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Sample records for generalidades variantes fisiologicas

  1. PET/TAC: Basic principles, physiological variants and artifacts; PET/TAC: Generalidades, variantes fisiologicas y artefactos

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez V, A.M. [Especialista en Medicina Nuclear, Profa. Depto. Radiologia de la Facultad de Medicina, Universidad Complutense de Madrid, Madrid (Spain)

    2007-07-01

    This presentation is about the basic principles, physiologic variants and devices that work in the PET/TAC technique. Next the conclusions obtained in the same one are presented: For a correct evaluation of the PET/TAC images with FDG is necessary the knowledge of the image acquisition technique, as well as of the physiologic distribution of the FDG, variants of the normality, benign causes of captation and more frequent devices. The introduction of this hybrid procedure allows the correct anatomical localization and identification of the deposits of FDG largely avoiding false or doubtful interpretations, but it can also originate not specific devices existent in the conventional PET. The previous knowledge of the possible devices will make possible in certain cases its elimination and in other its identification avoiding incorrect interpretations. (Author)

  2. Generalidades

    Directory of Open Access Journals (Sweden)

    Hidalgo Fernández-Cano, Amalio

    1960-01-01

    Full Text Available La pequeña producción de chatarra en España, por no estar avanzada la industrialización del país, obligaba a que en una nueva planta siderúrgica no se considerara en principio más consumo' de chatarra que la que ella misma produjese. Por consiguiente, se ha concebido una Siderúrgica básica para obtener acero, partiendo de carbón y de mineral de hierro. Otra de las condiciones que debía satisfacer la nueva planta industrial era la de producir chapa gruesa y fina, lo que aconsejaba conseguir el afino del acero en hornos de solera.

  3. Generalidades de la imagen corporal y sus implicaciones en el deporte

    OpenAIRE

    Diego Fabricio Rodríguez-Camacho; Karim Martina Alvis-Gome

    2015-01-01

    Antecedentes. La imagen corporal es la representación del cuerpo que cada individuo construye en su mente. Estarepresentación contempla dos componentes: imagen corporal propiamente dicha y esquema corporal, los cuales son influenciados a partir de la interacción de los individuos con su entorno. Objetivo. El presente documento hace parte del marco teórico del estudio Imagen corporal en futbolistas, y revisa las generalidades de la imagen corporal en relación con su construcción, desarrollo, c...

  4. Generalidades de la imagen corporal y sus implicaciones en el deporte

    Directory of Open Access Journals (Sweden)

    Diego Fabricio Rodríguez-Camacho

    2015-04-01

    Full Text Available Antecedentes. La imagen corporal es la representación del cuerpo que cada individuo construye en su mente. Estarepresentación contempla dos componentes: imagen corporal propiamente dicha y esquema corporal, los cuales son influenciados a partir de la interacción de los individuos con su entorno. Objetivo. El presente documento hace parte del marco teórico del estudio Imagen corporal en futbolistas, y revisa las generalidades de la imagen corporal en relación con su construcción, desarrollo, componentes, dimensiones e implicaciones en el deporte. Materiales y métodos. Se realizó una búsqueda en las bases de datos Pubmed, SciELO, Science Direct y Google Académico entre los años 1996 y 2014, introduciendo los términos: Imagen corporal en deporte, modelo interno en control motor, evaluación de imagen corporal y esquema corporal. Resultados. Se encontraron 48 artículos, 11 en español, 36 en inglés y uno en portugués, los cuales abordaron la imagen corporal como un constructo multidimensional que tiene implicación directa sobre el movimiento corporal de los individuos y su entorno. Conclusiones. La imagen corporal es dinámica, se construye y modifica a lo largo de la vida a partir de estímulos sensoriales en términos de cuerpo y espacio, así como de estímulos socioculturales involucrados en la autoestima y el rendimiento deportivo. El desarrollo de programas de actividad físico-deportiva genera un impacto positivo sobre la imagen corporal en todas las edades, siempre y cuando se tengan presentes parámetros específicos de entrenamiento.

  5. Los principios de generalidad e igualdad en la normativa tributaria municipal y su infracción por las ordenanzas fiscales.

    OpenAIRE

    Hernández Guijarro, Fernando

    2015-01-01

    Los principios constitucionales del Derecho Financiero y Tributario dan el marco y la atmósfera jurídica en donde deben convivir las diversas normas tributarias. Los principios de generalidad e igualdad son un claro ejemplo de los principios que establece el art. 31.1 CE y sobre los que se debe edificar un sistema tributario justo. Las Ordenanzas Fiscales que dictan los municipios deberán respetar estos principios y no generar ningún tipo de desigualdad de trato que pueda derivar ...

  6. Generalidades sobre Rocas y Análisis Químicos de Suelos.

    Directory of Open Access Journals (Sweden)

    Orozco R. Aycardo

    1940-06-01

    Full Text Available Piedra caliza, o simplemente Caliza. La piedra caliza cuando tiene un alto grado de pureza y su dureza es de un alto título, su facilidad a la descomposición es escasa, debido a que las anteriores características la hacen resistente a la acción del agua carbonatada. Cuando su condición no es como la anterior, se desintegra con facilidad, dando origen a suelos muy ricos en Calcio, por consiguiente muy buenos para la agricultura, toda vez que el calcio es uno de los primordiales elementos biogenéticos. De allí el adagio popular, que no es otra cosa que la verdad virtualizando una frase: "Suelo calizo, es suelo rico". En general, la caliza es de fácil descomposición por su baja dureza, carácter éste que la ha, hecho aplicable el nombre que se le da en varios países: "'Piedra podrida". Cascajo, Gravas, Arenas, Conglomerados. Debido a la heterogeneidad física y mineralógica de estas su descomposición y los suelos resultantes están poco popularizados o democratizados. De ellas diré que sufren desintegraciones físicas acompañadas de variantes químicas, que van formando suelos cada vez más pesados, según concepto del doctor Shamblenberger. En las regiones húmedas, los suelos constituí dos por estas rocas son pobres para la vegetación, por la percolación que sufren los elementos biogeníticos que pasan al estado de solución. La naturaleza de los suelos a que dan origen depende en gran parte de dos factores: de la del cemento, que une las partículas de tales rocas, y del carácter de las partículas. En cuanto a la naturaleza del cemento, se hallará una razonable diferencia en descomposición si el cemento es cuarzoso o silicoso, si es calcáreo, ferruginoso, aluminoso o arcilloso y zoolítico. Es lógico que estas rocas con cemento silicoso exhibirán una mayor dificultad a su desintegración que las mismas en cualquiera de los otros cementos, ya que tal proceso se inicia por él. Cuando el cemento es calc

  7. Cellulase variants

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Generalidades sobre os tumores renais

    OpenAIRE

    2008-01-01

    O aumento na incidência do carcinoma de células renais, na maior parte da população, deve-se em parte ao aumento do número de tumores detectados incidentalmente com novos métodos de diagnósticos por imagem. As sofisticações dos instrumentos diagnósticos e terapêuticos modificam as perspectivas dos pacientes com carcinoma de células renais. Um aumento na taxa de sobrevivência e uma redução da morbidade foram alcançados. As neoplasias malignas do trato gênito-urinário compreendem, aproximadamen...

  9. Generalidades sobre las fibras artificiales

    OpenAIRE

    González Salcedo, Luis Octavio

    2012-01-01

    Las fibras han sido utilizadas como materia prima en la elaboración de otros productos, como telas, papel, artesanías, entre otros, y como material de refuerzo en diversas matrices cerámicas y metálicas, con el fin mejorar o ganar propiedades, en materiales compuestos denominados composites. Las fibras pueden ser clasificadas de acuerdo con su origen, en fibras naturales y fibras artificiales. Una amplia exploración sobre el uso de fibras vegetales ha sido realizada, sin embargo su uso ...

  10. Generalidades sobre las fibras artificiales

    OpenAIRE

    González Salcedo, Luis Octavio

    2012-01-01

    Las fibras han sido utilizadas como materia prima en la elaboración de otros productos, como telas, papel, artesanías, entre otros, y como material de refuerzo en diversas matrices cerámicas y metálicas, con el fin mejorar o ganar propiedades, en materiales compuestos denominados composites. Las fibras pueden ser clasificadas de acuerdo con su origen, en fibras naturales y fibras artificiales. Una amplia exploración sobre el uso de fibras vegetales ha sido realizada, sin embargo su uso ...

