, Maria Pina; Murgia, Federico; Biino, Ginevra; Vaccargiu, Simona; Nagaraja, Ramaiah; Lohmueller, Kirk E; Timpson, Nicholas J; Soranzo, Nicole; Tachmazidou, Ioanna; Dedoussis, George; Zeggini, Eleftheria; Uzzau, Sergio; Jones, Chris; Lyons, Robert; Angius, Andrea; Abecasis, Gonçalo R; Novembre, John; Schlessinger, David; Cucca, Francesco

We report sequencing-based whole-genome association analyses to evaluate the impact of rare and founder variants on stature in 6,307 individuals on the island of Sardinia. We identify two variants with large effects. One variant, which introduces a stop codon in the GHR gene, is relatively frequent

Splice variants of perlucin from Haliotis laevigata modulate the crystallisation of CaCO3.

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Tanja Dodenhof

Full Text Available Perlucin is one of the proteins of the organic matrix of nacre (mother of pearl playing an important role in biomineralisation. This nacreous layer can be predominately found in the mollusc lineages and is most intensively studied as a compound of the shell of the marine Australian abalone Haliotis laevigata. A more detailed analysis of Perlucin will elucidate some of the still unknown processes in the complex interplay of the organic/inorganic compounds involved in the formation of nacre as a very interesting composite material not only from a life science-based point of view. Within this study we discovered three unknown Perlucin splice variants of the Australian abalone H. laevigata. The amplified cDNAs vary from 562 to 815 base pairs and the resulting translation products differ predominantly in the absence or presence of a varying number of a 10 mer peptide C-terminal repeat. The splice variants could further be confirmed by matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF MS analysis as endogenous Perlucin, purified from decalcified abalone shell. Interestingly, we observed that the different variants expressed as maltose-binding protein (MBP fusion proteins in E. coli showed strong differences in their influence on precipitating CaCO3 and that these differences might be due to a splice variant-specific formation of large protein aggregates influenced by the number of the 10 mer peptide repeats. Our results are evidence for a more complex situation with respect to Perlucin functional regulation by demonstrating that Perlucin splice variants modulate the crystallisation of calcium carbonate. The identification of differentially behaving Perlucin variants may open a completely new perspective for the field of nacre biomineralisation.

Human papillomavirus type-16 variants in Quechua aboriginals from Argentina.

Science.gov (United States)

Picconi, María Alejandra; Alonio, Lidia Virginia; Sichero, Laura; Mbayed, Viviana; Villa, Luisa Lina; Gronda, Jorge; Campos, Rodolfo; Teyssié, Angélica

2003-04-01

Cervical carcinoma is the leading cause of cancer death in Quechua indians from Jujuy (northwestern Argentina). To determine the prevalence of HPV-16 variants, 106 HPV-16 positive cervical samples were studied, including 33 low-grade squamous intraepithelial lesions (LSIL), 28 high-grade squamous intraepithelial lesions (HSIL), 9 invasive cervical cancer (ICC), and 36 samples from women with normal colposcopy and cytology. HPV genome variability was examined in the L1 and E6 genes by PCR-hybridization. In a subset of 20 samples, a LCR fragment was also analyzed by PCR-sequencing. Most variants belonged to the European branch with subtle differences that depended on the viral gene fragment studied. Only about 10% of the specimens had non-European variants, including eight Asian-American, two Asian, and one North-American-1. E6 gene analysis revealed that 43% of the samples were identical to HPV-16 prototype, while 57% corresponded to variants. Interestingly, the majority (87%) of normal smears had HPV-16 prototype, whereas variants were detected mainly in SIL and ICC. LCR sequencing yielded 80% of variants, including 69% of European, 19% Asian-American, and 12% Asian. We identified a new variant, the Argentine Quechua-51 (AQ-51), similar to B-14 plus two additional changes: G7842-->A and A7837-->C; phylogenetic inference allocated it in the Asian-American branch. The high proportion of European variants may reflect Spanish colonial influence on these native Inca descendants. The predominance of HPV-16 variants in pathologic samples when compared to normal controls could have implications for the natural history of cervical lesions. Copyright 2003 Wiley-Liss, Inc.

Modal analysis of fluid flows using variants of proper orthogonal decomposition

Science.gov (United States)

Rowley, Clarence; Dawson, Scott

2017-11-01

This talk gives an overview of several methods for analyzing fluid flows, based on variants of proper orthogonal decomposition. These methods may be used to determine simplified, approximate models that capture the essential features of these flows, in order to better understand the dominant physical mechanisms, and potentially to develop appropriate strategies for model-based flow control. We discuss balanced proper orthogonal decomposition as an approximation of balanced truncation, and explain connections with system identification methods such as the eigensystem realization algorithm. We demonstrate the methods on several canonical examples, including a linearized channel flow and the flow past a circular cylinder. Supported by AFOSR, Grant FA9550-14-1-0289.

Quadratic Polynomial Regression using Serial Observation Processing:Implementation within DART

Science.gov (United States)

Hodyss, D.; Anderson, J. L.; Collins, N.; Campbell, W. F.; Reinecke, P. A.

2017-12-01

Many Ensemble-Based Kalman ltering (EBKF) algorithms process the observations serially. Serial observation processing views the data assimilation process as an iterative sequence of scalar update equations. What is useful about this data assimilation algorithm is that it has very low memory requirements and does not need complex methods to perform the typical high-dimensional inverse calculation of many other algorithms. Recently, the push has been towards the prediction, and therefore the assimilation of observations, for regions and phenomena for which high-resolution is required and/or highly nonlinear physical processes are operating. For these situations, a basic hypothesis is that the use of the EBKF is sub-optimal and performance gains could be achieved by accounting for aspects of the non-Gaussianty. To this end, we develop here a new component of the Data Assimilation Research Testbed [DART] to allow for a wide-variety of users to test this hypothesis. This new version of DART allows one to run several variants of the EBKF as well as several variants of the quadratic polynomial lter using the same forecast model and observations. Dierences between the results of the two systems will then highlight the degree of non-Gaussianity in the system being examined. We will illustrate in this work the differences between the performance of linear versus quadratic polynomial regression in a hierarchy of models from Lorenz-63 to a simple general circulation model.

EPR Studies of Spin-Spin Exchange Processes: A Physical Chemistry Experiment.

Science.gov (United States)

Eastman, Michael P.

1982-01-01

Theoretical background, experimental procedures, and analysis of experimental results are provided for an undergraduate physical chemistry experiment on electron paramagnetic resonance (EPR) linewidths. Source of line broadening observed in a spin-spin exchange process between radicals formed in aqueous solutions of potassium peroxylamine…

Epistemological foundation of the teaching-learning process of physics in high school

Directory of Open Access Journals (Sweden)

Ana Grethel Suárez-Stable

2016-07-01

Full Text Available This paper the principal fundaments of the teaching-learning process of the physics subject in the Senior High School are treated. The valuation of the conceptions more significant to this educational level that have signed the development of this process from an integrator researching approach taking into account the logical chain construction-integration-creation. The need of renew of the point of view regarding the teaching-learning of sciences in particular the physics, from power of the researching approach is discussed. Taking into account the development of the students though and the encourage toward a teaching learning based in new added values of the knowledge from the valuation of the significance of the experience, is analyzed in this paper

Genetics Home Reference: GM2-gangliosidosis, AB variant

Science.gov (United States)

... Resources Genetic Testing (1 link) Genetic Testing Registry: Tay-Sachs disease, variant AB General Information from MedlinePlus (5 links) ... AB variant Activator Deficiency/GM2 Gangliosidosis Activator-deficient Tay-Sachs disease GM2 Activator Deficiency Disease GM2 gangliosidosis, type AB ...

Physical processes in collapse driven supernova

International Nuclear Information System (INIS)

Mayle, R.W.

1985-11-01

A model of the supernova explosion is discussed. The method of neutrino transport is discussed, since the explosive mechanism depends on neutrino heating of the material behind the accretion shock. The core region of these exploding stars becomes unstable to convective motions during the supernova evolution. Convective mixing allows more neutrinos to escape from under the neutrinosphere, and thus increases the amount of heating by neutrinos. An approximate method of incorporating convection is described, and some results of including convection in a computer model is presented. Another phenomena is seen in computer simulations of supernova, oscillations in the neutrino luminosity and mass accretion rate onto the protoneutron star. The last topic discussed in this thesis describes the attempt to understand this oscillation by perturbation of the steady state solution to equations approximating the complex physical processes occurring in the late time supernova. 42 refs., 31 figs

Physical processes in collapse driven supernova

Energy Technology Data Exchange (ETDEWEB)

Mayle, R.W.

1985-11-01

A model of the supernova explosion is discussed. The method of neutrino transport is discussed, since the explosive mechanism depends on neutrino heating of the material behind the accretion shock. The core region of these exploding stars becomes unstable to convective motions during the supernova evolution. Convective mixing allows more neutrinos to escape from under the neutrinosphere, and thus increases the amount of heating by neutrinos. An approximate method of incorporating convection is described, and some results of including convection in a computer model is presented. Another phenomena is seen in computer simulations of supernova, oscillations in the neutrino luminosity and mass accretion rate onto the protoneutron star. The last topic discussed in this thesis describes the attempt to understand this oscillation by perturbation of the steady state solution to equations approximating the complex physical processes occurring in the late time supernova. 42 refs., 31 figs.

DEVELOPMENT OF COORDINATION ABILITIES OF SPECIAL MEDICAL GROUPS STUDENTS IN PHYSICAL EDUCATION PROCESS

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E. N. Dotsenko

2013-08-01

Full Text Available Purpose. To analyze the problem of motor abilities development and health of students of special medical group in the process of physical education in technical universities. Determine the major factors, characteristics, and the relationship of physical development, physical fitness and coordination abilities of female students in special medical group. Establish regularities in precise movements mastering of different coordination structure and develop model characteristics of the relationship of coordination abilities and motor characteristics of students in special medical group. To substantiate and verify efficiency of coordination abilities development method of female students with regard to their functional status in the course of physical education in higher school. Methodology. Theoretical and methodological argument, characteristic of the experimental program in physical education teaching process of students in special medical group was shown. Findings. Research is to develop the training content in special medical groups with the use of coordinating elements and exercises to enhance the motor abilities of female students. Their influence on the level of physical development, functional training, as well as regularities in mastering and movement control of different coordinating structure at the female students of special medical group was studied. The comparative characteristic of female students athletic ability in the dynamics of the educational process, differentiated into groups according to nosology was presented. The criterion of spare capacities upgrade of the motor system in controlling the movements of different coordination structure was determined. Originality. The method of coordination abilities development of female students in special medical group, that aims on the formation and correction of motor control system of different coordination structure, a sense of body position and its individual parts in space, improving

[Hemoglobin variants in Colombian patients referred to discard hemoglobinopathies].

Science.gov (United States)

Romero-Sánchez, Consuelo; Gómez Gutiérrez, Alberto; Duarte, Yurani; Amazo, Constanza; Manosalva, Clara; Chila M, Lorena; Casas-Gómez, María Consuelo; Briceño Balcázar, Ignacio

2015-10-01

Oxygen transport is altered in hemoglobinopathies. To study the distribution of hemoglobinopathies in Andean subjects without African ancestry. We analyzed blood samples of 1,407 subjects aged 18 to 59 years (58% females), living in the central Andean region of Colombia, referred to discard hemoglobinopathies. The frequency and type of hemoglobinopathy was established by capillary and agarose gel electrophoresis. The frequency of hemoglobinopathies was 34.5% and higher among females. The structural variants found were: AS-heterozygous hemoglobin (8.1%), homozygous SS (3.7%), heterozygous SC (2.2%), AC heterozygotes (0.5%) and heterozygous AE (0.3%). Quantitative variants found were Hb A-Beta thalassemia (13.91%) and Hb H (0.06%), Beta-thalassemia heterozygotes C (0.88%), S-Beta thalassemia heterozygotes (6.07%) and compound heterozygous SC/Beta thalassemia (0.25%), with a persistence of fetal hemoglobin 0. Composite thalassemia was also found in 31%. All techniques showed good correlation and capillary electrophoresis demonstrated a greater detection of hemoglobin variants. The frequency of hemoglobin variants in the analyzed population was high, which is an important public health indicator. The most common hemoglobin variant was HbA/Increased structural Hb A2 and the mos frequent structural hemoglobinopathy was sickle cell trait. Capillary electrophoresis can discern any Hb variants present in the population.

Genetics in psychiatry: common variant association studies

Directory of Open Access Journals (Sweden)

Buxbaum Joseph D

2010-03-01

Full Text Available Abstract Many psychiatric conditions and traits are associated with significant heritability. Genetic risk for psychiatric conditions encompass rare variants, identified due to major effect, as well as common variants, the latter analyzed by association analyses. We review guidelines for common variant association analyses, undertaking after assessing evidence of heritability. We highlight the importance of: suitably large sample sizes; an experimental design that controls for ancestry; careful data cleaning; correction for multiple testing; small P values for positive findings; assessment of effect size for positive findings; and, inclusion of an independent replication sample. We also note the importance of a critical discussion of any prior findings, biological follow-up where possible, and a means of accessing the raw data.

Hemoglobin Variants: Biochemical Properties and Clinical Correlates

Science.gov (United States)

Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

2013-01-01

Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

Comparative analysis of metastasis variants derived from human prostate carcinoma cells: roles in intravasation of VEGF-mediated angiogenesis and uPA-mediated invasion

DEFF Research Database (Denmark)

Conn, Erin M; Bøtkjær, Kenneth Alrø; Kupriyanova, Tatyana A

2009-01-01

To analyze the process of tumor cell intravasation, we used the human tumor-chick embryo spontaneous metastasis model to select in vivo high (PC-hi/diss) and low (PC-lo/diss) disseminating variants from the human PC-3 prostate carcinoma cell line. These variants dramatically differed in their int...