  11. FATORES AMBIENTAIS NA RESPOSTA FISIOLOGICA E COMPORTAMENTAL DE VACAS LEITEIRAS

    Directory of Open Access Journals (Sweden)

    Raphael Chiarelo Zero

    2015-12-01

    Full Text Available This paper was developed in the dairy cattle sector from the university FAFRAM (Faculdade Dr. Francisco Maeda – FAFRAM located inItuverava, SP. Ten Girolando multiparous cows in intermediate stage of lactation were used, with average weight of 450 kg and average daily production of 9 liters of milk. The study was conducted during 2013 winter season.The objective of this study was to evaluate the conditions of heat stress, through collection and analysis of these data: the dry and wet bulb temperature, black globe temperature, airrelative humidity, and then calculating the black globe humidity index (BGHI. All data were collected under shade and sun. Physiological and behavioral parameters of lactating cows were also assessed. The data relating to environmental, behavioral and physiological factors were collected every sixty minutes in the period between milking, from 9:00 am to 2:00 pm, in the shade and in the sun. From the analysis of the data and the averages of all parameters, we have come to the results. It was noticed that the environmental conditions on the shade locations indicated values of thermal comfort in almost all times that were evaluated, but the results obtained for the unshaded environment presented themselves very high at all times, indicating a state of alert and emergency, confirming the thermal stress for lactating cows. Vast majority of physiological and behavioral parameters evaluated was not compatible with the ones from the literature. Even though in the winter season, the climate of the city Ituverava proves unfavorable for lactating cows, indicating high values of BGHI and consequently causing heat stress in the animals. O estudo foi desenvolvido na bovinocultura leiteira da Faculdade Dr. Francisco Maeda, localizada no município de Ituverava, SP. Utilizaram-se dez vacas girolandas, multíparas, com peso médio de 450 kg e produção média diária de 9 litros de leite. O experimento foi conduzido durante a estação de inverno de 2013. Objetivou-se avaliar as condições de estresse térmico, por meio de coletas e análises dos dados de temperatura de bulbo seco, bulbo úmido, temperatura de globo negro, umidade relativa do ar, e posteriormente o cálculo do índice de temperatura de globo e umidade (ITGU. Todos os dados foram coletados no ambiente sombreado e ao sol. Avaliaram-se parâmetros fisiológicos e comportamentais dos animais. Os dados referentes aos fatores ambientais, comportamentais e fisiológicos foram coletados a cada sessenta minutos, no período entre ordenhas, das 9:00 as 14:00 horas. Verificou-se que as condições ambientais referentes à sombra indicaram valores de conforto térmico em quase todos os horários, com exceção das 14:00 horas, com ITGU médio de 77,44, indicando condição de alerta. Os resultados obtidos para o ambiente exposto ao sol apresentaram índices estressantes em todos os horários, indicando situação de alerta e emergência, respectivamente, caracterizando condições de estresse térmico para as vacas em lactação. Grande parte dos parâmetros fisiológicos e comportamentais avaliados não se mostrou compatíveis com os presentes na literatura. Mesmo na estação de inverno, o clima da região avaliada mostrou-se desfavorável para as vacas em lactação, indicando altos valores de ITGU e consequentemente estresse térmico.

  12. Histone Variants and Epigenetics

    Science.gov (United States)

    Henikoff, Steven; Smith, M. Mitchell

    2015-01-01

    Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory. PMID:25561719

  13. Desmoplastic variant of ameloblastoma

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Jeong Ick; Kim, Dong Youn; Choi, Karp Shik [Dept. of Dental Radiology, College of Dentistry, Kyungpook National University, Daegu (Korea, Republic of)

    1995-02-15

    Desmoplastic variant of ameloblastoma is new and unusual variant of ameloblastoma with extensive stromal desmoplastic proliferation. The authors experienced a case of desmoplastic variant of amleloblastoma with moderate-defined radiolucency on the right maxillary anterior area in 62-year-old female. As a result of careful analysis of clinical, radiological examinations, we diagnosed it as desmoplastic variant of ameloblastoma. The following results were obtained; 1. Main clinical symptoms were nontender bony swelling with normal intact overlying mucosa on the right maxillary anterior area. 2. Radiographically, moderate-defined, multilocular radioluceney on the right maxillary anterior area were shown, and severe cortical bony thinning and expansion to labial and palatal sides were also observed. And this lesion was shown to be extended to the right nasal cavity. 3. Histopathologically, follicle-like epithelial islands with densely abundant collagenous stroma were morphologically compressed.

  14. Generalidades sobre el 68 en la narrativa

    OpenAIRE

    Ocampo, Aurora M.

    2013-01-01

    Es mucho lo que se ha escrito sobre el movimiento estudiantil de 1968, según mis registros, cerca de un centenar de libros, además de innumerables artículos, ensayos, narraciones, poemas, teatro y reseñas a los libros como a los grandes ensayos, aparecidos en publicaciones periódicas. Por otro lado, muchos de los libros, ya sean testimoniales, de reflexión sobre lo sucedido, antologías de poesías, ensayos, cuentos, teatro y narrativa en general se han reeditado varias veces; ahora, con motivo...

  15. Hemoglobin Variants in Mice

    Energy Technology Data Exchange (ETDEWEB)

    Popp, Raymond A.

    1965-04-22

    Variability among mammalian hemoglobins was observed many years ago (35). The chemical basis for differences among hemoglobins from different species of mammals has been studied by several investigators (5, 11, 18, 48). As well as interspecies differences, hemoglobin variants are frequently found within a species of mammals (2, 3, 7, 16) The inheritance of these intraspecies variants can be studied, and pedigrees indicate that the type of hemoglobin synthesized in an individual is genetically controlled (20). Several of the variant human hemoglobins are f'unctionally deficient (7, 16). Such hemoglobin anomalies are of basic interest to man because of the vital role of hemoglobin for transporting oxygen to all tissues of the body.

  16. 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

  17. Migraine Variants And Beyond

    Directory of Open Access Journals (Sweden)

    Chakravarty A

    2002-01-01

    Full Text Available The Classic presenting features of both migraine with and without aura have been clearly defined. Occasionally however migrainous headaches are accompanied by abrupt appearance of focal and ominous neurological signs. Such attacks can be labelled as migraine variants and the diagnosis in reality is one made by exclusion of other CNS diseases. Some but not all such conditions are mentioned in the International Headache Society (IHS classification under the general heading of migraine with aura. Rarely, the focal neurological deficit may outlast the migraine attack by days and occasionally with appearance of structural brain lesions on neuroimaging. Such attacks have been labelled as complicated Migraine by the IHS. The present review deal with the clinical, radiologic and pathophysiologic aspects of both these conditions - migraine variants and complicated migraine.

  18. Variants of Uncertainty

    Science.gov (United States)

    1981-05-15

    Variants of Uncertainty Daniel Kahneman University of British Columbia Amos Tversky Stanford University DTI-C &%E-IECTE ~JUNO 1i 19 8 1j May 15, 1981... Dennett , 1979) in which different parts have ac- cess to different data, assign then different weights and hold different views of the situation...2robable and t..h1 provable. Oxford- Claredor Press, 1977. Dennett , D.C. Brainstorms. Hassocks: Harvester, 1979. Donchin, E., Ritter, W. & McCallum, W.C

  19. Variants of glycoside hydrolases

    Energy Technology Data Exchange (ETDEWEB)

    Teter, Sarah; Ward, Connie; Cherry, Joel; Jones, Aubrey; Harris, Paul; Yi, Jung

    2017-07-11

    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.

  20. Variants of glycoside hydrolases

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. 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

    The overall time requiered to design a new product variant relies on two factor: how good the methods to design the new variant are and how good these method are supported by computers.It has been estimated that 80% of all design tasks are variational in that the goal of the design is to adapt an...

  2. Variants of windmill nystagmus.

    Science.gov (United States)

    Choi, Kwang-Dong; Shin, Hae Kyung; Kim, Ji-Soo; Kim, Sung-Hee; Choi, Jae-Hwan; Kim, Hyo-Jung; Zee, David S

    2016-07-01

    Windmill nystagmus is characterized by a clock-like rotation of the beating direction of a jerk nystagmus suggesting separate horizontal and vertical oscillators, usually 90° out of phase. We report oculographic characteristics in three patients with variants of windmill nystagmus in whom the common denominator was profound visual loss due to retinal diseases. Two patients showed a clock-like pattern, while in the third, the nystagmus was largely diagonal (in phase or 180° out of phase) but also periodically changed direction by 180°. We hypothesize that windmill nystagmus is a unique manifestation of "eye movements of the blind." It emerges when the central structures, including the cerebellum, that normally keep eye movements calibrated and gaze steady can no longer perform their task, because they are deprived of the retinal image motion that signals a need for adaptive recalibration.

  3. 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 i

  4. Cellobiohydrolase variants and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Wogulis, Mark

    2017-04-04

    The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

  5. Certain variants of multipermutohedron ideals

    Indian Academy of Sciences (India)

    AJAY KUMAR; CHANCHAL KUMAR

    2016-10-01

    Multipermutohedron ideals have rich combinatorial properties. An explicit combinatorial formula for the multigraded Betti numbers of a multipermutohedron ideal and their Alexander duals are known. Also, the dimension of the Artinian quotient of an Alexander dual of a multipermutohedron ideal is the number of generalized parking functions. In this paper, monomial ideals which are certain variants of multipermutohedron ideals are studied. Multigraded Betti numbers of these variant monomial ideals and their Alexander duals are obtained. Further, many interesting combinatorial properties of multipermutohedron ideals are extended to these variant monomial ideals.

  6. Gene Variants Reduce Opioid Risks

    Science.gov (United States)

    ... Opioids Prescription Drugs & Cold Medicines Steroids (Anabolic) Synthetic Cannabinoids (K2/Spice) Synthetic Cathinones (Bath Salts) Tobacco/Nicotine ... variant of the gene for the μ-opioid receptor (OPRM1) with a decreased risk for addiction to ...

  7. 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

  8. Variant Creutzfeldt-Jakob disease

    NARCIS (Netherlands)

    E.A. Croes (Esther); C.M. van Duijn (Cock)

    2003-01-01

    textabstractA variant form of Creutzfeldt-Jakob disease (vCJD) has had major impact in Europe during the last decade. In this article, we review the aetiology of vCJD and its relation with bovine spongiform encephalopathy. Further, treatment of the disease, the strategies focusing on prevention of t

  9. 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 Other Information on Swine Influenza/Variant Influenza Virus Language: English (US) Español ...

  10. Resistance of Abaca Somaclonal Variant Against Fusarium

    OpenAIRE

    RULLY DYAH PURWATI; SUDARSONO

    2007-01-01

    The objectives of this study were (i) to evaluate responses against F. oxysporum f.sp. cubense (Foc) infection of abaca variants regenerated using four different methods, (ii) to determine initial root length and plant height effects on survival of inoculated abaca variants, and (iii) to identify Foc resistance abaca variants. In the previous experiment, four abaca variant lines were regenerated from (i) embryogenic calli (TC line), (ii) ethyl methyl sulphonate (EMS) treated embryogenic calli...

  11. Variant Humicola grisea CBH1.1

    Energy Technology Data Exchange (ETDEWEB)

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Larenas, Edmund

    2017-05-09

    Disclosed are variants of Humicola grisea CeI7A (CBH1.1), H. jecorina CBH1 variant or S. thermophilium CBH1, nucleic acids encoding the same and methods for producing the same. The variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted.

  12. DHAD variants and methods of screening

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, Kristen J.; Ye, Rick W.

    2017-02-28

    Methods of screening for dihydroxy-acid dehydratase (DHAD) variants that display increased DHAD activity are disclosed, along with DHAD variants identified by these methods. Such enzymes can result in increased production of compounds from DHAD requiring biosynthetic pathways. Also disclosed are isolated nucleic acids encoding the DHAD variants, recombinant host cells comprising the isolated nucleic acid molecules, and methods of producing butanol.

  13. Clinical variants of lichen planus.

    Science.gov (United States)

    Wagner, Gunnar; Rose, Christian; Sachse, Michael Max

    2013-04-01

    Lichen planus is characterized by lichenoid, polygonal papules with fine white lines, called Wickham striae. Lesions most commonly occur on the limbs and on the dorsal aspect of the trunk. At the same time often leukoplakia of mucous membranes as well as nail disorders are seen. There are numerous variants of lichen planus which can be distinguished from the classical form on the basis of morphology and distribution of the lesions. The typical primary lesion of lichen planus may be replaced by other forms, such as patches, hyperkeratoses, ulcerations, or bullous lesions. Moreover, distribution patterns of these lesions may vary and include erythrodermic, inverse or linear arrangements. In contrast to these numerous clinical features, histologic findings remain characteristic in the variants, so that the diagnosis can be made securely. Differential diagnoses of lichen planus include diverse dermatoses such as bullous pemphigoid or paronychia.

  14. Coronary artery anatomy and variants

    Energy Technology Data Exchange (ETDEWEB)

    Malago, Roberto; Pezzato, Andrea; Barbiani, Camilla; Alfonsi, Ugolino; Nicoli, Lisa; Caliari, Giuliana; Pozzi Mucelli, Roberto [Policlinico G.B. Rossi, University of Verona, Department of Radiology, Verona (Italy)

    2011-12-15

    Variants and congenital anomalies of the coronary arteries are usually asymptomatic, but may present with severe chest pain or cardiac arrest. The introduction of multidetector CT coronary angiography (MDCT-CA) allows the detection of significant coronary artery stenosis. Improved performance with isotropic spatial resolution and higher temporal resolution provides a valid alternative to conventional coronary angiography (CCA) in many patients. MDCT-CA is now considered the ideal tool for three-dimensional visualization of the complex and tortuous anatomy of the coronary arteries. With multiplanar and volume-rendered reconstructions, MDCT-CA may even outperform CCA in determining the relative position of vessels, thus providing a better view of the coronary vascular anatomy. The purpose of this review is to describe the normal anatomy of the coronary arteries and their main variants based on MDCT-CA with appropriate reconstructions. (orig.)

  15. [Mirizzi syndrome and its variants].

    Science.gov (United States)

    Meyer, G J; Runge, D; Gebhardt, J

    1990-04-01

    Between 1981 and 1987 5434 patients were studied by ERCP in Allgemeines Krankenhaus Hamburg-Barmbeck. 26 (i.e. 0.43%) suffered from Mirizze syndrome with the triad of cholelithiasis, cholecystitis and obstructive biliary disease. They were classified in four different types according to the variable localisation and origin of the biliary obstruction. 16 patients corresponded to the classical type (I and II) with compression, penetration, and obturation by the concrement, five patients matched borderline with infiltration (III) and five patients were classified as variants of this syndrome. A mild elevation of serum bilirubine and alkaline phosphatase indicated more likely the benign etiology of type I to III, however, a marked elevation of alkaline phosphatase in the variants suggested more likely a malignant underlying disease. The diagnosis was ascertained in all cases by ERC and sonography preoperatively and was verified by laparotomy (n = 18) and follow-up (n = 6).

  16. Variants of lumbosacral elastic band.

    Directory of Open Access Journals (Sweden)

    Carlos Cesar Santín Alfaro

    2011-06-01

    Full Text Available It is made an intervention research, qualitative and quantitative of two variants of lumbosacral elastic bands used in Provincial Laboratory of Technical Orthopedics in Sancti Spiritus Province, taking into account the high demand for this device and that the laboratory do not often count with the raw material needed for the original lumbosacral belt made by denim cloth which is the conventional belt. The main goal of this research is to explain the technological process and to compare the cost of production of both elastic variants with lumbosacral belt made by cloth which are offer to patients who look for this service , giving them a rapid solution so that they can feel comfortable.

  17. Unusual variant of Cantrell's pentalogy?

    OpenAIRE

    Kumar, Basant; Sharma, S.B.; Kandpal, Deepak K.; Agrawal, L. D.

    2008-01-01

    A 12-hour-old male infant presented with prolapsed abdominal content through a defect on left side of chest wall with respiratory distress. A thorough clinical examination suggested absence of ectopia cordis, abdominal wall defect, and any bony anomaly. The child expired after 6 hours of admission because of respiratory distress and electrolyte imbalance. Is congenital defect of chest wall associated with diaphragmatic hernia without ectopia cordis and omphalocele, an unusual variant of Cantr...

  18. Dorsal variant blister aneurysm repair.

    Science.gov (United States)

    Couldwell, William T; Chamoun, Roukoz

    2012-01-01

    Dorsal variant proximal carotid blister aneurysms are treacherous lesions to manage. It is important to recognize this variant on preoperative angiographic imaging, in anticipation of surgical strategies for their treatment. Strategies include trapping the involved segment and revascularization if necessary. Other options include repair of the aneurysm rupture site directly. Given that these are not true berry aneurysms, repair of the rupture site involves wrapping or clip-grafting techniques. The case presented here was a young woman with a subarachnoid hemorrhage from a ruptured dorsal variant blister aneurysm. The technique used is demonstrated in the video and is a modified clip-wrap technique using woven polyester graft material. The patient was given aspirin preoperatively as preparation for the clip-wrap technique. It is the authors' current protocol to attempt a direct repair with clip-wrapping and leaving artery sacrifice with or without bypass as a salvage therapy if direct repair is not possible. Assessment of vessel patency after repair is performed by intraoperative Doppler and indocyanine green angiography. Intraoperative somatosensory and motor evoked potential monitoring is performed in all cases. The video can be found here: http://youtu.be/crUreWGQdGo.

  19. Microcystic Variant of Urothelial Carcinoma

    Directory of Open Access Journals (Sweden)

    Anthony Kodzo-Grey Venyo

    2013-01-01

    Full Text Available Background. Microcystic variant of urothelial carcinoma is one of the new variants of urothelial carcinoma that was added to the WHO classification in 2004. Aims. To review the literature on microcystic variant of urothelial carcinoma. Methods. Various internet search engines were used to identify reported cases of the tumour. Results. Microscopic features of the tumour include: (i Conspicuous intracellular and intercellular lumina/microcysts encompassed by malignant urothelial or squamous cells. (ii The lumina are usually empty; may contain granular eosinophilic debris, mucin, or necrotic cells. (iii The cysts may be variable in size; round, or oval, up to 2 mm; lined by urothelium which are either flattened cells or low columnar cells however, they do not contain colonic epithelium or goblet cells; are infiltrative; invade the muscularis propria; mimic cystitis cystica and cystitis glandularis; occasionally exhibit neuroendocrine differentiation. (iv Elongated and irregular branching spaces are usually seen. About 17 cases of the tumour have been reported with only 2 patients who have survived. The tumour tends to be of high-grade and high-stage. There is no consensus opinion on the best option of treatment of the tumour. Conclusions. It would prove difficult at the moment to be dogmatic regarding its prognosis but it is a highly aggressive tumour. New cases of the tumour should be reported in order to document its biological behaviour.