Physical Processes Involved In Yellow Sea Solitary Waves

Science.gov (United States)

Warn-Varnas, A.; Chin-Bing, S.; King, D.; Lamb, K.; Hawkins, J.; Teixeira, M.

The study area is located south of the Shandong peninsula. In this area, soliton gener- ation and propagation studies are per formed with the Lamb(1994) model. The model is nonhydrostatic and is formulated in 2 1/2 dimensions for terrain following c oordi- nates. In the area, 20 to 30 m topographic variations over distances of 10 to 20 km are found to occur in the digit al atlas of Choi (1999). The area is shallow with maximum depths ranging from 40 m to 70 m. Along the southern boundary of the region the semi-diurnal tidal strength magnitude varies from .6 m/sec to 1.2 m/sec, Fang(1994). We show that, for sum mer conditions, the existing physical processes associated with the semi-diurnal tidal flow over the topographic variations , in the shelfbreak region, lead to the formation of internal bores in the model simulations. Through acting phys- ical proce sses, the internal bores propagate on and off the shelf. A disintegration process of internal bores into solitary waves occ urs through frequency and ampli- tude dispersion. SAR observations of the area show images containing six events con- sisting of internal bores and solitary waves that travel in a well-defined direction for two and a half days. The origin of the trains appeared to be at a point along a steep topo graphic drop. The SAR observations are used for guiding and tuning the model simulations, by comparing spectra of observed and modeled wavelengths. The tuned model yields wavelengths that are within a factor of 2 of the SAR data. The modeled amp litudes are within a factor of 2 of amplitudes obtained with a two-layer model and the SAR data The signature on the acoustical field of ongoing physical processes through the interaction of the resultant oceanic struct ure with the acoustical field is pursued. Internal bore and solitary wave structures interact with the acoustic field. A re distribution of acoustical energy to higher acoustical modes occurs at some fre- quencies. Mode decomposition of the

Genetics Home Reference: Ohdo syndrome, Say-Barber-Biesecker-Young-Simpson variant

Science.gov (United States)

... SBBYS variant Ohdo syndrome, Say-Barber-Biesecker-Young-Simpson variant Printable PDF Open All Close All Enable ... collapse boxes. Description The Say-Barber-Biesecker-Young-Simpson (SBBYS) variant of Ohdo syndrome is a rare ...

A Trusted Autonomic Architecture to Safeguard Cyber-Physical Control Leaf Nodes and Protect Process Integrity

OpenAIRE

Chiluvuri, Nayana Teja

2015-01-01

Cyber-physical systems are networked through IT infrastructure and susceptible to malware. Threats targeting process control are much more safety-critical than traditional computing systems since they jeopardize the integrity of physical infrastructure. Existing defence mechanisms address security at the network nodes but do not protect the physical infrastructure if network integrity is compromised. An interface guardian architecture is implemented on cyber-physical control leaf nodes to mai...

Warty Carcinoma Penis: An Uncommon Variant

Directory of Open Access Journals (Sweden)

Sushma Thapa

2017-01-01

Full Text Available Penile carcinoma frequency varies widely in different parts of the world and comprises 1–10% of all the malignancies in males. Majority of the cases of penile carcinoma are squamous cell carcinoma of penis comprising 60% to 70% of all cases. Warty carcinoma of penis is an unusual neoplasm and a variant of penile squamous cell carcinoma comprising 5%–10% of all the variants. The other histological variants include basaloid, verrucous, papillary, sarcomatous, mixed, and adenosquamous carcinoma. The various histological entities with an exophytic papillary lesions including warty carcinoma are together referred to as the “verruciform” group of neoplasms. The warty carcinoma has to be differentiated from these lesions and is typically distinguished by histological features of hyperkeratosis, arborescent papillomatosis, acanthosis, and prominent koilocytosis with nuclear pleomorphism. We present a case of 65-year-old male with growth measuring 6×4 cm in the penis who underwent total penectomy and was diagnosed as warty carcinoma penis.

Cryptanalysis of RSA and its variants

CERN Document Server

Hinek, M Jason

2009-01-01

Thirty years after RSA was first publicized, it remains an active research area. Although several good surveys exist, they are either slightly outdated or only focus on one type of attack. Offering an updated look at this field, Cryptanalysis of RSA and Its Variants presents the best known mathematical attacks on RSA and its main variants, including CRT-RSA, multi-prime RSA, and multi-power RSA. Divided into three parts, the book first introduces RSA and reviews the mathematical background needed for the majority of attacks described in the remainder of the text. It then brings together all of the most popular mathematical attacks on RSA and its variants. For each attack presented, the author includes a mathematical proof if possible or a mathematical justification for attacks that rely on assumptions. For the attacks that cannot be proven, he gives experimental evidence to illustrate their practical effectiveness. Focusing on mathematical attacks that exploit the structure of RSA and specific parameter choic...

Assessment of Functional Effects of Unclassified Genetic Variants

NARCIS (Netherlands)

Couch, Fergus J.; Rasmussen, Lene Juel; Hofstra, Robert; Monteiro, Alvaro N. A.; Greenblatt, Marc S.; de Wind, Niels

2008-01-01

Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been

Assessment of Functional Effects of Unclassified Genetic Variants

NARCIS (Netherlands)

Couch, Fergus J.; Rasmussen, Lene Juel; Hofstra, Robert; Monteiro, Alvaro N. A.; Greenblatt, Marc S.; de Wind, Niels

Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been

Canine parvovirus: the worldwide occurrence of antigenic variants.

Science.gov (United States)

Miranda, Carla; Thompson, Gertrude

2016-09-01

The most important enteric virus infecting canids is canine parvovirus type 2 (CPV-2). CPV is the aetiologic agent of a contagious disease, mainly characterized by clinical gastroenteritis signs in younger dogs. CPV-2 emerged as a new virus in the late 1970s, which could infect domestic dogs, and became distributed in the global dog population within 2 years. A few years later, the virus's original type was replaced by a new genetic and antigenic variant, called CPV-2a. Around 1984 and 2000, virus variants with the single change to Asp or Glu in the VP2 residue 426 were detected (sometimes termed CPV-2b and -2c). The genetic and antigenic changes in the variants have also been correlated with changes in their host range; in particular, in the ability to replicate in cats and also host range differences in canine and other tissue culture cells. CPV-2 variants have been circulating among wild carnivores and have been well-documented in several countries around the world. Here, we have reviewed and summarized the current information about the worldwide distribution and evolution of CPV-2 variants since they emerged, as well as the host ranges they are associated with.

Minimal-post-processing 320-Gbps true random bit generation using physical white chaos.

Science.gov (United States)

Wang, Anbang; Wang, Longsheng; Li, Pu; Wang, Yuncai

2017-02-20

Chaotic external-cavity semiconductor laser (ECL) is a promising entropy source for generation of high-speed physical random bits or digital keys. The rate and randomness is unfortunately limited by laser relaxation oscillation and external-cavity resonance, and is usually improved by complicated post processing. Here, we propose using a physical broadband white chaos generated by optical heterodyning of two ECLs as entropy source to construct high-speed random bit generation (RBG) with minimal post processing. The optical heterodyne chaos not only has a white spectrum without signature of relaxation oscillation and external-cavity resonance but also has a symmetric amplitude distribution. Thus, after quantization with a multi-bit analog-digital-convertor (ADC), random bits can be obtained by extracting several least significant bits (LSBs) without any other processing. In experiments, a white chaos with a 3-dB bandwidth of 16.7 GHz is generated. Its entropy rate is estimated as 16 Gbps by single-bit quantization which means a spectrum efficiency of 96%. With quantization using an 8-bit ADC, 320-Gbps physical RBG is achieved by directly extracting 4 LSBs at 80-GHz sampling rate.

FORMULATION OF MATHEMATICAL PROBLEM DESCRIBING PHYSICAL AND CHEMICAL PROCESSES AT CONCRETE CORROSION

Directory of Open Access Journals (Sweden)

Sergey V. Fedosov

2017-06-01

Full Text Available The article deals with the relevance of new scientific research focused on modeling of physical and chemical processes occurring in the cement concrete at their exploitation. The basic types of concrete corrosion are described. The problem of mass transfer processes in a flat reinforced concrete wall at concrete corrosion of the first and the second types has been mathematically formulated.

Migraine Variants in Children

Science.gov (United States)

... Headaches in Children FAQ Migraine Variants In Children Children Get Migraines Too! Learn More Migraine Information Find Help Doctors & Resources Get Connected Join the Conversation Follow Us on Social Media Company About News Resources Privacy Policy Contact Phone: ...

Apolipoprotein L1 gene variants in deceased organ donors are associated with renal allograft failure.

Science.gov (United States)

Freedman, B I; Julian, B A; Pastan, S O; Israni, A K; Schladt, D; Gautreaux, M D; Hauptfeld, V; Bray, R A; Gebel, H M; Kirk, A D; Gaston, R S; Rogers, J; Farney, A C; Orlando, G; Stratta, R J; Mohan, S; Ma, L; Langefeld, C D; Hicks, P J; Palmer, N D; Adams, P L; Palanisamy, A; Reeves-Daniel, A M; Divers, J

2015-06-01

Apolipoprotein L1 gene (APOL1) nephropathy variants in African American deceased kidney donors were associated with shorter renal allograft survival in a prior single-center report. APOL1 G1 and G2 variants were genotyped in newly accrued DNA samples from African American deceased donors of kidneys recovered and/or transplanted in Alabama and North Carolina. APOL1 genotypes and allograft outcomes in subsequent transplants from 55 U.S. centers were linked, adjusting for age, sex and race/ethnicity of recipients, HLA match, cold ischemia time, panel reactive antibody levels, and donor type. For 221 transplantations from kidneys recovered in Alabama, there was a statistical trend toward shorter allograft survival in recipients of two-APOL1-nephropathy-variant kidneys (hazard ratio [HR] 2.71; p = 0.06). For all 675 kidneys transplanted from donors at both centers, APOL1 genotype (HR 2.26; p = 0.001) and African American recipient race/ethnicity (HR 1.60; p = 0.03) were associated with allograft failure. Kidneys from African American deceased donors with two APOL1 nephropathy variants reproducibly associate with higher risk for allograft failure after transplantation. These findings warrant consideration of rapidly genotyping deceased African American kidney donors for APOL1 risk variants at organ recovery and incorporation of results into allocation and informed-consent processes. © Copyright 2015 The American Society of Transplantation and the American Society of Transplant Surgeons.

The pathogenicity of genetic variants previously associated with left ventricular non-compaction

DEFF Research Database (Denmark)

Abbasi, Yeganeh; Jabbari, Javad; Jabbari, Reza

2016-01-01

BACKGROUND: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy. Many genetic variants have been associated with LVNC. However, the number of the previous LVNC-associated variants that are common in the background population remains unknown. The aim of this study was to provide...... an updated list of previously reported LVNC-associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false-positive LVNC-associated variants. METHODS AND RESULTS: The Human Gene Mutation Database and PubMed were systematically...... searched to identify all previously reported LVNC-associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine...

Misfolding, degradation, and aggregation of variant proteins. The molecular pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency

DEFF Research Database (Denmark)

Pedersen, Christina Bak; Bross, P.; Winter, V.S.

2003-01-01

and aggregation of variant SCAD proteins. In this study we investigated the processing of a set of disease-causing variant SCAD proteins (R22W, G68C, W153R, R359C, and Q341H) and two common variant proteins (R147W and G185S) that lead to reduced SCAD activity. All SCAD proteins, including the wild type, associate...... proteolytic degradation by mitochondrial proteases or, especially at elevated temperature, aggregation of non-native conformers. The latter finding may indicate that accumulation of aggregated SCAD proteins may play a role in the pathogenesis of SCAD deficiency.......Short chain acyl-CoA dehydrogenase (SCAD) deficiency is an inborn error of the mitochondrial fatty acid metabolism caused by rare variations as well as common susceptibility variations in the SCAD gene. Earlier studies have shown that a common variant SCAD protein (R147W) was impaired in folding...

Students' inclusion to the value of physical culture during the process of athletic training.

Directory of Open Access Journals (Sweden)

Sychov S.O.

2010-12-01

Full Text Available Means and methods of students' inclusion to the value of physical culture, during the process of athletic training on the classes of physical education are opened in this article. 52 students took part in research. It is developed the recommendation for the application of pedagogical conditions of use in the expressway strength and strength training, ability to determine dosing load for students with different level of physical background, methods of power properties development both for boys and for girls. It is shown that using of athletic training at the classes of physical education is contributing of students' inclusion to the value of physical culture.

Managing Variant Calling Files the Big Data Way: Using HDFS and Apache Parquet

NARCIS (Netherlands)

Boufea, Aikaterini; Finkers, H.J.; Kaauwen, van M.P.W.; Kramer, M.R.; Athanasiadis, I.N.

2017-01-01

Big Data has been seen as a remedy for the efficient management of the ever-increasing genomic data. In this paper, we investigate the use of Apache Spark to store and process Variant Calling Files (VCF) on a Hadoop cluster. We demonstrate Tomatula, a software tool for converting VCF files to Apache

Network perturbation by recurrent regulatory variants in cancer.

Directory of Open Access Journals (Sweden)

Kiwon Jang

2017-03-01

Full Text Available Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis. In the protein interactome, the identified transcriptional drivers were not as highly connected as coding driver genes but appeared to form a network module centered on the coding drivers. The coding and regulatory variants associated via these interactions between the coding and transcriptional drivers showed exclusive and complementary occurrence patterns across tumor samples. Transcriptional cancer drivers may act through an extensive perturbation of the regulatory network and by altering protein network modules through interactions with coding driver genes.