  20. Monitoreo neurointensivo en pediatría (I: Generalidades

    Directory of Open Access Journals (Sweden)

    Eduardo M. Pleguezuelo Rodríguez

    2001-06-01

    Full Text Available Se reporta que el traumatismo craneoencefálico grave (TCEG continúa siendo la principal causa de muerte y discapacidad en pediatría, de la misma manera es el factor determinante del pronóstico en niños con trauma multisistémico, no sólo ocasionando la desaparición del ser físico, sino también dejándolo en ocasiones en estados limítrofes entre la vida y la muerte, tales son los llamados estados vegetativos. En las últimas décadas se ha revolucionado el modo de tratamiento de estos pacientes, y se ha pasado del tratamiento neuroquirúrgico convencional, el cual se realizaba en salas de neurocirugía y se comportaba con una mortalidad mayor del 70 %, al tratamiento neurointensivo, en unidades de cuidados intensivos (UCI, y se define por neuromonitoreo continuo, intensivo e invasivo, que permite identificar una serie de fenómenos fisiopatológicos que son diferentes para cada paciente y de esta manera tratarlos de forma racional, con lo cual se ha conseguido reducir la mortalidad a niveles inferiores al 30 %. Después de más de 5 años de experiencia con esta metodología en el Hospital provincial General de la provincia de Camagüey, y más de 2 años de realizarla en el Hospital Pediátrico Provincial Docente "Eduardo Agramonte Piña" se decidió en este trabajo describir detalladamente la forma de realizar el monitoreo, así como los valores normales, utilidad clínica y las principales desviaciones patológicas de las variables más importantes en el neuromonitoreo intensivo, como son: presión intracraneal (PIC, hemodinámicas, metabólicas, las cuales pueden ser realizadas con modestos recursos, disponibles en la mayoría de nuestras salas de terapia intensiva. Este primer trabajo recoge definiciones y elementos generales del monitoreo de la PIC, así como información que se puede obtener con los valores numéricos reflejados en el monitor y con el análisis de la morfología de onda.It is reported that severe cranioencephalic trauma (SCET is still the main cause of death and disability in Pediatrics. It is also the determinant of prognosis in children with multisystemic trauma, causing not only death but leaving the child in limiting states between death and life, such as the so-called vegetative states. During the last decades the treatment of these patients has been revolutionized and it has passed from the conventional neurosurgical treatment, which was received at neurosurgery wards and had a mortality rate higher than 70%, to neurointensive treatment, which is given at intensive care units (ICU and is defined by continuous, intensive and invasive monitoring that allow to identify a series of physiopathological phenomena different for each patient and to treat patients in a rational way. This has made possible the reduction of mortality to less than 30 %. After more of 5 years of experience with this methodology at the Provincial General Hospital of Camagüey and more than 2 years of its application at "Eduardo Agramonte" Provincial Pediatric Teaching Hospital, it was decided to describe in detail in this paper the way of monitoring the patient, as well as the normal values, clinical usefulness and the main pathological deviations of the most important variables, such as: intracranial pressure (ICP, hemodynamic and metabolic variables, which may be determined with modest resources available in most of our intensive care units. This first paper contains general definitions and elements related to the monitoring of ICP and information that may be obtained by using the numerical values appearing in the monitor and by analyzing wave morphology.

  1. Proceso de recuperación de CO2. Generalidades

    Directory of Open Access Journals (Sweden)

    Arianna Núñez-Caraballo

    2015-01-01

    Full Text Available En el presente trabajo se muestra una recopilación sobre las propiedades físicas y químicas del CO 2 , la influencia del mismo en el efecto invernadero, sus apli- caciones en la industria, los sistemas de captura del gas y algunas estrategias que actualmente se siguen para la reducción de las emisiones.

  2. PSICOLOGÍA DE LAS EMOCIONES POSITIVAS: GENERALIDADES Y BENEFICIOS

    Directory of Open Access Journals (Sweden)

    Ahmad Ramsés Barragán Estrada

    2014-01-01

    Full Text Available Se presenta un análisis conceptual en relación con la psicología de las emociones positivas y sus principales implicaciones en la vida de las personas. El estudio de las emociones positivas se ha visto hasta cierto punto limitado, pues pocas son las investigaciones que se orientan hacia este tema, en comparación con el estudio de las emociones negativas. Sin embargo, las investigaciones y propuestas que se han elaborado hasta ahora han sido lo suficientemente concisas para poder cimentar afirmaciones y teorías. Se describen ciertos estados emocion a les positivos, como la fluidez, el humor, la elevación y el bienestar, y se revisan los resultados de diversas investigaciones en torno al cultivo de las emociones positivas.

  3. PSICOLOGÍA DE LAS EMOCIONES POSITIVAS: GENERALIDADES Y BENEFICIOS

    OpenAIRE

    2014-01-01

    Se presenta un análisis conceptual en relación con la psicología de las emociones positivas y sus principales implicaciones en la vida de las personas. El estudio de las emociones positivas se ha visto hasta cierto punto limitado, pues pocas son las investigaciones que se orientan hacia este tema, en comparación con el estudio de las emociones negativas. Sin embargo, las investigaciones y propuestas que se han elaborado hasta ahora han sido lo suficientemente concisas para poder cimentar afir...

  4. Mesas de dinero: generalidades y experiencia en Colombia

    Directory of Open Access Journals (Sweden)

    Johnny Alvarez Jaramillo

    1989-04-01

    Full Text Available RESUMEN   Las necesidades de financiamiento de corto plazo, ha determinado el aguzamiento  de la imaginación para garantizar los recursos. Generalmente, las prácticas financieras en Colombia se extienden sin ningún control institucional; hasta que desafortunadamente, las prácticas desleales  o fraudulentas, llevan al estado a intervenir y reglamentar. Las llamadas MESAS DE DINERO, se han generalizado en nuestro medio en la medida en que proveen recursos financieros de corto plazo, difíciles de conseguir por los canales tradicionales. Los recientes escándalos del sector bursátil y anteriormente, la crisis bancaria, desaceleraron el crecimiento del mercado financiero extrainstitucional, pero no lo han acabado  del todo.El presente artículo, pretende informar brevemente sobre las experiencias de las llamadas  MESAS DE DINERO, su práctica y desarrollo.

  5. Resistance of Abaca Somaclonal Variant Against Fusarium

    Directory of Open Access Journals (Sweden)

    RULLY DYAH PURWATI

    2007-12-01

    Full Text Available The objectives of this study were (i to evaluate responses against F. oxysporum f.sp. cubense (Foc infection of abaca variants regenerated using four different methods, (ii to determine initial root length and plant height effects on survival of inoculated abaca variants, and (iii to identify Foc resistance abaca variants. In the previous experiment, four abaca variant lines were regenerated from (i embryogenic calli (TC line, (ii ethyl methyl sulphonate (EMS treated embryogenic calli (EMS line, (iii EMS treated embryogenic calli, followed by in vitro selection on Foc culture filtrate (EMS+CF line, and (iv EMS treated embryogenic calli, followed by in vitro selection on fusaric acid (EMS+FA line. All abaca variants were grown in a glasshouse and inoculated with Banyuwangi isolate of Foc (Foc Bw. Initial root length (RL and plant height (PH of the abaca variants were recorded before inoculation, while scores of plant damage (SPD, and their survival were recorded at 60 days after inoculation (DAI. The results showed that the initial RL and PH did not affect survival of the tested abaca variants. Regardless of their initial RL and PH, susceptible abaca variants died before 60 DAI while resistance ones still survived. Abaca variants regenerated from single clump of embryogenic callus showed an array of responses against Foc Bw infection, indicating the existence of a mix cells population. The Foc Bw resistance abaca variants were successfully identified from four tested abaca variant lines, although with different frequencies. However, more Foc Bw resistance abaca plants were identified from EMS+CF line than the others. Using the developed procedures, 8 resistance abaca plants were identified from abaca cv. Tangongon and 12 from abaca cv. Sangihe-1.

  6. Semantic prioritization of novel causative genomic variants

    KAUST Repository

    Boudellioua, Imane

    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.

  7. 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...

  8. Beta-glucosidase I variants with improved properties

    Energy Technology Data Exchange (ETDEWEB)

    Bott, Richard R.; Kaper, Thijs; Kelemen, Bradley; Goedegebuur, Frits; Hommes, Ronaldus Wilhelmus; Kralj, Slavko; Kruithof, Paulien; Nikolaev, Igor; Van Der Kley, Wilhelmus Antonious Hendricus; Van Lieshout, Johannes Franciscus Thomas; Van Stigt Thans, Sander

    2016-09-20

    The present disclosure is generally directed to enzymes and in particular beta-glucosidase variants. Also described are nucleic acids encoding beta-glucosidase variants, compositions comprising beta-glucosidase variants, methods of using beta-glucosidase variants, and methods of identifying additional useful beta-glucosidase variants.

  9. 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.

  10. Histones in functional diversification. Core histone variants.

    Science.gov (United States)

    Pusarla, Rama-Haritha; Bhargava, Purnima

    2005-10-01

    Recent research suggests that minor changes in the primary sequence of the conserved histones may become major determinants for the chromatin structure regulating gene expression and other DNA-related processes. An analysis of the involvement of different core histone variants in different nuclear processes and the structure of different variant nucleosome cores shows that this may indeed be so. Histone variants may also be involved in demarcating functional regions of the chromatin. We discuss in this review why two of the four core histones show higher variation. A comparison of the status of variants in yeast with those from higher eukaryotes suggests that histone variants have evolved in synchrony with functional requirement of the cell.