Variants at the 9p21 locus and melanoma risk

International Nuclear Information System (INIS)

Maccioni, Livia; Rachakonda, Panduranga Sivaramakrishna; Bermejo, Justo Lorenzo; Planelles, Dolores; Requena, Celia; Hemminki, Kari; Nagore, Eduardo; Kumar, Rajiv

2013-01-01

The influence of variants at the 9p21 locus on melanoma risk has been reported through investigation of CDKN2A variants through candidate gene approach as well as by genome wide association studies (GWAS). In the present study we genotyped, 25 SNPs that tag 273 variants on chromosome 9p21 in 837 melanoma cases and 1154 controls from Spain. Ten SNPs were selected based on previous associations, reported in GWAS, with either melanocytic nevi or melanoma risk or both. The other 15 SNPs were selected to fine map the CDKN2A gene region. All the 10 variants selected from the GWAS showed statistically significant association with melanoma risk. Statistically significant association with melanoma risk was also observed for the carriers of the variant T-allele of rs3088440 (540 C>T) at the 3’ UTR of CDKN2A gene with an OR 1.52 (95% CI 1.14-2.04). Interaction analysis between risk associated polymorphisms and previously genotyped MC1R variants, in the present study, did not show any statistically significant association. Statistical significant association was observed for the interaction between phototypes and the rs10811629 (located in intron 5 of MTAP). The strongest association was observed between the homozygous carrier of the A–allele and phototype II with an OR of 15.93 (95% CI 5.34-47.54). Our data confirmed the association of different variants at chromosome 9p21 with melanoma risk and we also found an association of a variant with skin phototypes

Spatial distributions of Pseudomonas fluorescens colony variants in mixed-culture biofilms.

Science.gov (United States)

Workentine, Matthew L; Wang, Siyuan; Ceri, Howard; Turner, Raymond J

2013-07-28

The emergence of colony morphology variants in structured environments is being recognized as important to both niche specialization and stress tolerance. Pseudomonas fluorescens demonstrates diversity in both its natural environment, the rhizosphere, and in laboratory grown biofilms. Sub-populations of these variants within a biofilm have been suggested as important contributors to antimicrobial stress tolerance given their altered susceptibility to various agents. As such it is of interest to determine how these variants might be distributed in the biofilm environment. Here we present an analysis of the spatial distribution of Pseudomonas fluorescens colony morphology variants in mixed-culture biofilms with the wildtype phenotype. These findings reveal that two variant colony morphotypes demonstrate a significant growth advantage over the wildtype morphotype in the biofilm environment. The two variant morphotypes out-grew the wildtype across the entire biofilm and this occurred within 24 h and was maintained through to 96 h. This competitive advantage was not observed in homogeneous broth culture. The significant advantage that the variants demonstrate in biofilm colonization over the wildtype denotes the importance of this phenotype in structured environments.

Photo-physics of third-order nonlinear optical processes in organic dyes

International Nuclear Information System (INIS)

Delysse, Stephane

1997-01-01

We study some aspects of the nonlinear picosecond photo-physics in organic dyes using Kerr ellipsometry. The aim is to establish link between the photo-physics and nonlinear optics in these compounds. First, we study coherent processes directly linked to the third-order susceptibility. Thus, we measure two-photon absorption spectra of large internal charge transfer dyes. We take into account all coupling between three electronic states which can interfere to explain the particular response of some stilbene dyes. On the second hand, we expose a more photophysical approach to determine the S 1 → S n transition energies and moments using the measurement of excited state absorption cross sections. These results allow the prediction of the susceptibilities relevant to alternative nonlinear optical methods. Nevertheless, the stationary approach hides the complex relaxation processes which can take place in organic dyes. As an illustration, we study the formation and disappearance of a TICT (Twisted intramolecular charge transfer) in a pyrylium salt in solvents of increasing viscosity. (author) [fr

Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

CERN Document Server

Demirel, Yasar

2014-01-01

Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

McRunjob: A High Energy Physics Workflow Planner for Grid Production Processing

OpenAIRE

Graham, G E; Evans, D; Bertram, I

2003-01-01

McRunjob is a powerful grid workflow manager used to manage the generation of large numbers of production processing jobs in High Energy Physics. In use at both the DZero and CMS experiments, McRunjob has been used to manage large Monte Carlo production processing since 1999 and is being extended to uses in regular production processing for analysis and reconstruction. Described at CHEP 2001, McRunjob converts core metadata into jobs submittable in a variety of environments. The powerful core...

Regionally variant collagen alignment correlates with viscoelastic properties of the disc of the human temporomandibular joint.

Science.gov (United States)

Gutman, Shawn; Kim, Daniel; Tarafder, Solaiman; Velez, Sergio; Jeong, Julia; Lee, Chang H

2018-02-01

To determine the regionally variant quality of collagen alignment in human TMJ discs and its statistical correlation with viscoelastic properties. For quantitative analysis of the quality of collagen alignment, horizontal sections of human TMJ discs with Pricrosirius Red staining were imaged under circularly polarized microscopy. Mean angle and angular deviation of collagen fibers in each region were analyzed using a well-established automated image-processing for angular gradient. Instantaneous and relaxation moduli of each disc region were measured under stress-relaxation test both in tensile and compression. Then Spearman correlation analysis was performed between the angular deviation and the moduli. To understand the effect of glycosaminoglycans on the correlation, TMJ disc samples were treated by chondroitinase ABC (C-ABC). Our imaging processing analysis showed the region-variant direction of collagen alignment, consistently with previous findings. Interestingly, the quality of collagen alignment, not only the directions, was significantly different in between the regions. The angular deviation of fiber alignment in the anterior and intermediate regions were significantly smaller than the posterior region. Medial and lateral regions showed significantly bigger angular deviation than all the other regions. The regionally variant angular deviation values showed statistically significant correlation with the tensile instantaneous modulus and the relaxation modulus, partially dependent on C-ABC treatment. Our findings suggest the region-variant degree of collagen fiber alignment is likely attributed to the heterogeneous viscoelastic properties of TMJ disc that may have significant implications in development of regenerative therapy for TMJ disc. Copyright © 2017 Elsevier Ltd. All rights reserved.

Familial Risk and a Genome-Wide Supported DRD2 Variant for Schizophrenia Predict Lateral Prefrontal-Amygdala Effective Connectivity During Emotion Processing.

Science.gov (United States)

Quarto, Tiziana; Paparella, Isabella; De Tullio, Davide; Viscanti, Giovanna; Fazio, Leonardo; Taurisano, Paolo; Romano, Raffaella; Rampino, Antonio; Masellis, Rita; Popolizio, Teresa; Selvaggi, Pierluigi; Pergola, Giulio; Bertolino, Alessandro; Blasi, Giuseppe

2017-09-16

The brain functional mechanisms translating genetic risk into emotional symptoms in schizophrenia (SCZ) may include abnormal functional integration between areas key for emotion processing, such as the amygdala and the lateral prefrontal cortex (LPFC). Indeed, investigation of these mechanisms is also complicated by emotion processing comprising different subcomponents and by disease-associated state variables. Here, our aim was to investigate the relationship between risk for SCZ and effective connectivity between the amygdala and the LPFC during different subcomponents of emotion processing. Thus, we first characterized with dynamic causal modeling (DCM) physiological patterns of LPFC-amygdala effective connectivity in healthy controls (HC) during implicit and explicit emotion processing. Then, we compared DCM patterns in a subsample of HC, in patients with SCZ and in healthy siblings of patients (SIB), matched for demographics. Finally, we investigated in HC association of LPFC-amygdala effective connectivity with a genome-wide supported variant increasing genetic risk for SCZ and possibly relevant to emotion processing (DRD2 rs2514218). In HC, we found that a "bottom-up" amygdala-to-LPFC pattern during implicit processing and a "top-down" LPFC-to-amygdala pattern during explicit processing were the most likely directional models of effective connectivity. Differently, implicit emotion processing in SIB, SCZ, and HC homozygous for the SCZ risk rs2514218 C allele was associated with decreased probability for the "bottom-up" as well as with increased probability for the "top-down" model. These findings suggest that task-specific anomaly in the directional flow of information or disconnection between the amygdala and the LPFC is a good candidate endophenotype of SCZ. © The Author 2017. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

About forming of personality physical culture of students in the process of physical education (in aspect of presence of abilities

Directory of Open Access Journals (Sweden)

S.I. Belykh

2013-01-01

Full Text Available It is shown that practice of teaching of discipline «Physical education» does not provide forming of volume of abilities, sufficient for the origin of athletic activity. Prevail ability to pick up a place, sporting form, inventory depending on the type of physical exercises and ability on the observance of rules of the personal hygiene. In the questionnaire questioning 650 students (324 youths and 326 girls of the first and fourth courses took part. All of students visited employments on physical education at school and institute of higher. It is marked that the important task of amateurish athletic education is forming for the students of the personal experience of independent athletic, health and рекреационных employments. It is underlined that sense of amateurish athletic education of students consists in achievement by a man unity of mental and activity processes. Such processes are needed for an estimation and understanding of the state of the health, programming and residence of healthy way of life.

Novel Variants in Individuals with RYR1-Related Congenital Myopathies: Genetic, Laboratory, and Clinical Findings

Directory of Open Access Journals (Sweden)

Joshua J. Todd

2018-03-01

Full Text Available The ryanodine receptor 1-related congenital myopathies (RYR1-RM comprise a spectrum of slow, rare neuromuscular diseases. Affected individuals present with a mild-to-severe symptomatology ranging from proximal muscle weakness, hypotonia and joint contractures to scoliosis, ophthalmoplegia, and respiratory involvement. Although there is currently no FDA-approved treatment for RYR1-RM, our group recently conducted the first clinical trial in this patient population (NCT02362425. This study aimed to characterize novel RYR1 variants with regard to genetic, laboratory, muscle magnetic resonance imaging (MRI, and clinical findings. Genetic and histopathology reports were obtained from participant’s medical records. Alamut Visual Software was used to determine if participant’s variants had been previously reported and to assess predicted pathogenicity. Physical exams, pulmonary function tests, T1-weighted muscle MRI scans, and blood measures were completed during the abovementioned clinical trial. Six novel variants (two de novo, three dominant, and one recessive were identified in individuals with RYR1-RM. Consistent with established RYR1-RM histopathology, cores were observed in all biopsies, except Case 6 who exhibited fiber-type disproportion. Muscle atrophy and impaired mobility with Trendelenburg gait were the most common clinical symptoms and were identified in all cases. Muscle MRI revealed substantial inter-individual variation in fatty infiltration corroborating the heterogeneity of the disease. Two individuals with dominant RYR1 variants exhibited respiratory insufficiency: a clinical symptom more commonly associated with recessive RYR1-RM cases. This study demonstrates that a genetics-led approach is suitable for the diagnosis of suspected RYR1-RM which can be corroborated through histopathology, muscle MRI and clinical examination.

Contributions of Function-Altering Variants in Genes Implicated in Pubertal Timing and Body Mass for Self-Limited Delayed Puberty.

Science.gov (United States)

Howard, Sasha R; Guasti, Leonardo; Poliandri, Ariel; David, Alessia; Cabrera, Claudia P; Barnes, Michael R; Wehkalampi, Karoliina; O'Rahilly, Stephen; Aiken, Catherine E; Coll, Anthony P; Ma, Marcella; Rimmington, Debra; Yeo, Giles S H; Dunkel, Leo

2018-02-01

Self-limited delayed puberty (DP) is often associated with a delay in physical maturation, but although highly heritable the causal genetic factors remain elusive. Genome-wide association studies of the timing of puberty have identified multiple loci for age at menarche in females and voice break in males, particularly in pathways controlling energy balance. We sought to assess the contribution of rare variants in such genes to the phenotype of familial DP. We performed whole-exome sequencing in 67 pedigrees (125 individuals with DP and 35 unaffected controls) from our unique cohort of familial self-limited DP. Using a whole-exome sequencing filtering pipeline one candidate gene [fat mass and obesity-associated gene (FTO)] was identified. In silico, in vitro, and mouse model studies were performed to investigate the pathogenicity of FTO variants and timing of puberty in FTO+/- mice. We identified potentially pathogenic, rare variants in genes in linkage disequilibrium with genome-wide association studies of age at menarche loci in 283 genes. Of these, five genes were implicated in the control of body mass. After filtering for segregation with trait, one candidate, FTO, was retained. Two FTO variants, found in 14 affected individuals from three families, were also associated with leanness in these patients with DP. One variant (p.Leu44Val) demonstrated altered demethylation activity of the mutant protein in vitro. Fto+/- mice displayed a significantly delayed timing of pubertal onset (P puberty in the general population may contribute to the pathogenesis of self-limited DP. Copyright © 2017 Endocrine Society

Genomic constitution of an H-2:Tla variant leukemia.

Science.gov (United States)

Shen, F W; Chaganti, R S; Doucette, L A; Litman, G W; Steinmetz, M; Hood, L; Boyse, E A

1984-10-01

A TL+ leukemia of a (B6 X A)F1 hybrid mouse (H-2b/H-2a) was previously subjected to immunoselection against H-2a by passage in (B6 X A.SW)F1 mice (H-2b/H-2s). A variant leukemia line was obtained that serologically lacked not only the H-2a phenotype but also the TL phenotype determined by the linked cis Tlaa allele of strain A. The H-2b phenotype and the TL phenotype of the Tlab allele of the B6 strain, which is expressed only by leukemia cells, were retained by the variant. Southern blotting with an H-2 cDNA probe that identifies restriction fragment polymorphisms distinguishing alleles of the H-2 and Tla regions of the B6 and A strains indicates that both the H-2a and Tlaa alleles are missing from the genome of this H-2a:Tlaa negative variant. Since the variant has two apparently unaltered chromosomes 17, where the H-2:Tla complex is situated, and since the intensity of bands in Southern blotting is suggestive of H-2b homozygosity, it is considered that loss of the H-2a:Tlaa haplotype by the variant was accompanied by duplication of the H-2b:Tlab haplotype. The implied change from heterozygosity to homozygosity that the variant has undergone with respect to H-2:Tla was not paralleled by a similar change at the three other loci tested, since the variant retained heterozygosity for Pep-3 (chromosome 1), Gpi-1 (chromosome 7), and Es-1 (chromosome 8).