  11. Fundamental Characteristics of Industrial Variant Specification Systems

    DEFF Research Database (Denmark)

    Hansen, Benjamin Loer; Hvam, Lars

    2004-01-01

    This paper focuses on the operational task of creating customised variants of industrial specifications (e.g. drawings, routings and bill-of-materials). Rooted in a lack of existing literature on the subject the paper describes the nature of variant specification systems. It introduces some funda...... examples. In general the paper discusses an important focus area within mass customization and build-to-order production: the nature of industrial variant specification systems.......This paper focuses on the operational task of creating customised variants of industrial specifications (e.g. drawings, routings and bill-of-materials). Rooted in a lack of existing literature on the subject the paper describes the nature of variant specification systems. It introduces some...

  12. Different Variants of Fundamental Portfolio

    Directory of Open Access Journals (Sweden)

    Tarczyński Waldemar

    2014-06-01

    Full Text Available The paper proposes the fundamental portfolio of securities. This portfolio is an alternative for the classic Markowitz model, which combines fundamental analysis with portfolio analysis. The method’s main idea is based on the use of the TMAI1 synthetic measure and, in limiting conditions, the use of risk and the portfolio’s rate of return in the objective function. Different variants of fundamental portfolio have been considered under an empirical study. The effectiveness of the proposed solutions has been related to the classic portfolio constructed with the help of the Markowitz model and the WIG20 market index’s rate of return. All portfolios were constructed with data on rates of return for 2005. Their effectiveness in 2006- 2013 was then evaluated. The studied period comprises the end of the bull market, the 2007-2009 crisis, the 2010 bull market and the 2011 crisis. This allows for the evaluation of the solutions’ flexibility in various extreme situations. For the construction of the fundamental portfolio’s objective function and the TMAI, the study made use of financial and economic data on selected indicators retrieved from Notoria Serwis for 2005.

  13. Chemokine gene variants in schizophrenia.

    Science.gov (United States)

    Dasdemir, Selcuk; Kucukali, Cem Ismail; Bireller, Elif Sinem; Tuzun, Erdem; Cakmakoglu, Bedia

    2016-08-01

    Background Chemokines are known to play a major role in driving inflammation and immune responses in several neuroinflammatory diseases, including multiple sclerosis, Alzheimer's disease and Parkinson's disease. Inflammation has also been implicated in the pathogenesis of schizophrenia. Aim We aimed to investigate a potential link between chemokines and schizophrenia and analyze the role of MCP-1-A2518G, SDF-1-3'A, CCR5-delta32, CCR5-A55029G, CXCR4-C138T and CCR2-V64I gene polymorphisms in the Turkish population. Methods Genotyping was conducted by PCR-RFLP based on 140 patients and 123 unrelated healthy controls to show the relation between chemokine gene variants and schizophrenia risk. Results Frequencies of CCR5-A55029G A genotypes and CCR5-A55029G AG genotypes were found higher in patients than the controls and even also CCR2-V64I WT: CCR5-A55029G A and CCR2-V64I 64I: CCR5-A55029G A haplotypes significantly associated according to Bonferroni correction. However, no significant association was found for any of the other polymorphisms with the risk of schizophrenia. Conclusions Our findings suggest that CCR5-A55029G polymorphisms and CCR2-V64I WT: CCR5-A55029G A and CCR2-V64I 64I: CCR5-A55029G A haplotypes might have association with schizophrenia pathogenesis.

  14. Histological variants of cutaneous Kaposi sarcoma

    Directory of Open Access Journals (Sweden)

    Pantanowitz Liron

    2008-07-01

    Full Text Available Abstract This review provides a comprehensive overview of the broad clinicopathologic spectrum of cutaneous Kaposi sarcoma (KS lesions. Variants discussed include: usual KS lesions associated with disease progression (i.e. patch, plaque and nodular stage; morphologic subtypes alluded to in the older literature such as anaplastic and telangiectatic KS, as well as several lymphedematous variants; and numerous recently described variants including hyperkeratotic, keloidal, micronodular, pyogenic granuloma-like, ecchymotic, and intravascular KS. Involuting lesions as a result of treatment related regression are also presented.

  15. 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.

  16. Histone variants in plant transcriptional regulation.

    Science.gov (United States)

    Jiang, Danhua; Berger, Frédéric

    2017-01-01

    Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

  17. TCM Differential Treatment of Cough Variant Asthma

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhong-de; DENG Yi-qi; ZHANG Yu; HAN Yun; LIN Lin; CHAO En-xiang

    2010-01-01

    @@ Cough variant asthma (CVA), also called latent asthma or cough asthma, is a special type of asthma. With gradually deepened understanding of CVA in recent years, good curative effect has been achieved in TCM treatment of CVA.

  18. Variant profiling of evolving prokaryotic populations

    Science.gov (United States)

    Zojer, Markus; Schuster, Lisa N.; Schulz, Frederik; Pfundner, Alexander; Horn, Matthias

    2017-01-01

    Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community

  19. Bisalbuminemia. A new molecular variant, albumin Vancouver.

    Science.gov (United States)

    Frohlich, J; Kozier, J; Campbell, D J; Curnow, J V; Tárnoky, A L

    1978-11-01

    Of 18 members of a Fiji Indian family investigated, eight of the 12 males and two of the six females had an electrophoretically slow-type bisalbuminemia (alloalbuminemia). The albumin was characterized by the hiterto unique ratio of the two bands (Al A 35%: variant 65%), and by dye-binding studies and electrophoretic mobility in different media. The data suggest that this is a new variant, which we propose to call albumin Vancouver (Al Va).

  20. Another new variant of Bouveret's syndrome

    Institute of Scientific and Technical Information of China (English)

    Seong-Heum Park; Sang-Woo Lee; Tae-Jin Song

    2009-01-01

    Although Bouveret's syndrome, i.e. gastric outlet obstruction by a large gallstone impacted in the proximal duodenum secondary to a cholecystoduodenal fistula,is rare, its pathogenesis and clinical features are well characterized. However, existence of variant forms of the syndrome are not well known, and as far as we have been described in the English-language literature.We present a case of another new variant of Bouveret's syndrome in a 54-year-old Korean woman.

  1. Brief Analysis of Regional Variants in English%Brief Analysis of Regional Variants in Enghsh

    Institute of Scientific and Technical Information of China (English)

    张炳科

    2008-01-01

    It is universally acknowledged that regional variants exist in each language, for it is impossible that people always employ the same pronunciation or vocabulary or even grammar to express the same meaning no matter how large the scope in which a language is used may be. The author of this paper is just to exemplify some regional variants in English and to analyze the factors that account for the variants ,with the purpose of teaching English well in the most efficient way.

  2. Histone variants: key players of chromatin.

    Science.gov (United States)

    Biterge, Burcu; Schneider, Robert

    2014-06-01

    Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.

  3. Beta-glucosidase variants and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Maisonneuve-hyperplantarflexion variant ankle fracture.

    Science.gov (United States)

    Hinds, Richard M; Tran, Wesley H; Lorich, Dean G

    2014-11-01

    Maisonneuve fractures are rare ankle injuries, accounting for up to 7% of all ankle fractures. They consist of a proximal third fibula fracture, syndesmotic disruption, and medial ankle injury (either a deltoid ligament disruption or a medial malleolus fracture), and are often successfully managed with nonoperative treatment of the proximal fibula fracture and open reduction and internal fixation (ORIF) of the medial ankle injury and syndesmotic disruption. The hyperplantarflexion variant ankle fracture comprises approximately 7% of all ankle fractures and features dual posterior tibial lip fractures featuring a posterolateral fragment and a posteromedial fragment. Good functional results have been reported in the literature after ORIF of both the posterolateral and posteromedial fragments of this variant fracture that is not described by the Lauge-Hansen classification. In this report, the authors present the unique case of an isolated ankle fracture demonstrating characteristics of both a Maisonneuve fracture and a hyperplantarflexion variant ankle fracture. They also highlight the diagnostic imaging characteristics, including magnetic resonance imaging (MRI) and preoperative radiograph findings, surgical treatment, and postoperative clinical outcome for this patient with a Maisonneuve-hyperplantarflexion variant ankle fracture. To the authors' knowledge, this unique fracture pattern has not been reported previously in the literature. The authors conclude that although good results were seen postoperatively in this case, the importance of ORIF of both the posteromedial and posterolateral fragments of variant fractures cannot be overstated. They also found MRI to be a particularly helpful adjunct in formulating the correct diagnosis and treatment plan.

  5. Word Variant Identification in Old French

    Directory of Open Access Journals (Sweden)

    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.

  6. Variants of Monteggia Type Injury: Case Reports

    Directory of Open Access Journals (Sweden)

    Kamudin NAF

    2015-03-01

    Full Text Available Background: Monteggia fracture-dislocation is rare in children. Various reports attest to its rarity, while recording the many variant of this injury. It is, therefore, easy to miss the diagnosis in the absence of proper clinical examination and radiographs. Case Report : This report highlights two rare variants of Monteggia fracture-dislocation seen in children. The first case was a 12-year old girl alleged to have fallen from a 15-feet tall tree and sustaining a combined type III Monteggia injury with ipsilateral Type II Salter-Harris injury of distal end radius with a metaphyseal fracture of the distal third of the ulna. The second case was a 13-year old who had sustained a closed fracture of atypical Type I Monteggia hybrid lesion, in a road traffic accident. Conclusion: This report highlights the rare variants of Monteggia fracture dislocation which could have been missed without proper clinical examinations and radiographs.

  7. Variants of Monteggia Type Injury: Case Reports

    Science.gov (United States)

    Firdouse, M; Han, CS; M Yusof, A

    2015-01-01

    Background Monteggia fracture-dislocation is rare in children. Various reports attest to its rarity, while recording the many variant of this injury. It is, therefore, easy to miss the diagnosis in the absence of proper clinical examination and radiographs. Case Report This report highlights two rare variants of Monteggia fracture-dislocation seen in children. The first case was a 12-year old girl alleged to have fallen from a 15- feet tall tree and sustaining a combined type III Monteggia injury with ipsilateral Type II Salter-Harris injury of distal end radius with a metaphyseal fracture of the distal third of the ulna. The second case was a 13-year old who had sustained a closed fracture of atypical Type I Monteggia hybrid lesion, in a road traffic accident. Conclusion This report highlights the rare variants of Monteggia fracture dislocation which could have been missed without proper clinical examinations and radiographs. PMID:28435591

  8. 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.

  9. A case of reninoma with variant angina

    Directory of Open Access Journals (Sweden)

    Hyung Ah Jo

    2014-06-01

    Full Text Available Reninoma is a tumor of the renal juxtaglomerular cell apparatus that causes hypertension and hypokalemia because of hypersecretion of renin. We present a case of a 29-year-old female patient with reninoma and concomitant variant angina. The patient had uncontrolled hypertension and elevated plasma renin activity and aldosterone levels. Imaging studies revealed a mass in the left kidney, which was further confirmed as a renin-producing lesion via selective venous catheterization. During the evaluation, the patient had acute-onset chest pain that was diagnosed as variant angina after a provocation test. After partial nephrectomy, the plasma renin activity and plasma aldosterone levels decreased and blood pressure normalized. We report a case of reninoma with variant angina.

  10. Hemoglobin variants: biochemical properties and clinical correlates.

    Science.gov (United States)

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

    2013-03-01

    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.

  11. Cryptanalysis of SIMON Variants with Connections

    DEFF Research Database (Denmark)

    Alizadeh, Javad; Alkhzaimi, Hoda A.; Aref, Mohammad Reza

    2014-01-01

    SIMON is a family of 10 lightweight block ciphers published by Beaulieu et al. from the United States National Security Agency (NSA). A cipher in this family with K-bit key and N-bit block is called SIMONN/K. We present several linear characteristics for reduced-round SIMON32/64 that can be used...... the presented observations do not directly yield an attack, but provide a basis for further analysis for the specific SIMON variant. Finally, we exploit a connection between linear and differential characteristics for SIMON to construct linear characteristics for different variants of reduced-round SIMON. Our...

  12. Histone variants and melanoma: facts and hypotheses.

    Science.gov (United States)

    Konstantinov, Nikifor K; Ulff-Møller, Constance J; Dimitrov, Stefan

    2016-07-01

    Melanoma is the most aggressive form of skin cancer with rising incidence and morbidity. Despite advances in treatment, the 10-yr survival for patients with metastatic disease is less than 10%. During the past few years, ongoing research on different epigenomic aberrations in melanoma has catalyzed better understanding of its pathogenesis and identification of new therapeutics. In our review, we will focus on the role of histone variants, key epigenetic players in melanoma initiation and progression. Specifically, incorporation of histone variants enables additional layers of chromatin structure, and here, we will describe how alterations in this epigenetic behavior impact melanoma.

  13. Variant profiling of evolving prokaryotic populations

    Directory of Open Access Journals (Sweden)

    Markus Zojer

    2017-02-01

    Full Text Available Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to

  14. The current state of clinical interpretation of sequence variants.

    Science.gov (United States)

    Hoskinson, Derick C; Dubuc, Adrian M; Mason-Suares, Heather

    2017-01-31

    Accurate and consistent variant classification is required for Precision Medicine. But clinical variant classification remains in its infancy. While recent guidelines put forth jointly by the American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) for the classification of Mendelian variants has advanced the field, the degree of subjectivity allowed by these guidelines can still lead to inconsistent classification across clinical molecular genetic laboratories. In addition, there are currently no such guidelines for somatic cancer variants, only published institutional practices. Additional variant classification guidelines, including disease- or gene-specific criteria, along with inter-laboratory data sharing is critical for accurate and consistent variant interpretation.

  15. Cellobiohydrolase I gene and improved variants

    Science.gov (United States)

    Adney, William S.; Decker, Stephen R.; Mc Carter, Suzanne; Baker, John O.; Nieves, Raphael; Himmel, Michael E.; Vinzant, Todd B.

    2008-05-20

    The disclosure provides a method for preparing an active exoglucanase in a heterologous host of eukaryotic origin. The method includes mutagenesis to reduce glycosylation of the exoglucanase when expressed in a heterologous host. It is further disclosed a method to produce variant cellobiohydrolase that is stable at high temperature through mutagenesis.

  16. Developing consistent pronunciation models for phonemic variants

    CSIR Research Space (South Africa)

    Davel, M

    2006-09-01

    Full Text Available from a lexicon containing variants. In this paper we (the authors) address both these issues by creating ‘pseudo-phonemes’ associated with sets of ‘generation restriction rules’ to model those pronunciations that are consistently realised as two or more...

  17. Mining Process Variants: Goals and Issues

    NARCIS (Netherlands)

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

    2008-01-01

    Recently, Process-Aware Information Systems (PAIS) were introduced, which allow for dynamic process and service changes. This, in turn, has led to a large number of process model variants, which are difficult to maintain and expensive to configure. This paper deals with goals and issues related to t

  18. Splicing variants of porcine synphilin-1

    DEFF Research Database (Denmark)

    Larsen, Knud Erik; Madsen, Lone Bruhn; Farajzadeh, Leila

    2015-01-01

    RNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa) synphilin-1 cDNA (SNCAIP) and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1) of 919 amino acids which shows a high similarity to human (90...

  19. Report of a rare anatomic variant

    DEFF Research Database (Denmark)

    De Brucker, Y; Ilsen, B; Muylaert, C;

    2015-01-01

    We report the CT findings in a case of partial anomalous pulmonary venous return (PAPVR) from the left upper lobe in an adult. PAPVR is an anatomic variant in which one to three pulmonary veins drain into the right atrium or its tributaries, rather than into the left atrium. This results in a lef...

  20. Splicing variants of porcine synphilin-1

    Directory of Open Access Journals (Sweden)

    Knud Larsen

    2015-09-01

    Full Text Available Parkinson's disease (PD, idiopathic and familial, is characterized by degradation of dopaminergic neurons and the presence of Lewy bodies (LB in the substantia nigra. LBs contain aggregated proteins of which α-synuclein is the major component. The protein synphilin-1 interacts and colocalizes with α-synuclein in LBs. The aim of this study was to isolate and characterize porcine synphilin-1 and isoforms hereof with the future perspective to use the pig as a model for Parkinson's disease. The porcine SNCAIP cDNA was cloned by reverse transcriptase PCR. The spatial expression of SNCAIP mRNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa synphilin-1 cDNA (SNCAIP and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1 of 919 amino acids which shows a high similarity to human (90% and to mouse (84% synphilin-1. Three shorter transcript variants of the synphilin-1 gene were identified, all lacking one or more exons. SNCAIP transcripts were detected in most examined organs and tissues and the highest expression was found in brain tissues and lung. Conserved splicing variants and a novel splice form of synhilin-1 were found in this study. All synphilin-1 isoforms encoded by the identified transcript variants lack functional domains important for protein degradation.

  1. HLogo: a parallel Haskell variant of Netlogo

    NARCIS (Netherlands)

    N. Bezirgiannis (Nikolaos); Prasetya, I.S.W.B.; Sakellariou, I.

    2016-01-01

    textabstractAgent-based Modeling (ABM) has become quite popular to the simulation community for its usability and wide area of applicability. However, speed is not usually a trait that ABM tools are characterized of attaining. This paper presents HLogo, a parallel variant of the NetLogo ABM framewor

  2. PIN1 gene variants in Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Siedlecki Janusz

    2009-11-01

    Full Text Available Abstract Background Peptidyl-prolyl isomerase, NIMA-interacting 1 (PIN1 plays a significant role in the brain and is implicated in numerous cellular processes related to Alzheimer's disease (AD and other neurodegenerative conditions. There are confounding results concerning PIN1 activity in AD brains. Also PIN1 genetic variation was inconsistently associated with AD risk. Methods We performed analysis of coding and promoter regions of PIN1 in early- and late-onset AD and frontotemporal dementia (FTD patients in comparison with healthy controls. Results Analysis of eighteen PIN1 common polymorphisms and their haplotypes in EOAD, LOAD and FTD individuals in comparison with the control group did not reveal their contribution to disease risk. In six unrelated familial AD patients four novel PIN1 sequence variants were detected. c.58+64C>T substitution that was identified in three patients, was located in an alternative exon. In silico analysis suggested that this variant highly increases a potential affinity for a splicing factor and introduces two intronic splicing enhancers. In the peripheral leukocytes of one living patient carrying the variant, a 2.82 fold decrease in PIN1 expression was observed. Conclusion Our data does not support the role of PIN1 common polymorphisms as AD risk factor. However, we suggest that the identified rare sequence variants could be directly connected with AD pathology, influencing PIN1 splicing and/or expression.