Efficient utilization of rare variants for detection of disease-related genomic regions.

Directory of Open Access Journals (Sweden)

Lei Zhang

2010-12-01

Full Text Available When testing association between rare variants and diseases, an efficient analytical approach involves considering a set of variants in a genomic region as the unit of analysis. One factor complicating this approach is that the vast majority of rare variants in practical applications are believed to represent background neutral variation. As a result, analyzing a single set with all variants may not represent a powerful approach. Here, we propose two alternative strategies. In the first, we analyze the subsets of rare variants exhaustively. In the second, we categorize variants selectively into two subsets: one in which variants are overrepresented in cases, and the other in which variants are overrepresented in controls. When the proportion of neutral variants is moderate to large we show, by simulations, that the both proposed strategies improve the statistical power over methods analyzing a single set with total variants. When applied to a real sequencing association study, the proposed methods consistently produce smaller p-values than their competitors. When applied to another real sequencing dataset to study the difference of rare allele distributions between ethnic populations, the proposed methods detect the overrepresentation of variants between the CHB (Chinese Han in Beijing and YRI (Yoruba people of Ibadan populations with small p-values. Additional analyses suggest that there is no difference between the CHB and CHD (Chinese Han in Denver datasets, as expected. Finally, when applied to the CHB and JPT (Japanese people in Tokyo populations, existing methods fail to detect any difference, while it is detected by the proposed methods in several regions.

Changes in classification of genetic variants in BRCA1 and BRCA2.

Science.gov (United States)

Kast, Karin; Wimberger, Pauline; Arnold, Norbert

2018-02-01

Classification of variants of unknown significance (VUS) in the breast cancer genes BRCA1 and BRCA2 changes with accumulating evidence for clinical relevance. In most cases down-staging towards neutral variants without clinical significance is possible. We searched the database of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) for changes in classification of genetic variants as an update to our earlier publication on genetic variants in the Centre of Dresden. Changes between 2015 and 2017 were recorded. In the group of variants of unclassified significance (VUS, Class 3, uncertain), only changes of classification towards neutral genetic variants were noted. In BRCA1, 25% of the Class 3 variants (n = 2/8) changed to Class 2 (likely benign) and Class 1 (benign). In BRCA2, in 50% of the Class 3 variants (n = 16/32), a change to Class 2 (n = 10/16) or Class 1 (n = 6/16) was observed. No change in classification was noted in Class 4 (likely pathogenic) and Class 5 (pathogenic) genetic variants in both genes. No up-staging from Class 1, Class 2 or Class 3 to more clinical significance was observed. All variants with a change in classification in our cohort were down-staged towards no clinical significance by a panel of experts of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC). Prevention in families with Class 3 variants should be based on pedigree based risks and should not be guided by the presence of a VUS.

Identifying genetic variants that affect viability in large cohorts.

Directory of Open Access Journals (Sweden)

Hakhamanesh Mostafavi

2017-09-01

Full Text Available A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10-6 for fathers and P~2.0 × 10-3 for mothers, consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10-3. Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD, body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans.

Protein variants in Hiroshima and Nagasaki: tales of two cities.

Science.gov (United States)

Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

1988-12-01

The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation

Hepatitis E Virus Variant in Farmed Mink, Denmark

DEFF Research Database (Denmark)

Krog, Jesper Schak; Breum, Solvej Østergaard; Jensen, Trine Hammer

2013-01-01

Hepatitis E virus (HEV) is a zoonotic virus for which pigs are the primary animal reservoir. To investigate whether HEV occurs in mink in Denmark, we screened feces and tissues from domestic and wild mink. Our finding of a novel HEV variant supports previous findings of HEV variants in a variety...

Efficient population-scale variant analysis and prioritization with VAPr.

Science.gov (United States)

Birmingham, Amanda; Mark, Adam M; Mazzaferro, Carlo; Xu, Guorong; Fisch, Kathleen M

2018-04-06

With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package VAPr (Variant Analysis and Prioritization). VAPr leverages existing annotation tools ANNOVAR and MyVariant.info with MongoDB-based flexible storage and filtering functionality. It offers biologists and bioinformatics generalists easy-to-use and scalable analysis and prioritization of genomic variants from large cohort studies. VAPr is developed in Python and is available for free use and extension under the MIT License. An install package is available on PyPi at https://pypi.python.org/pypi/VAPr, while source code and extensive documentation are on GitHub at https://github.com/ucsd-ccbb/VAPr. kfisch@ucsd.edu.

Physics Colloquium: The optical route to quantum information processing

CERN Multimedia

Université de Genève

2011-01-01

Geneva University Physics Department 24, Quai Ernest Ansermet CH-1211 Geneva 4 Monday 11 April 2011 17h00 - Ecole de Physique, Auditoire Stückelberg The optical route to quantum information processing Prof. Terry Rudolph/Imperial College, London Photons are attractive as carriers of quantum information both because they travel, and can thus transmit information, but also because of their good coherence properties and ease in undergoing single-qubit manipulations. The main obstacle to their use in information processing is inducing an effective interaction between them in order to produce entanglement. The most promising approach in photon-based information processing architectures is so-called measurement-based quantum computing. This relies on creating upfront a multi-qubit highly entangled state (the cluster state) which has the remarkable property that, once prepared, it can be used to perform quantum computation by making only single qubit measurements. In this talk I will discuss generically the...

IL10 low-frequency variants in Behçet's disease patients.

Science.gov (United States)

Matos, Mafalda; Xavier, Joana M; Abrantes, Patrícia; Sousa, Inês; Rei, Nádia; Davatchi, Fereydoun; Shahram, Farhad; Jesus, Gorete; Barcelos, Filipe; Vedes, Joana; Salgado, Manuel; Abdollahi, Bahar Sadeghi; Nadji, Abdolhadi; Moraes-Fontes, Maria Francisca; Shafiee, Niloofar Mojarad; Ghaderibarmi, Fahmida; Vaz Patto, José; Crespo, Jorge; Oliveira, Sofia A

2017-05-01

To explain the missing heritability after the genome-wide association studies era, sequencing studies allow the identification of low-frequency variants with a stronger effect on disease risk. Common variants in the interleukin 10 gene (IL10) have been consistently associated with Behçet's disease (BD) and the goal of this study is to investigate the role of low-frequency IL10 variants in BD susceptibility. To identify IL10 low-frequency variants, a discovery group of 50 Portuguese BD patients were Sanger-sequenced in a 7.7 kb genomic region encompassing the complete IL10 gene, 0.9 kb upstream and 2 kb downstream, and two conserved regions in the putative promoter. To assess if the novel variants are BD- and/or Portuguese-specific, they were assayed in an additional group of BD patients (26 Portuguese and 964 Iranian) and controls (104 Portuguese and 823 Iranian). Rare IL10 coding variants were not detected in BD patients, but we identified 28 known single nucleotide polymorphisms with minor allele frequencies ranging from 0.010 to 0.390, and five novel non-coding variants in five heterozygous cases. ss836185595, located in the IL10 3' untranslated region, was also detected in one Iranian control individual and therefore is not specific to BD. The remaining novel IL10 variants (ss836185596 and ss836185602 in intron 3, ss836185598 and ss836185604 in the putative promoter region) were not found in the replication dataset. This study highlights the importance of screening the whole gene and regulatory regions when searching for novel variants associated with complex diseases, and the need to develop bioinformatics tools to predict the functional impact of non-coding variants and statistical tests which incorporate these predictions. © 2014 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death

Directory of Open Access Journals (Sweden)

Mohammad K. Eldomery

2016-11-01

Full Text Available Abstract Background Mitochondrial presequence proteases perform fundamental functions as they process about 70 % of all mitochondrial preproteins that are encoded in the nucleus and imported posttranslationally. The mitochondrial intermediate presequence protease MIP/Oct1, which carries out precursor processing, has not yet been established to have a role in human disease. Methods Whole exome sequencing was performed on four unrelated probands with left ventricular non-compaction (LVNC, developmental delay (DD, seizures, and severe hypotonia. Proposed pathogenic variants were confirmed by Sanger sequencing or array comparative genomic hybridization. Functional analysis of the identified MIP variants was performed using the model organism Saccharomyces cerevisiae as the protein and its functions are highly conserved from yeast to human. Results Biallelic single nucleotide variants (SNVs or copy number variants (CNVs in MIPEP, which encodes MIP, were present in all four probands, three of whom had infantile/childhood death. Two patients had compound heterozygous SNVs (p.L582R/p.L71Q and p.E602*/p.L306F and one patient from a consanguineous family had a homozygous SNV (p.K343E. The fourth patient, identified through the GeneMatcher tool, a part of the Matchmaker Exchange Project, was found to have inherited a paternal SNV (p.H512D and a maternal CNV (1.4-Mb deletion of 13q12.12 that includes MIPEP. All amino acids affected in the patients’ missense variants are highly conserved from yeast to human and therefore S. cerevisiae was employed for functional analysis (for p.L71Q, p.L306F, and p.K343E. The mutations p.L339F (human p.L306F and p.K376E (human p.K343E resulted in a severe decrease of Oct1 protease activity and accumulation of non-processed Oct1 substrates and consequently impaired viability under respiratory growth conditions. The p.L83Q (human p.L71Q failed to localize to the mitochondria. Conclusions Our findings reveal for the first

Two Novel Variants Affecting CDKL5 Transcript Associated with Epileptic Encephalopathy.

Science.gov (United States)

Neupauerová, Jana; Štěrbová, Katalin; Vlčková, Markéta; Sebroňová, Věra; Maříková, Tat'ána; Krůtová, Marcela; David, Staněk; Kršek, Pavel; Žaliová, Markéta; Seeman, Pavel; Laššuthová, Petra

2017-10-01

Variants in the human X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been reported as being etiologically associated with early infantile epileptic encephalopathy type 2 (EIEE2). We report on two patients, a boy and a girl, with EIEE2 that present with early onset epilepsy, hypotonia, severe intellectual disability, and poor eye contact. Massively parallel sequencing (MPS) of a custom-designed gene panel for epilepsy and epileptic encephalopathy containing 112 epilepsy-related genes was performed. Sanger sequencing was used to confirm the novel variants. For confirmation of the functional consequence of an intronic CDKL5 variant in patient 2, an RNA study was done. DNA sequencing revealed de novo variants in CDKL5, a c.2578C>T (p. Gln860*) present in a hemizygous state in a 3-year-old boy, and a potential splice site variant c.463+5G>A in heterozygous state in a 5-year-old girl. Multiple in silico splicing algorithms predicted a highly reduced splice site score for c.463+5G>A. A subsequent mRNA study confirmed an aberrant shorter transcript lacking exon 7. Our data confirmed that variants in the CDKL5 are associated with EIEE2. There is credible evidence that the novel identified variants are pathogenic and, therefore, are likely the cause of the disease in the presented patients. In one of the patients a stop codon variant is predicted to produce a truncated protein, and in the other patient an intronic variant results in aberrant splicing.

Processing-structure-property relationships in electron beam physical vapor deposited yttria stabilized zirconia coatings

International Nuclear Information System (INIS)

Rao, D. Srinivasa; Valleti, Krishna; Joshi, S. V.; Janardhan, G. Ranga

2011-01-01

The physical and mechanical properties of yttria stabilized zirconia (YSZ) coatings deposited by the electron beam physical vapor deposition technique have been investigated by varying the key process variables such as vapor incidence angle and sample rotation speed. The tetragonal zirconia coatings formed under varying process conditions employed were found to have widely different surface and cross-sectional morphologies. The porosity, phase composition, planar orientation, hardness, adhesion, and surface residual stresses in the coated specimens were comprehensively evaluated to develop a correlation with the process variables. Under transverse scratch test conditions, the YSZ coatings exhibited two different crack formation modes, depending on the magnitude of residual stress. The influence of processing conditions on the coating deposition rate, column orientation angle, and adhesion strength has been established. Key relationships between porosity, hardness, and adhesion are also presented.