  3. New genetic variants associated with prostate cancer

    Science.gov (United States)

    Researchers have newly identified 23 common genetic variants -- one-letter changes in DNA known as single-nucleotide polymorphisms or SNPs -- that are associated with risk of prostate cancer. These results come from an analysis of more than 10 million SNP

  4. Histone Variants in Development and Diseases

    Institute of Scientific and Technical Information of China (English)

    Ping Chen; Jicheng Zhao; Guohong Li

    2013-01-01

    Eukaryotic genomic DNA is highly packaged into chromatin by histones to fit inside the nucleus.Other than the bulk packaging role of canonical histones with an expression peak at S phase and replication-coupled deposition,different histone variants have evolved distinct regulatory mechanisms for their expression,deposition and functional implications.The diversity of histone variants results in structural plasticity of chromatin and highlights functionally distinct chromosomal domain,which plays critical roles in development from a fertilized egg into a complex organism,as well as in aging and diseases.However,the mechanisms of this fundamental process are poorly understood so far.It is of particular interest to investigate how the variants are incorporated into chromatin and mark specific chromatin states to regulate gene expression,and how they are involved in development and diseases.In this review,we focus on recent progress in studies of epigenetic regulation of three extensively investigated variants including H2A.Z,macroH2A and H3.3,and their functional implications in development and diseases.

  5. A compendium of genetic variant data

    DEFF Research Database (Denmark)

    Cardoso, Joao; Schöning, Lars Yannik; Herrgard, Markus

    2014-01-01

    Laboratory strains are genetically unstable if exposed to selective pressure as encountered, for example, during molecular cloning, fermentation, or adaptive laboratory evolution experiments. This genetic variation is the consequence of an adaptation process of the microorganism to stress...... obtained from distinct experiments. This compendium of genetic variant is a critical step to develop approaches to automatically and systematically characterize mutated strains in the future....

  6. Gene variants as risk factors for gastroschisis

    Science.gov (United States)

    Yang, Wei; Schultz, Kathleen; Tom, Lauren; Lin, Bin; Carmichael, Suzan L.; Lammer, Edward J.; Shaw, Gary M.

    2016-01-01

    In a population‐based case‐control study in California of 228 infants, we investigated 75 genetic variants in 20 genes and risk of gastroschisis with regard to maternal age, race/ethnicity, vitamin use, and smoking exposure. We hypothesized that genes related to vascular compromise may interact with environmental factors to affect the risk of gastroschisis. Haplotypes were constructed for 75 gene variants using the HaploView program. Risk for gastroschisis associated with each gene variant was calculated for both the homozygotes and the heterozygotes, with the homozygous wildtypes as the referent. Risks were estimated as odds ratios (ORs) with 95% confidence intervals (CIs) by logistic regression. We found 11 gene variants with increased risk and four variants with decreased risk of gastroschisis for heterozygous (ORh) or homozygous variants (ORv) genotypes. These included NOS3 (rs1036145) ORh = 0.4 (95% CI: 0.2–0.7); NOS3 (rs10277237) ORv = 2.7 (95% CI: 1.3–6.0); ADD1 (rs12503220) ORh = 2.9 (95% CI: 1.6–5.4), GNB3 (rs5443) ORh = 0.2 (95% CI: 0.1–0.5), ORv = 0.4 (95% CI: 0.2–0.9); ICAM1 (rs281428) ORv = 6.9 (95% CI: 2.1–22.9), ICAM1 (rs3093030) ORv = 2.6 (95% CI: 1.2–5.6); ICAM4 (rs281438) ORv = 4.9 (95% CI: 1.4–16.6), ICAM5 (rs281417) ORh = 2.1 (95% CI: 1.1–4.1), ORv = 4.8 (95% CI: 1.7–13.6); ICAM5 (rs281440) ORh = 23.7 (95% CI: 5.5–102.5), ORv = 20.6 (95% CI: 3.4–124.3); ICAM5 (rs2075741) ORv = 2.2 (95% CI: 1.1–4.4); NAT1 ORv = 0.3 (95% CI: 0.1–0.9). There were additional associations between several gene variants and gastroschisis among women aged 20–24 and among mothers with and without vitamin use. NOS3, ADD1, ICAM1, ICAM4, and ICAM5 warrant further investigation in additional populations and with the interaction of additional environmental exposures. © 2016 Wiley Periodicals, Inc. PMID:27616475

  7. Gene Variant from Africa Linked to Black Obesity

    Science.gov (United States)

    ... html Gene Variant From Africa Linked to Black Obesity Study sees first biological pathway to weight gain ... identified an Africa-specific gene variant associated with obesity. The team found that about 1 percent of ...

  8. Rare variant density across the genome and across populations

    OpenAIRE

    Raska Paola; Zhu Xiaofeng

    2011-01-01

    Abstract Next-generation sequencing allows for a new focus on rare variant density for conducting analyses of association to disease and for narrowing down the genomic regions that show evidence of functionality. In this study we use the 1000 Genomes Project pilot data as distributed by Genetic Analysis Workshop 17 to compare rare variant densities across seven populations. We made the comparisons using regressions of rare variants on total variant counts per gene for each population and Taji...

  9. 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....

  10. Processing of No-Release Variants in Connected Speech

    Science.gov (United States)

    LoCasto, Paul C.; Connine, Cynthia M.

    2011-01-01

    The cross modal repetition priming paradigm was used to investigate how potential lexically ambiguous no-release variants are processed. In particular we focus on segmental regularities that affect the variant's frequency of occurrence (voicing of the critical segment) and phonological context in which the variant occurs (status of the following…

  11. Rare ADH Variant Constellations are Specific for Alcohol Dependence

    OpenAIRE

    Zuo, Lingjun; Zhang, Heping; Malison, Robert T; Li, Chiang-shan R.; Zhang, Xiang-Yang; Wang, Fei; Lu, Lingeng; Lu, Lin; Wang, Xiaoping; Krystal, John H.; Zhang, Fengyu; Deng, Hong-Wen; Luo, Xingguang

    2012-01-01

    Aims: Some of the well-known functional alcohol dehydrogenase (ADH) gene variants (e.g. ADH1B*2, ADH1B*3 and ADH1C*2) that significantly affect the risk of alcohol dependence are rare variants in most populations. In the present study, we comprehensively examined the associations between rare ADH variants [minor allele frequency (MAF)

  12. GenOVa: a computer program to generate orientational variants

    OpenAIRE

    Cayron, Cyril

    2007-01-01

    A computer program called GenOVa, written in Python, calculates the orientational variants, the operators (special types of misorientations between variants) and the composition table associated with a groupoid structure. The variants can be represented by three-dimensional shapes or by pole figures.

  13. Variants in CUL4B are Associated with Cerebral Malformations

    NARCIS (Netherlands)

    Vulto-van Silfhout, Anneke T.; Nakagawa, Tadashi; Bahi-Buisson, Nadia; Haas, Stefan A.; Hu, Hao; Bienek, Melanie; Vissers, Lisenka E. L. M.; Gilissen, Christian; Tzschach, Andreas; Busche, Andreas; Muesebeck, Joerg; Rump, Patrick; Mathijssen, Inge B.; Avela, Kristiina; Somer, Mirja; Doagu, Fatma; Philips, Anju K.; Rauch, Anita; Baumer, Alessandra; Voesenek, Krysta; Poirier, Karine; Vigneron, Jacqueline; Amram, Daniel; Odent, Sylvie; Nawara, Magdalena; Obersztyn, Ewa; Lenart, Jacek; Charzewska, Agnieszka; Lebrun, Nicolas; Fischer, Ute; Nillesen, Willy M.; Yntema, Helger G.; Jarvela, Irma; Ropers, Hans-Hilger; de Vries, Bert B. A.; Brunner, Han G.; van Bokhoven, Hans; Raymond, F. Lucy; Willemsen, Michel A. A. P.; Chelly, Jamel; Xiong, Yue; Barkovich, A. James; Kalscheuer, Vera M.; Kleefstra, Tjitske; de Brouwer, Arjan P. M.