Common genetic variants influence human subcortical brain structures

Science.gov (United States)

Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S.; Armstrong, Nicola J.; Bernard, Manon; Bohlken, Marc M.; Boks, Marco P.; Bralten, Janita; Brown, Andrew A.; Chakravarty, M. Mallar; Chen, Qiang; Ching, Christopher R. K.; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L.; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J.; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H.; Olde Loohuis, Loes M.; Luciano, Michelle; Macare, Christine; Mather, Karen A.; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L.; Roiz-Santiañez, Roberto; Rose, Emma J.; Salami, Alireza; Sämann, Philipp G.; Schmaal, Lianne; Schork, Andrew J.; Shin, Jean; Strike, Lachlan T.; Teumer, Alexander; van Donkelaar, Marjolein M. J.; van Eijk, Kristel R.; Walters, Raymond K.; Westlye, Lars T.; Whelan, Christopher D.; Winkler, Anderson M.; Zwiers, Marcel P.; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M. H.; Hartberg, Cecilie B.; Haukvik, Unn K.; Heister, Angelien J. G. A. M.; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C. M.; Lopez, Lorna M.; Makkinje, Remco R. R.; Matarin, Mar; Naber, Marlies A. M.; McKay, D. Reese; Needham, Margaret; Nugent, Allison C.; Pütz, Benno; Royle, Natalie A.; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S. L.; van Hulzen, Kimm J. E.; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A.; Bastin, Mark E.; Brodaty, Henry; Bulayeva, Kazima B.; Carless, Melanie A.; Cichon, Sven; Corvin, Aiden; Curran, Joanne E.; Czisch, Michael; de Zubicaray, Greig I.; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D.; Erk, Susanne; Fedko, Iryna O.; Ferrucci, Luigi; Foroud, Tatiana M.; Fox, Peter T.; Fukunaga, Masaki; Gibbs, J. Raphael; Göring, Harald H. H.; Green, Robert C.; Guelfi, Sebastian; Hansell, Narelle K.; Hartman, Catharina A.; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G.; Heslenfeld, Dirk J.; Hoekstra, Pieter J.; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R.; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W.; Kochunov, Peter; Kwok, John B.; Lawrie, Stephen M.; Liu, Xinmin; Longo, Dan L.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W.; Mostert, Jeanette C.; Mühleisen, Thomas W.; Nalls, Michael A.; Nichols, Thomas E.; Nilsson, Lars G.; Nöthen, Markus M.; Ohi, Kazutaka; Olvera, Rene L.; Perez-Iglesias, Rocio; Pike, G. Bruce; Potkin, Steven G.; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D.; Rujescu, Dan; Schnell, Knut; Schofield, Peter R.; Smith, Colin; Steen, Vidar M.; Sussmann, Jessika E.; Thalamuthu, Anbupalam; Toga, Arthur W.; Traynor, Bryan J.; Troncoso, Juan; Turner, Jessica A.; Valdés Hernández, Maria C.; van ’t Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J. A.; van Tol, Marie-Jose; Veltman, Dick J.; Wassink, Thomas H.; Westman, Eric; Zielke, Ronald H.; Zonderman, Alan B.; Ashbrook, David G.; Hager, Reinmar; Lu, Lu; McMahon, Francis J.; Morris, Derek W.; Williams, Robert W.; Brunner, Han G.; Buckner, Randy L.; Buitelaar, Jan K.; Cahn, Wiepke; Calhoun, Vince D.; Cavalleri, Gianpiero L.; Crespo-Facorro, Benedicto; Dale, Anders M.; Davies, Gareth E.; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C.; Espeseth, Thomas; Gollub, Randy L.; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S.; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W. J. H.; Roffman, Joshua L.; Sisodiya, Sanjay M.; Smoller, Jordan W.; van Bokhoven, Hans; van Haren, Neeltje E. M.; Völzke, Henry; Walter, Henrik; Weiner, Michael W.; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A.; Blangero, John; Boomsma, Dorret I.; Brouwer, Rachel M.; Cannon, Dara M.; Cookson, Mark R.; de Geus, Eco J. C.; Deary, Ian J.; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E.; Francks, Clyde; Glahn, David C.; Grabe, Hans J.; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E.; Jönsson, Erik G.; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S.; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M.; Ophoff, Roel A.; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S.; Saykin, Andrew J.; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M.; Weale, Michael E.; Weinberger, Daniel R.; Adams, Hieab H. H.; Launer, Lenore J.; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L.; Becker, James T.; Yanek, Lisa; van der Lee, Sven J.; Ebling, Maritza; Fischl, Bruce; Longstreth, W. T.; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N.; van Duijn, Cornelia M.; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C.; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M. Arfan; Martin, Nicholas G.; Wright, Margaret J.; Schumann, Gunter; Franke, Barbara; Thompson, Paul M.; Medland, Sarah E.

2015-01-01

The highly complex structure of the human brain is strongly shaped by genetic influences1. Subcortical brain regions form circuits with cortical areas to coordinate movement2, learning, memory3 and motivation4, and altered circuits can lead to abnormal behaviour and disease2. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume5 and intracranial volume6. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10−33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability inhuman brain development, and may help to determine mechanisms of neuropsychiatric dysfunction. PMID:25607358

Common genetic variants influence human subcortical brain structures.

Science.gov (United States)

Hibar, Derrek P; Stein, Jason L; Renteria, Miguel E; Arias-Vasquez, Alejandro; Desrivières, Sylvane; Jahanshad, Neda; Toro, Roberto; Wittfeld, Katharina; Abramovic, Lucija; Andersson, Micael; Aribisala, Benjamin S; Armstrong, Nicola J; Bernard, Manon; Bohlken, Marc M; Boks, Marco P; Bralten, Janita; Brown, Andrew A; Chakravarty, M Mallar; Chen, Qiang; Ching, Christopher R K; Cuellar-Partida, Gabriel; den Braber, Anouk; Giddaluru, Sudheer; Goldman, Aaron L; Grimm, Oliver; Guadalupe, Tulio; Hass, Johanna; Woldehawariat, Girma; Holmes, Avram J; Hoogman, Martine; Janowitz, Deborah; Jia, Tianye; Kim, Sungeun; Klein, Marieke; Kraemer, Bernd; Lee, Phil H; Olde Loohuis, Loes M; Luciano, Michelle; Macare, Christine; Mather, Karen A; Mattheisen, Manuel; Milaneschi, Yuri; Nho, Kwangsik; Papmeyer, Martina; Ramasamy, Adaikalavan; Risacher, Shannon L; Roiz-Santiañez, Roberto; Rose, Emma J; Salami, Alireza; Sämann, Philipp G; Schmaal, Lianne; Schork, Andrew J; Shin, Jean; Strike, Lachlan T; Teumer, Alexander; van Donkelaar, Marjolein M J; van Eijk, Kristel R; Walters, Raymond K; Westlye, Lars T; Whelan, Christopher D; Winkler, Anderson M; Zwiers, Marcel P; Alhusaini, Saud; Athanasiu, Lavinia; Ehrlich, Stefan; Hakobjan, Marina M H; Hartberg, Cecilie B; Haukvik, Unn K; Heister, Angelien J G A M; Hoehn, David; Kasperaviciute, Dalia; Liewald, David C M; Lopez, Lorna M; Makkinje, Remco R R; Matarin, Mar; Naber, Marlies A M; McKay, D Reese; Needham, Margaret; Nugent, Allison C; Pütz, Benno; Royle, Natalie A; Shen, Li; Sprooten, Emma; Trabzuni, Daniah; van der Marel, Saskia S L; van Hulzen, Kimm J E; Walton, Esther; Wolf, Christiane; Almasy, Laura; Ames, David; Arepalli, Sampath; Assareh, Amelia A; Bastin, Mark E; Brodaty, Henry; Bulayeva, Kazima B; Carless, Melanie A; Cichon, Sven; Corvin, Aiden; Curran, Joanne E; Czisch, Michael; de Zubicaray, Greig I; Dillman, Allissa; Duggirala, Ravi; Dyer, Thomas D; Erk, Susanne; Fedko, Iryna O; Ferrucci, Luigi; Foroud, Tatiana M; Fox, Peter T; Fukunaga, Masaki; Gibbs, J Raphael; Göring, Harald H H; Green, Robert C; Guelfi, Sebastian; Hansell, Narelle K; Hartman, Catharina A; Hegenscheid, Katrin; Heinz, Andreas; Hernandez, Dena G; Heslenfeld, Dirk J; Hoekstra, Pieter J; Holsboer, Florian; Homuth, Georg; Hottenga, Jouke-Jan; Ikeda, Masashi; Jack, Clifford R; Jenkinson, Mark; Johnson, Robert; Kanai, Ryota; Keil, Maria; Kent, Jack W; Kochunov, Peter; Kwok, John B; Lawrie, Stephen M; Liu, Xinmin; Longo, Dan L; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Mohnke, Sebastian; Montgomery, Grant W; Mostert, Jeanette C; Mühleisen, Thomas W; Nalls, Michael A; Nichols, Thomas E; Nilsson, Lars G; Nöthen, Markus M; Ohi, Kazutaka; Olvera, Rene L; Perez-Iglesias, Rocio; Pike, G Bruce; Potkin, Steven G; Reinvang, Ivar; Reppermund, Simone; Rietschel, Marcella; Romanczuk-Seiferth, Nina; Rosen, Glenn D; Rujescu, Dan; Schnell, Knut; Schofield, Peter R; Smith, Colin; Steen, Vidar M; Sussmann, Jessika E; Thalamuthu, Anbupalam; Toga, Arthur W; Traynor, Bryan J; Troncoso, Juan; Turner, Jessica A; Valdés Hernández, Maria C; van 't Ent, Dennis; van der Brug, Marcel; van der Wee, Nic J A; van Tol, Marie-Jose; Veltman, Dick J; Wassink, Thomas H; Westman, Eric; Zielke, Ronald H; Zonderman, Alan B; Ashbrook, David G; Hager, Reinmar; Lu, Lu; McMahon, Francis J; Morris, Derek W; Williams, Robert W; Brunner, Han G; Buckner, Randy L; Buitelaar, Jan K; Cahn, Wiepke; Calhoun, Vince D; Cavalleri, Gianpiero L; Crespo-Facorro, Benedicto; Dale, Anders M; Davies, Gareth E; Delanty, Norman; Depondt, Chantal; Djurovic, Srdjan; Drevets, Wayne C; Espeseth, Thomas; Gollub, Randy L; Ho, Beng-Choon; Hoffmann, Wolfgang; Hosten, Norbert; Kahn, René S; Le Hellard, Stephanie; Meyer-Lindenberg, Andreas; Müller-Myhsok, Bertram; Nauck, Matthias; Nyberg, Lars; Pandolfo, Massimo; Penninx, Brenda W J H; Roffman, Joshua L; Sisodiya, Sanjay M; Smoller, Jordan W; van Bokhoven, Hans; van Haren, Neeltje E M; Völzke, Henry; Walter, Henrik; Weiner, Michael W; Wen, Wei; White, Tonya; Agartz, Ingrid; Andreassen, Ole A; Blangero, John; Boomsma, Dorret I; Brouwer, Rachel M; Cannon, Dara M; Cookson, Mark R; de Geus, Eco J C; Deary, Ian J; Donohoe, Gary; Fernández, Guillén; Fisher, Simon E; Francks, Clyde; Glahn, David C; Grabe, Hans J; Gruber, Oliver; Hardy, John; Hashimoto, Ryota; Hulshoff Pol, Hilleke E; Jönsson, Erik G; Kloszewska, Iwona; Lovestone, Simon; Mattay, Venkata S; Mecocci, Patrizia; McDonald, Colm; McIntosh, Andrew M; Ophoff, Roel A; Paus, Tomas; Pausova, Zdenka; Ryten, Mina; Sachdev, Perminder S; Saykin, Andrew J; Simmons, Andy; Singleton, Andrew; Soininen, Hilkka; Wardlaw, Joanna M; Weale, Michael E; Weinberger, Daniel R; Adams, Hieab H H; Launer, Lenore J; Seiler, Stephan; Schmidt, Reinhold; Chauhan, Ganesh; Satizabal, Claudia L; Becker, James T; Yanek, Lisa; van der Lee, Sven J; Ebling, Maritza; Fischl, Bruce; Longstreth, W T; Greve, Douglas; Schmidt, Helena; Nyquist, Paul; Vinke, Louis N; van Duijn, Cornelia M; Xue, Luting; Mazoyer, Bernard; Bis, Joshua C; Gudnason, Vilmundur; Seshadri, Sudha; Ikram, M Arfan; Martin, Nicholas G; Wright, Margaret J; Schumann, Gunter; Franke, Barbara; Thompson, Paul M; Medland, Sarah E

2015-04-09

The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

Description of intensity of physical education in a structure educational educate and health-improvement-educate processes.

Directory of Open Access Journals (Sweden)

Bondar T.S.

2012-12-01

Full Text Available Comparison of intensity of physical education is presented in child's establishments of making healthy and rest and general educational establishments. Questioning of 183 students-practice and analysis of document of the Kharkov regional management is conducted on physical education and sport. It is set that health-improvement-educate process is directed on forming for children and young people of culture of health. It is marked that the result of pedagogical activity in establishments and establishments of education is physical, spiritual and social development of personality of children and young people. Witnessed, that process of physical education in out-of-town child's establishments of making healthy and rest almost in three times more intensive by comparison to general educational establishments and school summer camps. It contingently a presence for the children of plenty of spare time, by the use in practice of camps of non-standard facilities and forms of increase of motive activity of children, by the features of structure health-improvement-educate process.

Functional significance of SPINK1 promoter variants in chronic pancreatitis.

Science.gov (United States)

Derikx, Monique H M; Geisz, Andrea; Kereszturi, Éva; Sahin-Tóth, Miklós

2015-05-01

Chronic pancreatitis is a progressive inflammatory disorder of the pancreas, which often develops as a result of genetic predisposition. Some of the most frequently identified risk factors affect the serine protease inhibitor Kazal type 1 (SPINK1) gene, which encodes a trypsin inhibitor responsible for protecting the pancreas from premature trypsinogen activation. Recent genetic and functional studies indicated that promoter variants in the SPINK1 gene might contribute to disease risk in carriers. Here, we investigated the functional effects of 17 SPINK1 promoter variants using luciferase reporter gene expression assay in four different cell lines, including three pancreatic acinar cell lines (rat AR42J with or without dexamethasone-induced differentiation and mouse 266-6) and human embryonic kidney 293T cells. We found that most variants caused relatively small changes in promoter activity. Surprisingly, however, we observed significant variations in the effects of the promoter variants in the different cell lines. Only four variants exhibited consistently reduced promoter activity in all acinar cell lines, confirming previous reports that variants c.-108G>T, c.-142T>C, and c.-147A>G are risk factors for chronic pancreatitis and identifying c.-52G>T as a novel risk variant. In contrast, variant c.-215G>A, which is linked with the disease-associated splice-site mutation c.194 + 2T>C, caused increased promoter activity, which may mitigate the overall effect of the pathogenic haplotype. Our study lends further support to the notion that sequence evaluation of the SPINK1 promoter region in patients with chronic pancreatitis is justified as part of the etiological investigation. Copyright © 2015 the American Physiological Society.

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.

Differences in the Load-Velocity Profile Between 4 Bench-Press Variants.

Science.gov (United States)

García-Ramos, Amador; Pestaña-Melero, Francisco Luis; Pérez-Castilla, Alejandro; Rojas, Francisco Javier; Haff, Guy Gregory

2018-03-01

To compare the load-velocity relationship between 4 variants of the bench-press (BP) exercise. The full load-velocity relationship of 30 men was evaluated by means of an incremental loading test starting at 17 kg and progressing to the individual 1-repetition maximum (1RM) in 4 BP variants: concentric-only BP, concentric-only BP throw (BPT), eccentric-concentric BP, and eccentric-concentric BPT. A strong and fairly linear relationship between mean velocity (MV) and %1RM was observed for the 4 BP variants (r 2  > .96 for pooled data and r 2  > .98 for individual data). The MV associated with each %1RM was significantly higher in the eccentric-concentric technique than in the concentric-only technique. The only significant difference between the BP and BPT variants was the higher MV with the light to moderate loads (20-70%1RM) in the BPT using the concentric-only technique. MV was significantly and positively correlated between the 4 BP variants (r = .44-.76), which suggests that the subjects with higher velocities for each %1RM in 1 BP variant also tend to have higher velocities for each %1RM in the 3 other BP variants. These results highlight the need for obtaining specific equations for each BP variant and the existence of individual load-velocity profiles.

Changes in localization of human discs large (hDlg) during keratinocyte differentiation is associated with expression of alternatively spliced hDlg variants

International Nuclear Information System (INIS)

Roberts, S.; Calautti, E.; Vanderweil, S.; Nguyen, H.O.; Foley, A.; Baden, H.P.; Viel, A.

2007-01-01

Alternative spliced variants of the human discs large (hDlg) tumour suppressor are characterized by combinations of insertions. Here, using insertions I2- and I3-specific antibodies, we show that I2 and I3 variants have distinct distributions in epidermal and cervical epithelia. In skin and cervix, I3 variants are found in the cytoplasm. Cytoplasmic localization of I3 variants decreases as cervical keratinocytes differentiate, concomitant with relocalization to the cell periphery. I2 variants are found at the cell periphery of differentiated epidermal and cervical keratinocytes. Nuclear localization of I2 variants was evident in both tissues, with concentration of nuclear I2 variants in basal and parabasal cervical keratinocytes. A prominent nuclear localization of hDlg in cells of hyperproliferative layers of psoriatic lesions, but not in mature differentiated keratinocytes, together with I2 redistribution in differentiating keratinocytes, suggests that nuclear hDlg functions may be pertinent to growth of undifferentiated cells. Supporting our findings in squamous tissues, a decrease of nuclear hDlg and an increase of membrane-bound and cytoplasmic hDlg upon calcium-induced keratinocyte differentiation were not concomitant processes. Furthermore, we confirm that the exit of I2 variants from the nucleus is linked to stimulation of epithelial differentiation. The dynamic redistribution of hDlg also correlated with a marked increase in the expression of I3 variants while the level of I2 variants showed only a moderate decrease. Because changes in the intracellular distribution of hDlg splice variants, and in their expression levels, correlate with changes in differentiation state we hypothesize that the different hDlg isoforms play distinct roles at various stages of epithelial differentiation

A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

Science.gov (United States)

Genser, Krzysztof; Hatcher, Robert; Kelsey, Michael; Perdue, Gabriel; Wenzel, Hans; Wright, Dennis H.; Yarba, Julia

2017-10-01

The Geant4 simulation toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models rely on measured cross-sections and phenomenological models with the physically motivated parameters that are tuned to cover many application domains. To study what uncertainties are associated with the Geant4 physics models we have designed and implemented a comprehensive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies. It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertainties associated with the simulation model choices. Based on modern event-processing infrastructure software, the toolkit offers a variety of attractive features, e.g. flexible run-time configurable workflow, comprehensive bookkeeping, easy to expand collection of analytical components. Design, implementation technology, and key functionalities of the toolkit are presented in this paper and illustrated with selected results.

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Science.gov (United States)

Karbassi, Izabela; Maston, Glenn A; Love, Angela; DiVincenzo, Christina; Braastad, Corey D; Elzinga, Christopher D; Bright, Alison R; Previte, Domenic; Zhang, Ke; Rowland, Charles M; McCarthy, Michele; Lapierre, Jennifer L; Dubois, Felicita; Medeiros, Katelyn A; Batish, Sat Dev; Jones, Jeffrey; Liaquat, Khalida; Hoffman, Carol A; Jaremko, Malgorzata; Wang, Zhenyuan; Sun, Weimin; Buller-Burckle, Arlene; Strom, Charles M; Keiles, Steven B; Higgins, Joseph J

2016-01-01

We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies collected from internal and external sources. Scores were calculated by trained scientists using a quantitative framework that assigned differential weighting to these five types of data. We performed descriptive and comparative statistics on the dataset and tested interobserver concordance among the trained scientists. Private variants defined as variants found within single families (n = 5,182), were either VUS (80.5%; n = 4,169) or likely pathogenic (19.5%; n = 1,013). The remaining variants (n = 6,712) were VUS (38.4%; n = 2,577) or likely benign/benign (34.7%; n = 2,327) or likely pathogenic/pathogenic (26.9%, n = 1,808). Exact agreement between the trained scientists on the final variant score was 98.5% [95% confidence interval (CI) (98.0, 98.9)] with an interobserver consistency of 97% [95% CI (91.5, 99.4)]. Variant scores were stable and showed increasing odds of being in agreement with new data when re-evaluated periodically. This carefully curated, standardized variant pathogenicity scoring system provides reliable pathogenicity scores for DNA variants encountered in a clinical laboratory setting. © 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Autism as an adaptive common variant pathway for human brain development.

Science.gov (United States)

Johnson, Mark H

2017-06-01

While research on focal perinatal lesions has provided evidence for recovery of function, much less is known about processes of brain adaptation resulting from mild but widespread disturbances to neural processing over the early years (such as alterations in synaptic efficiency). Rather than being viewed as a direct behavioral consequence of life-long neural dysfunction, I propose that autism is best viewed as the end result of engaging adaptive processes during a sensitive period. From this perspective, autism is not appropriately described as a disorder of neurodevelopment, but rather as an adaptive common variant pathway of human functional brain development. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

Gene × physical activity interactions in obesity

DEFF Research Database (Denmark)

Ahmad, Shafqat; Rukh, Gull; Varga, Tibor V

2013-01-01

Numerous obesity loci have been identified using genome-wide association studies. A UK study indicated that physical activity may attenuate the cumulative effect of 12 of these loci, but replication studies are lacking. Therefore, we tested whether the aggregate effect of these loci is diminished...... in adults of European ancestry reporting high levels of physical activity. Twelve obesity-susceptibility loci were genotyped or imputed in 111,421 participants. A genetic risk score (GRS) was calculated by summing the BMI-associated alleles of each genetic variant. Physical activity was assessed using self...... combined using meta-analysis weighted by cohort sample size. The meta-analysis yielded a statistically significant GRS × physical activity interaction effect estimate (Pinteraction  = 0.015). However, a statistically significant interaction effect was only apparent in North American cohorts (n = 39...

Guillain-Barré Syndrome: A Variant Consisting of Facial Diplegia and Paresthesia with Left Facial Hemiplegia Associated with Antibodies to Galactocerebroside and Phosphatidic Acid.

Science.gov (United States)

Nishiguchi, Sho; Branch, Joel; Tsuchiya, Tsubasa; Ito, Ryoji; Kawada, Junya

2017-10-02

BACKGROUND A rare variant of Guillain-Barré syndrome (GBS) consists of facial diplegia and paresthesia, but an even more rare association is with facial hemiplegia, similar to Bell's palsy. This case report is of this rare variant of GBS that was associated with IgG antibodies to galactocerebroside and phosphatidic acid. CASE REPORT A 54-year-old man presented with lower left facial palsy and paresthesia of his extremities, following an upper respiratory tract infection. Physical examination confirmed lower left facial palsy and paresthesia of his extremities with hyporeflexia of his lower limbs and sensory loss of all four extremities. The differential diagnosis was between a variant of GBS and Bell's palsy. Following initial treatment with glucocorticoids followed by intravenous immunoglobulin (IVIG), his sensory abnormalities resolved. Serum IgG antibodies to galactocerebroside and phosphatidic acid were positive in this patient, but not other antibodies to glycolipids or phospholipids were found. Five months following discharge from hospital, his left facial palsy had improved. CONCLUSIONS A case of a rare variant of GBS is presented with facial diplegia and paresthesia and with unilateral facial palsy. This rare variant of GBS may which may mimic Bell's palsy. In this case, IgG antibodies to galactocerebroside and phosphatidic acid were detected.

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

Directory of Open Access Journals (Sweden)

D. G. Georgakopoulos

2009-04-01

Full Text Available The interest in bioaerosols has traditionally been linked to health hazards for humans, animals and plants. However, several components of bioaerosols exhibit physical properties of great significance for cloud processes, such as ice nucleation and cloud condensation. To gain a better understanding of their influence on climate, it is therefore important to determine the composition, concentration, seasonal fluctuation, regional diversity and evolution of bioaerosols. In this paper, we will review briefly the existing techniques for detection, quantification, physical and chemical analysis of biological particles, attempting to bridge physical, chemical and biological methods for analysis of biological particles and integrate them with aerosol sampling techniques. We will also explore some emerging spectroscopy techniques for bulk and single-particle analysis that have potential for in-situ physical and chemical analysis. Lastly, we will outline open questions and further desired capabilities (e.g., in-situ, sensitive, both broad and selective, on-line, time-resolved, rapid, versatile, cost-effective techniques required prior to comprehensive understanding of chemical and physical characterization of bioaerosols.

Behavioural-variant frontotemporal dementia: An update

Directory of Open Access Journals (Sweden)

Olivier Piguet

Full Text Available ABSTRACT Behavioural-variant frontotemporal dementia (bvFTD is characterised by insidious changes in personality and interpersonal conduct that reflect progressive disintegration of the neural circuits involved in social cognition, emotion regulation, motivation and decision making. The underlying pathology is heterogeneous and classified according to the presence of intraneuronal inclusions of tau, TDP-43 or occasionally FUS. Biomarkers to detect these histopathological changes in life are increasingly important with the development of disease-modifying drugs. Gene mutations have been found which collectively account for around 10-20% of cases including a novel hexanucleotide repeat on chromosome 9 (C9orf72. The recently reviewed International Consensus Criteria for bvFTD propose three levels of diagnostic certainly: possible, probable and definite. Detailed history taking from family members to elicit behavioural features underpins the diagnostic process with support from neuropsychological testing designed to detect impairment in decision-making, emotion processing and social cognition. Brain imaging is important for increasing the level of diagnosis certainty. Carer education and support remain of paramount importance.

Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA.

Science.gov (United States)

Schrader, Kasmintan A; Cheng, Donavan T; Joseph, Vijai; Prasad, Meera; Walsh, Michael; Zehir, Ahmet; Ni, Ai; Thomas, Tinu; Benayed, Ryma; Ashraf, Asad; Lincoln, Annie; Arcila, Maria; Stadler, Zsofia; Solit, David; Hyman, David M; Hyman, David; Zhang, Liying; Klimstra, David; Ladanyi, Marc; Offit, Kenneth; Berger, Michael; Robson, Mark

2016-01-01

Tumor genetic sequencing identifies potentially targetable genetic alterations with therapeutic implications. Analysis has concentrated on detecting tumor-specific variants, but recognition of germline variants may prove valuable as well. To estimate the burden of germline variants identified through routine clinical tumor sequencing. Patients with advanced cancer diagnoses eligible for studies of targeted agents at Memorial Sloan Kettering Cancer Center are offered tumor-normal sequencing with MSK-IMPACT, a 341-gene panel. We surveyed the germline variants seen in 187 overlapping genes with Mendelian disease associations in 1566 patients who had undergone tumor profiling between March and October 2014. The number of presumed pathogenic germline variants (PPGVs) and variants of uncertain significance per person in 187 genes associated with single-gene disorders and the proportions of individuals with PPGVs in clinically relevant gene subsets, in genes consistent with known tumor phenotypes, and in genes with evidence of second somatic hits in their tumors. The mean age of the 1566 patients was 58 years, and 54% were women. Presumed pathogenic germline variants in known Mendelian disease-associated genes were identified in 246 of 1566 patients (15.7%; 95% CI, 14.0%-17.6%), including 198 individuals with mutations in genes associated with cancer susceptibility. Germline findings in cancer susceptibility genes were concordant with the individual's cancer type in only 81 of 198 cases (40.9%; 95% CI, 34.3%-47.9%). In individuals with PPGVs retained in the tumor, somatic alteration of the other allele was seen in 39 of 182 cases (21.4%; 95% CI, 16.1%-28.0%), of which 13 cases did not show a known correlation of the germline mutation and a known syndrome. Mutations in non-cancer-related Mendelian disease genes were seen in 55 of 1566 cases (3.5%; 95% CI, 27.1%-45.4%). Almost every individual had more than 1 variant of uncertain significance (1565 of 1566 patients; 99

Extension twin variant selection during uniaxial compression of a magnesium alloy

DEFF Research Database (Denmark)

Pei, Y.; Godfrey, A.; Jiang, J.

2012-01-01

is also observed in that smaller grains are less likely to contain lower ranked twin variants. For both 5% and 10% compression no clear relationship exists between the volume fraction of each twin variant in a given grain population and the Schmid factor for the twin variant. A positive linear......Samples of the magnesium alloy AZ31 have been deformed by compression to strains of 5% and 10% and microstructural observations made to investigate the activation of specific {1 0 1¯ 2} extension twin variants. The twinning has been analyzed on a grain-by-grain basis for more than 260 grains...... to determine both the number of extension twin variants in each grain, and the volume fraction of each. At 5% strain approx. 30% of the grains contain twins corresponding to variants with the third or lower ranked Schmid factor, with the fraction increasing to 40% after 10% compression. A grain size effect...

DeepPVP: phenotype-based prioritization of causative variants using deep learning

KAUST Repository

Boudellioua, Imene

2018-05-02

Background: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity prediction is combined with a semantic similarity measure to prioritize not only variants that are likely to be dysfunctional but those that are likely involved in the pathogenesis of a patient\\'s phenotype. Results: We have developed DeepPVP, a variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data. We demonstrate that DeepPVP performs significantly better than existing methods, including phenotype-based methods that use similar features. DeepPVP is freely available at https://github.com/bio-ontology-research-group/phenomenet-vp Conclusions: DeepPVP further improves on existing variant prioritization methods both in terms of speed as well as accuracy.

Discovering deviating cases and process variants using trace clustering

NARCIS (Netherlands)

Hompes, B.F.A.; Buijs, J.C.A.M.; van der Aalst, W.M.P.; Dixit, P.M.; Buurman, J.

2015-01-01

Information systems supporting business processes generate event data which provide the starting point for a range of process mining techniques. Lion's share of real-life processes are complex and ad-hoc, which creates problems for traditional process mining techniques, that cannot deal with such

A geometric framework for evaluating rare variant tests of association.

Science.gov (United States)

Liu, Keli; Fast, Shannon; Zawistowski, Matthew; Tintle, Nathan L

2013-05-01

The wave of next-generation sequencing data has arrived. However, many questions still remain about how to best analyze sequence data, particularly the contribution of rare genetic variants to human disease. Numerous statistical methods have been proposed to aggregate association signals across multiple rare variant sites in an effort to increase statistical power; however, the precise relation between the tests is often not well understood. We present a geometric representation for rare variant data in which rare allele counts in case and control samples are treated as vectors in Euclidean space. The geometric framework facilitates a rigorous classification of existing rare variant tests into two broad categories: tests for a difference in the lengths of the case and control vectors, and joint tests for a difference in either the lengths or angles of the two vectors. We demonstrate that genetic architecture of a trait, including the number and frequency of risk alleles, directly relates to the behavior of the length and joint tests. Hence, the geometric framework allows prediction of which tests will perform best under different disease models. Furthermore, the structure of the geometric framework immediately suggests additional classes and types of rare variant tests. We consider two general classes of tests which show robustness to noncausal and protective variants. The geometric framework introduces a novel and unique method to assess current rare variant methodology and provides guidelines for both applied and theoretical researchers. © 2013 Wiley Periodicals, Inc.

CEACAM6 gene variants in inflammatory bowel disease.

Science.gov (United States)

Glas, Jürgen; Seiderer, Julia; Fries, Christoph; Tillack, Cornelia; Pfennig, Simone; Weidinger, Maria; Beigel, Florian; Olszak, Torsten; Lass, Ulrich; Göke, Burkhard; Ochsenkühn, Thomas; Wolf, Christiane; Lohse, Peter; Müller-Myhsok, Bertram; Diegelmann, Julia; Czamara, Darina; Brand, Stephan

2011-04-29

The carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) acts as a receptor for adherent-invasive E. coli (AIEC) and its ileal expression is increased in patients with Crohn's disease (CD). Given its contribution to the pathogenesis of CD, we aimed to investigate the role of genetic variants in the CEACAM6 region in patients with inflammatory bowel diseases (IBD). In this study, a total of 2,683 genomic DNA samples (including DNA from 858 CD patients, 475 patients with ulcerative colitis (UC), and 1,350 healthy, unrelated controls) was analyzed for eight CEACAM6 SNPs (rs10415946, rs1805223 = p.Pro42Pro, rs4803507, rs4803508, rs11548735 = p.Gly239Val, rs7246116 = pHis260His, rs2701, rs10416839). In addition, a detailed haplotype analysis and genotype-phenotype analysis were performed. Overall, our genotype analysis did not reveal any significant association of the investigated CEACAM6 SNPs and haplotypes with CD or UC susceptibility, although certain CEACAM6 SNPs modulated CEACAM6 expression in intestinal epithelial cell lines. Despite its function as receptor of AIEC in ileal CD, we found no association of the CEACAM6 SNPs with ileal or ileocolonic CD. Moreover, there was no evidence of epistasis between the analyzed CEACAM6 variants and the main CD-associated NOD2, IL23R and ATG16L1 variants. This study represents the first detailed analysis of CEACAM6 variants in IBD patients. Despite its important role in bacterial attachment in ileal CD, we could not demonstrate a role for CEACAM6 variants in IBD susceptibility or regarding an ileal CD phenotype. Further functional studies are required to analyze if these gene variants modulate ileal bacterial attachment.

CEACAM6 gene variants in inflammatory bowel disease.

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Jürgen Glas

Full Text Available BACKGROUND: The carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6 acts as a receptor for adherent-invasive E. coli (AIEC and its ileal expression is increased in patients with Crohn's disease (CD. Given its contribution to the pathogenesis of CD, we aimed to investigate the role of genetic variants in the CEACAM6 region in patients with inflammatory bowel diseases (IBD. METHODOLOGY: In this study, a total of 2,683 genomic DNA samples (including DNA from 858 CD patients, 475 patients with ulcerative colitis (UC, and 1,350 healthy, unrelated controls was analyzed for eight CEACAM6 SNPs (rs10415946, rs1805223 = p.Pro42Pro, rs4803507, rs4803508, rs11548735 = p.Gly239Val, rs7246116 = pHis260His, rs2701, rs10416839. In addition, a detailed haplotype analysis and genotype-phenotype analysis were performed. Overall, our genotype analysis did not reveal any significant association of the investigated CEACAM6 SNPs and haplotypes with CD or UC susceptibility, although certain CEACAM6 SNPs modulated CEACAM6 expression in intestinal epithelial cell lines. Despite its function as receptor of AIEC in ileal CD, we found no association of the CEACAM6 SNPs with ileal or ileocolonic CD. Moreover, there was no evidence of epistasis between the analyzed CEACAM6 variants and the main CD-associated NOD2, IL23R and ATG16L1 variants. CONCLUSIONS: This study represents the first detailed analysis of CEACAM6 variants in IBD patients. Despite its important role in bacterial attachment in ileal CD, we could not demonstrate a role for CEACAM6 variants in IBD susceptibility or regarding an ileal CD phenotype. Further functional studies are required to analyze if these gene variants modulate ileal bacterial attachment.

Nuclear variants of bone morphogenetic proteins

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Meinhart Christopher A

2010-03-01

Full Text Available Abstract Background Bone morphogenetic proteins (BMPs contribute to many different aspects of development including mesoderm formation, heart development, neurogenesis, skeletal development, and axis formation. They have previously been recognized only as secreted growth factors, but the present study detected Bmp2, Bmp4, and Gdf5/CDMP1 in the nuclei of cultured cells using immunocytochemistry and immunoblotting of nuclear extracts. Results In all three proteins, a bipartite nuclear localization signal (NLS was found to overlap the site at which the proproteins are cleaved to release the mature growth factors from the propeptides. Mutational analyses indicated that the nuclear variants of these three proteins are produced by initiating translation from downstream alternative start codons. The resulting proteins lack N-terminal signal peptides and are therefore translated in the cytoplasm rather than the endoplasmic reticulum, thus avoiding proteolytic processing in the secretory pathway. Instead, the uncleaved proteins (designated nBmp2, nBmp4, and nGdf5 containing the intact NLSs are translocated to the nucleus. Immunostaining of endogenous nBmp2 in cultured cells demonstrated that the amount of nBmp2 as well as its nuclear/cytoplasmic distribution differs between cells that are in M-phase versus other phases of the cell cycle. Conclusions The observation that nBmp2 localization varies throughout the cell cycle, as well as the conservation of a nuclear localization mechanism among three different BMP family members, suggests that these novel nuclear variants of BMP family proteins play an important functional role in the cell.

BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

NARCIS (Netherlands)

Shimelis, Hermela; Mesman, Romy L. S.; Von Nicolai, Catharina; Ehlen, Asa; Guidugli, Lucia; Martin, Charlotte; Calléja, Fabienne M. G. R.; Meeks, Huong; Hallberg, Emily; Hinton, Jamie; Lilyquist, Jenna; Hu, Chunling; Aalfs, Cora M.; Aittomäki, Kristiina; Andrulis, Irene; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W.; Benitez, Javier; Bogdanova, Natalia V.; Bojesen, Stig E.; Bolla, Manjeet K.; Borresen-Dale, Anne-Lise; Brauch, Hiltrud; Brennan, Paul; Brenner, Hermann; Broeks, Annegien; Brouwers, Barbara; Brüning, Thomas; Burwinkel, Barbara; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Cheng, Ching-Yu; Choi, Ji-Yeob; Collée, J. Margriet; Cox, Angela; Cross, Simon S.; Czene, Kamila; Darabi, Hatef; Dennis, Joe; Dörk, Thilo; Dos-Santos-Silva, Isabel; Dunning, Alison M.; Fasching, Peter A.; Figueroa, Jonine; Flyger, Henrik; García-Closas, Montserrat; Giles, Graham G.; Glendon, Gord; Guénel, Pascal; Haiman, Christopher A.; Hall, Per; Hamann, Ute; Hartman, Mikael; Hogervorst, Frans B.; Hollestelle, Antoinette; Hopper, John L.; Ito, Hidemi; Jakubowska, Anna; Kang, Daehee; Kosma, Veli-Matti; Kristensen, Vessela; Lai, Kah-Nyin; Lambrechts, Diether; Marchand, Loic Le; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Machackova, Eva; Mannermaa, Arto; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; Miao, Hui; Michailidou, Kyriaki; Milne, Roger L.; Muir, Kenneth; Neuhausen, Susan L.; Nevanlinna, Heli; Olson, Janet E.; Olswold, Curtis; Oosterwijk, Jan J. C.; Osorio, Ana; Peterlongo, Paolo; Peto, Julian; Pharoah, Paul D. P.; Pylkäs, Katri; Radice, Paolo; Rashid, Muhammad Usman; Rhenius, Valerie; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schoemaker, Minouk J.; Seynaeve, Caroline; Shah, Mitul; Shen, Chen-Yang; Shrubsole, Martha; Shu, Xiao-Ou; Slager, Susan; Southey, Melissa C.; Stram, Daniel O.; Swerdlow, Anthony; teo, Soo H.; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; van Asperen, Christi J.; van der Kolk, Lizet E.; Wang, Qin; Winqvist, Robert; Wu, Anna H.; Yu, Jyh-Cherng; Zheng, Wei; Zheng, Ying; Leary, Jennifer; Walker, Logan; Foretova, Lenka; Fostira, Florentia; Claes, Kathleen B. M.; Varesco, Liliana; Moghadasi, Setareh; Easton, Douglas F.; Spurdle, Amanda; Devilee, Peter; Vrieling, Harry; Monteiro, Alvaro N. A.; Goldgar, David E.; Carreira, Aura; Vreeswijk, Maaike P. G.; Couch, Fergus J.

2017-01-01

Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk

Predicting effects of noncoding variants with deep learning-based sequence model.

Science.gov (United States)

Zhou, Jian; Troyanskaya, Olga G

2015-10-01

Identifying functional effects of noncoding variants is a major challenge in human genetics. To predict the noncoding-variant effects de novo from sequence, we developed a deep learning-based algorithmic framework, DeepSEA (http://deepsea.princeton.edu/), that directly learns a regulatory sequence code from large-scale chromatin-profiling data, enabling prediction of chromatin effects of sequence alterations with single-nucleotide sensitivity. We further used this capability to improve prioritization of functional variants including expression quantitative trait loci (eQTLs) and disease-associated variants.

THE EXAMINATION OF THE EFFECTS OF THE RHYTHMIC TEACHING OF PHYSICAL EDUCATION ON SPEED OF 9-10 YEARS OLD GIRLS

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Dragana Aleksić

2013-07-01

Full Text Available By different moving activities, learning about their body and its mothoric, a child develops its mothoric, acquires different motoric skills and habits and develops motoric activities. In this work, the subject of the research is just one segment of the anthropological area which refers to the appearance of appropriate motor abilities-speed. The research involved a total sample of 99 girls from the 3th and 4th grade of elementary school. The subjects were classified in experimental and control groups. The experimental group was made of 51 students and they were practicing according to planning instruction where the rhythmic gymnastics had the primary part. The control group of 48 students was practicing according to official instructional plan and program for P.E. of the Republic of Serbia. At the beginning of the academic year, initial (first measurement was performed, followed by experimental final (second measurement at the end of experiment. Research data was processed using SPSS standard statistics procedure. The multi-variant procedures were used in this research ant those were: the multi-variant analysis of the variable MANCOVA i MANOVA. Also, the mono-variant procedures were used and those were: the variable analysis ANCOVA, ANOVA and the interval of entrust. Considering the difference of the influence of the treatment, it can be pointed out that the experimental program, with all its characteristics, widely contributed to all its segments to the improvement of speed. It is known that the use of physical exercise stimulation only within regular physical education classes is not sufficient to provoke essential improvement of motoric abilities. Therefore it is very important not only to try to animate schoolboys for participation in additional sporting activities, especial rhythmic gymnastics, out of regular physical education classes, but, what is even more important, to increase the number of physical education classes a week, with the

The principle of least action history and physics

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Rojo, Alberto

2018-01-01

The principle of least action originates in the idea that, if nature has a purpose, it should follow a minimum or critical path. This simple principle, and its variants and generalizations, applies to optics, mechanics, electromagnetism, relativity, and quantum mechanics, and provides an essential guide to understanding the beauty of physics. This unique text provides an accessible introduction to the action principle across these various fields of physics, and examines its history and fundamental role in science. It includes - with varying levels of mathematical sophistication - explanations from historical sources, discussion of classic papers, and original worked examples. The result is a story that is understandable to those with a modest mathematical background, as well as to researchers and students in physics and the history of physics.

A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3

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Murthy, Aditya; Li, Yun; Peng, Ivan; Reichelt, Mike; Katakam, Anand Kumar; Noubade, Rajkumar; Roose-Girma, Merone; Devoss, Jason; Diehl, Lauri; Graham, Robert R.; van Lookeren Campagne, Menno

2014-02-01

Crohn's disease is a debilitating inflammatory bowel disease (IBD) that can involve the entire digestive tract. A single-nucleotide polymorphism (SNP) encoding a missense variant in the autophagy gene ATG16L1 (rs2241880, Thr300Ala) is strongly associated with the incidence of Crohn's disease. Numerous studies have demonstrated the effect of ATG16L1 deletion or deficiency; however, the molecular consequences of the Thr300Ala (T300A) variant remains unknown. Here we show that amino acids 296-299 constitute a caspase cleavage motif in ATG16L1 and that the T300A variant (T316A in mice) significantly increases ATG16L1 sensitization to caspase-3-mediated processing. We observed that death-receptor activation or starvation-induced metabolic stress in human and murine macrophages increased degradation of the T300A or T316A variants of ATG16L1, respectively, resulting in diminished autophagy. Knock-in mice harbouring the T316A variant showed defective clearance of the ileal pathogen Yersinia enterocolitica and an elevated inflammatory cytokine response. In turn, deletion of the caspase-3-encoding gene, Casp3, or elimination of the caspase cleavage site by site-directed mutagenesis rescued starvation-induced autophagy and pathogen clearance, respectively. These findings demonstrate that caspase 3 activation in the presence of a common risk allele leads to accelerated degradation of ATG16L1, placing cellular stress, apoptotic stimuli and impaired autophagy in a unified pathway that predisposes to Crohn's disease.

GBA Variants Influence Motor and Non-Motor Features of Parkinson's Disease.

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Jesús, Silvia; Huertas, Ismael; Bernal-Bernal, Inmaculada; Bonilla-Toribio, Marta; Cáceres-Redondo, María Teresa; Vargas-González, Laura; Gómez-Llamas, Myriam; Carrillo, Fátima; Calderón, Enrique; Carballo, Manuel; Gómez-Garre, Pilar; Mir, Pablo

2016-01-01

The presence of mutations in glucocerebrosidase (GBA) gene is a known factor increasing the risk of developing Parkinson's disease (PD). Mutations carriers have earlier disease onset and are more likely to develop neuropsychiatric symptoms than other sporadic PD cases. These symptoms have primarily been observed in Parkinson's patients carrying the most common pathogenic mutations L444P and N370S. However, recent findings suggest that other variants across the gene may have a different impact on the phenotype as well as on the disease progression. We aimed to explore the influence of variants across GBA gene on the clinical features and treatment related complications in PD. In this study, we screened the GBA gene in a cohort of 532 well-characterised PD patients and 542 controls from southern Spain. The potential pathogeniticy of the identified variants was assessed using in-silico analysis and subsequently classified as benign or deleterious. As a result, we observed a higher frequency of GBA variants in PD patients (12.2% vs. 7.9% in controls, p = 0.021), earlier mean age at disease onset in GBA variant carriers (50.6 vs. 56.6 years; p = 0.013), as well as more prevalent motor and non-motor symptoms in patients carrying deleterious variants. In addition, we found that dopaminergic motor complications are influenced by both benign and deleterious variants. Our results highlight the fact that the impact on the phenotype highly depends on the potential pathogenicity of the carried variants. Therefore, the course of motor and non-motor symptoms as well as treatment-related motor complications could be influenced by GBA variants.

GBA Variants Influence Motor and Non-Motor Features of Parkinson's Disease.

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Silvia Jesús

Full Text Available The presence of mutations in glucocerebrosidase (GBA gene is a known factor increasing the risk of developing Parkinson's disease (PD. Mutations carriers have earlier disease onset and are more likely to develop neuropsychiatric symptoms than other sporadic PD cases. These symptoms have primarily been observed in Parkinson's patients carrying the most common pathogenic mutations L444P and N370S. However, recent findings suggest that other variants across the gene may have a different impact on the phenotype as well as on the disease progression. We aimed to explore the influence of variants across GBA gene on the clinical features and treatment related complications in PD. In this study, we screened the GBA gene in a cohort of 532 well-characterised PD patients and 542 controls from southern Spain. The potential pathogeniticy of the identified variants was assessed using in-silico analysis and subsequently classified as benign or deleterious. As a result, we observed a higher frequency of GBA variants in PD patients (12.2% vs. 7.9% in controls, p = 0.021, earlier mean age at disease onset in GBA variant carriers (50.6 vs. 56.6 years; p = 0.013, as well as more prevalent motor and non-motor symptoms in patients carrying deleterious variants. In addition, we found that dopaminergic motor complications are influenced by both benign and deleterious variants. Our results highlight the fact that the impact on the phenotype highly depends on the potential pathogenicity of the carried variants. Therefore, the course of motor and non-motor symptoms as well as treatment-related motor complications could be influenced by GBA variants.

VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern

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Hu Qiang

2012-01-01

Full Text Available Abstract Background The massive amounts of genetic variant generated by the next generation sequencing systems demand the development of effective computational tools for variant prioritization. Findings VPA (Variant Pattern Analyzer is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. The tool starts from individual files of variant and sequence calls and extract variants with user-specified frequency pattern across the study subjects of interest. Several position level quality criteria can be incorporated into the variant extraction. It can be used in studies with matched pair design as well as studies with multiple groups of subjects. Conclusions VPA can be used as an automatic pipeline to prioritize variants for further functional exploration and hypothesis generation. The package is implemented in the R language and is freely available from http://vpa.r-forge.r-project.org.

Ossification variants of the femoral condyles are not associated with osteochondritis dissecans

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Jans, L., E-mail: lennartjans@hotmail.com [Department of Radiology and Medical Imaging, Ghent University Hospital, De Pintelaan 185, 9000 Gent (Belgium); Jaremko, J., E-mail: jjaremko@gmail.com [Department of Radiology, University of Alberta Hospital, 8440-112 Street, Edmonton T6G 2B7, Alberta (Canada); Ditchfield, M., E-mail: Michael.ditchfield@southernhealth.org.au [Department of Radiology, Monash University Clayton Campus, Wellington Road, Clayton 3800, VIC (Australia); De Coninck, T., E-mail: Tinekedeconinck@ugent.be [Department of Radiology and Medical Imaging, Ghent University Hospital, De Pintelaan 185, 9000 Gent (Belgium); Huysse, W., E-mail: Wouter.huysse@ugent.be [Department of Radiology and Medical Imaging, Ghent University Hospital, De Pintelaan 185, 9000 Gent (Belgium); Moon, A., E-mail: Anna.moon@rch.org.au [Department of Radiology, Royal Children' s Hospital, Flemington Road, Parkville 3052, VIC (Australia); Verstraete, K., E-mail: Koenraad.verstraete@ugent.be [Department of Radiology and Medical Imaging, Ghent University Hospital, De Pintelaan 185, 9000 Gent (Belgium)

2012-11-15

Purpose: To determine if ossification variants of the femoral condyles involving the subchondral bone plate are associated with osteochondritis dissecans (OCD). Materials and methods: The prevalence of ossification variants of the unaffected femoral condyle in 116 patients (aged 9-14 years) with unicondylar OCD on MRI (magnetic resonance imaging) of the knee was compared to a control group of 579 patients (aged 9-14 years) without OCD. The evolution of the ossification variants in both groups was studied by reviewing follow-up MR imaging side by side with the baseline study. Results: The prevalence of ossification variants in the unaffected condyle in patients with OCD (12.9%) and in the control group of patients without OCD (12.6%) was similar (p = 0.88). Evolution of ossification variants to OCD was not seen on follow-up MRI examinations. All variants had decreased in size or were no longer visible. Conclusion: Ossification variants of the femoral condyle that involve the subchondral bone plate are not associated with OCD. Clinical relevance statement: Ossification variants are not associated with OCD, indicating that routine MRI follow-up in affected children is not mandatory.

Ossification variants of the femoral condyles are not associated with osteochondritis dissecans

International Nuclear Information System (INIS)

Jans, L.; Jaremko, J.; Ditchfield, M.; De Coninck, T.; Huysse, W.; Moon, A.; Verstraete, K.

2012-01-01

Purpose: To determine if ossification variants of the femoral condyles involving the subchondral bone plate are associated with osteochondritis dissecans (OCD). Materials and methods: The prevalence of ossification variants of the unaffected femoral condyle in 116 patients (aged 9–14 years) with unicondylar OCD on MRI (magnetic resonance imaging) of the knee was compared to a control group of 579 patients (aged 9–14 years) without OCD. The evolution of the ossification variants in both groups was studied by reviewing follow-up MR imaging side by side with the baseline study. Results: The prevalence of ossification variants in the unaffected condyle in patients with OCD (12.9%) and in the control group of patients without OCD (12.6%) was similar (p = 0.88). Evolution of ossification variants to OCD was not seen on follow-up MRI examinations. All variants had decreased in size or were no longer visible. Conclusion: Ossification variants of the femoral condyle that involve the subchondral bone plate are not associated with OCD. Clinical relevance statement: Ossification variants are not associated with OCD, indicating that routine MRI follow-up in affected children is not mandatory.

[Surgical aspects of indications and techniques for adenomatous polyposis variants].

Science.gov (United States)

Möslein, Gabriela

2016-08-01

Due to the advances in molecular genetic diagnostics of adenomatous polyposis variants, identification of patients with a genetic predisposition and their at risk relatives is becoming increasingly important in clinical practice. Precise knowledge of the specific risk profile is gaining significance especially for surgeons and requires a clinically differentiated approach in order to correctly identify the indications for prophylactic surgery. In this article reference will be made to the technical details of the pouch operation rather than the decision-making process per se, since this has become common knowledge for specialized colorectal surgeons. Besides the more commonly known polyposis syndromes, such as familial adenomatous polyposis (FAP), surgeons should nowadays at least be able to clinically distinguish between attenuated and classical variants of FAP, be aware of MUTYH-associated polyposis (MAP) and also the new polyposis syndrome polymerase proofreading-associated polyposis (PPAP). Surgeons should be familiar with the specific indications and extent of surgery for prophylactic organ removal in the lower gastrointestinal tract in order to be able to competently advise patients.

An Experimental Study of the Dropwise Condensation on Physically Processed Surface

International Nuclear Information System (INIS)

Choi, Jaeyoung; Chang, Soonheung; Watanabe, N.; Sambuichi, T.; Shiota, D.; Aritomi, M.

2013-01-01

Recent research by Kawakubo et al. derived empirical condensation heat transfer correlation suitable for wider range of operating condition in presence of non-condensable gas. However, their proposals of PCCS are focused on plane tube surface. To design better PCCS heat exchanger with high heat transfer coefficient new treatment on condensation surface can be considered in order to maintain dropwise condensation, the heat transfer coefficient of which has an order of magnitude larger than those of film condensation. Advanced research measure dropwise condensation heat transfer coefficient of Au and Cr coated surface based on number of droplet and droplet growth rate. However, coated surface is not desirable in power plant due to its duration of few years. On the other hand, physical processing (micro holes and patterns) on stainless steel and titanium surface is expected to perform better heat transfer, also is durable for the whole reactor lifetime. Since there is no published research about dropwise condensation for physically processed surface on SUS and Ti, the purposes of this research are to measure the condensation heat transfer coefficient and analyze its mechanism of enhanced heat transfer of treated SUS and Ti commonly used to nuclear plant. In the comparison of theoretical equation and experiment, it shows same result that heat transfer coefficient is proportional to maximum droplet diameter power to -0.321. Moreover, in the comparison of bare and processed surface, heat transfer coefficient decreases in processed surface

Comparative study based on the physical self-concept in teenagers regarding gender and physical activity

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David Molero López-Barajas

2010-01-01

Full Text Available The aims of this article are to evaluate the physical self-concept in adolescence and to get to know the outcomes in the perceptions of the different dimensions in the physical self-concept. Furthermore, we aim to check the existence of noticeable differences in the outcomes regarding gender variables and regarding the level of physical activity of those polled. The sample consists of 81 individuals divided in two groups: secondary school teenager students and swimmers in adolescence. We use the Physical Self-concept Questionnaire (PSQ as a tool for getting information; there are six scales: physical skills, physical conditions, physical charming, strength, and general physical self-concept. We use the Physical Self-concept Questionnaire (PSQ as an instrument of collection of information which consists of 6 different scales: physical skills, physical condition, physical attractiveness, strength and general self-concept. We will show the results in two different analysis of the variant. In the first one we have found remarkable differences as far as the statistic point of view is concerned in gender perceptions in the scales of physical skills, physical condition, strength and general physical self-concept in favour of men (p<0,05. In the second analysis we have checked the existence of noticeable differences between the two groups of young people within the scales of physical skills and strength in favour of those who practice physical activity regularly (p<0,05.