    2015-01-01

    Variants in cullin 4B (CUL4B) are a known cause of syndromic X-linked intellectual disability. Here, we describe an additional 25 patients from 11 families with variants in CUL4B. We identified nine different novel variants in these families and confirmed the pathogenicity of all nontruncating varia

  14. Variants in CUL4B are associated with cerebral malformations

    NARCIS (Netherlands)

    Vulto-van Silfhout, A.T.; Nakagawa, T.; Bahi-Buisson, N.; Haas, S.A.; Hu, H; Bienek, M.; Vissers, L.E.L.M.; Gilissen, C.F.H.A.; Tzschach, A.; Busche, A.; Musebeck, J.; Rump, P.; Mathijssen, I.B.; Avela, K.; Somer, M.; Doagu, F.; Philips, A.K.; Rauch, A.; Baumer, A.; Voesenek, K.E.J.; Poirier, K.; Vigneron, J.; Amram, D.; Odent, S.; Nawara, M.; Obersztyn, E.; Lenart, J.; Charzewska, A.; Lebrun, N.; Fischer, U.; Nillesen, W.M.; Yntema, H.G.; Jarvela, I.; Ropers, H.H.; Vries, B. de; Brunner, H.G.; Bokhoven, H. van; Raymond, F.L.; Willemsen, M.A.A.P.; Chelly, J.; Xiong, Y.; Barkovich, A.J.; Kalscheuer, V.M.; Kleefstra, T.; Brouwer, A.P.M. de

    2015-01-01

    Variants in cullin 4B (CUL4B) are a known cause of syndromic X-linked intellectual disability. Here, we describe an additional 25 patients from 11 families with variants in CUL4B. We identified nine different novel variants in these families and confirmed the pathogenicity of all nontruncating varia

  15. The power of multiplexed functional analysis of genetic variants.

    Science.gov (United States)

    Gasperini, Molly; Starita, Lea; Shendure, Jay

    2016-10-01

    New technologies have recently enabled saturation mutagenesis and functional analysis of nearly all possible variants of regulatory elements or proteins of interest in single experiments. Here we discuss the past, present, and future of such multiplexed (functional) assays for variant effects (MAVEs). MAVEs provide detailed insight into sequence-function relationships, and they may prove critical for the prospective clinical interpretation of genetic variants.

  16. Processing of No-Release Variants in Connected Speech

    Science.gov (United States)

    LoCasto, Paul C.; Connine, Cynthia M.

    2011-01-01

    The cross modal repetition priming paradigm was used to investigate how potential lexically ambiguous no-release variants are processed. In particular we focus on segmental regularities that affect the variant's frequency of occurrence (voicing of the critical segment) and phonological context in which the variant occurs (status of the following…

  17. Wham: Identifying Structural Variants of Biological Consequence.

    Science.gov (United States)

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.

  18. Discussing and managing hematologic germ line variants.

    Science.gov (United States)

    Kohlmann, Wendy; Schiffman, Joshua D

    2016-11-24

    With the introduction of genomic technologies, more hereditary cancer syndromes with hematologic malignancies are being described. Up to 10% of hematologic malignancies in children and adults may be the result of an underlying inherited genetic risk. Managing these patients with hereditary hematologic malignancies, including familial leukemia, remains a clinical challenge because there is little information about these relatively rare disorders. This article covers some of the issues related to the diagnosis and interpretation of variants associated with hereditary hematologic malignancies, including the importance of an accurate family history in interpreting genetic variants associated with disease. The challenges of screening other family members and offering the most appropriate early malignancy detection is also discussed. We now have a good opportunity to better define hereditary cancer syndromes with associated hematologic malignancies and contribute to clinically effective guidelines.

  19. Wham: Identifying Structural Variants of Biological Consequence.

    Directory of Open Access Journals (Sweden)

    Zev N Kronenberg

    2015-12-01

    Full Text Available Existing methods for identifying structural variants (SVs from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham, with documentation on a wiki (http://zeeev.github.io/wham/. For community support please post questions to https://www.biostars.org/.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike

    2016-01-01

    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). PMID:27379672

  2. Unusual variant of Cantrell′s pentalogy?

    Directory of Open Access Journals (Sweden)

    Kumar Basant

    2008-01-01

    Full Text Available A 12-hour-old male infant presented with prolapsed abdominal content through a defect on left side of chest wall with respiratory distress. A thorough clinical examination suggested absence of ectopia cordis, abdominal wall defect, and any bony anomaly. The child expired after 6 hours of admission because of respiratory distress and electrolyte imbalance. Is congenital defect of chest wall associated with diaphragmatic hernia without ectopia cordis and omphalocele, an unusual variant of Cantrell′s pentalogy?

  3. Variant position of the medial plantar nerve

    OpenAIRE

    Astik RB; Dave UH; Gajendra KS

    2011-01-01

    Knowledge of variation of position of the medial plantar nerve is important for the forefoot surgeon for plantar reconstruction, local injection therapy and an excision of interdigital neuroma. During routine dissection of 50-year-old female cadaver, we found the medial plantar nerve and vessels variably located between plantar aponeurosis and the muscles of the first layer of the sole of the right foot. Due to this variant position, the medial plantar nerve and vessels lose their protection ...

  4. Small colony variants and their clinical significance

    Directory of Open Access Journals (Sweden)

    Venkataramana Venkataramana

    2016-01-01

    Full Text Available Among the many factors that contribute to bacterial colonization, persistence and development of infection, the ability of microorganisms to form small colony variants (SCVs assumes great significance. Although bacteria require intrinsic virulence factors to cause pathogenesis, some of them regularly evolve mechanisms to evade immune mechanisms, become resistant to antibiotics, and sustain in the human/animal cells to cause chronic infections. This mini review highlights the recent advances in the study of SCVs.

  5. Unusual variant of Cantrell′s pentalogy?

    OpenAIRE

    Kumar Basant; Sharma S.; Kandpal Deepak; Agrawal L

    2008-01-01

    A 12-hour-old male infant presented with prolapsed abdominal content through a defect on left side of chest wall with respiratory distress. A thorough clinical examination suggested absence of ectopia cordis, abdominal wall defect, and any bony anomaly. The child expired after 6 hours of admission because of respiratory distress and electrolyte imbalance. Is congenital defect of chest wall associated with diaphragmatic hernia without ectopia cordis and omphalocele, an unusual variant of Cantr...

  6. Association of genetic variants with diabetic nephropathy

    Institute of Scientific and Technical Information of China (English)

    Saliha; Rizvi; Syed; Tasleem; Raza; Farzana; Mahdi

    2014-01-01

    Diabetic nephropathy accounts for the most serious microvascular complication of diabetes mellitus. It is suggested that the prevalence of diabetic nephropathy will continue to increase in future posing a major challenge to the healthcare system resulting in increased morbidity and mortality. It occurs as a result of interaction between both genetic and environmental factors in individuals with both type 1 and type 2 diabetes. Genetic susceptibility has been proposed as an important factor for the development and progression of diabetic nephropathy, and various research efforts are being executed worldwide to identify the susceptibility gene for diabetic nephropathy. Numerous single nucleotide polymorphisms have been found in various genes giving rise to various gene variants which have been found to play a major role in genetic susceptibility to diabetic nephropathy. The risk of developing diabetic nephropathy is increased several times by inheriting risk alleles at susceptibility loci of various genes like ACE, IL, TNF-α, COL4A1, e NOS, SOD2, APOE, GLUT, etc. The identification of these genetic variants at a biomarker level could thus, allow the detection of those individuals at high risk for diabetic nephropathy which could thus help in the treatment, diagnosis and early prevention of the disease. The present review discusses about the various gene variants found till date to be associated with diabetic nephropathy.

  7. Primary Aldosteronism and ARMC5 Variants

    Science.gov (United States)

    Zilbermint, Mihail; Xekouki, Paraskevi; Faucz, Fabio R.; Berthon, Annabel; Gkourogianni, Alexandra; Schernthaner-Reiter, Marie Helene; Batsis, Maria; Sinaii, Ninet; Quezado, Martha M.; Merino, Maria; Hodes, Aaron; Abraham, Smita B.; Libé, Rossella; Assié, Guillaume; Espiard, Stéphanie; Drougat, Ludivine; Ragazzon, Bruno; Davis, Adam; Gebreab, Samson Y.; Neff, Ryan; Kebebew, Electron; Bertherat, Jérôme; Lodish, Maya B.

    2015-01-01

    Context: Primary aldosteronism is one of the leading causes of secondary hypertension, causing significant morbidity and mortality. A number of genetic defects have recently been identified in primary aldosteronism, whereas we identified mutations in ARMC5, a tumor-suppressor gene, in cortisol-producing primary macronodular adrenal hyperplasia. Objective: We investigated a cohort of 56 patients who were referred to the National Institutes of Health for evaluation of primary aldosteronism for ARMC5 defects. Methods: Patients underwent step-wise diagnosis, with measurement of serum aldosterone and plasma renin activity followed by imaging, saline suppression and/or oral salt loading tests, plus adrenal venous sampling. Cortisol secretion was also evaluated; unilateral or bilateral adrenalectomy was performed, if indicated. DNA, protein, and transfection studies in H295R cells were conducted by standard methods. Results: We identified 12 germline ARMC5 genetic alterations in 20 unrelated and two related individuals in our cohort (39.3%). ARMC5 sequence changes in 6 patients (10.7%) were predicted to be damaging by in silico analysis. All affected patients carrying a variant predicted to be damaging were African Americans (P = .0023). Conclusions: Germline ARMC5 variants may be associated with primary aldosteronism. Additional cohorts of patients with primary aldosteronism and metabolic syndrome, particularly African Americans, should be screened for ARMC5 sequence variants because these may underlie part of the known increased predisposition of African Americans to low renin hypertension. PMID:25822102

  8. Warty Carcinoma Penis: An Uncommon Variant

    Science.gov (United States)

    Ghosh, Arnab; Shrestha, Santosh; Ghartimagar, Dilasma; Narasimhan, Raghavan; Talwar, OP

    2017-01-01

    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. PMID:28154768

  9. Association of genetic variants with diabetic nephropathy.

    Science.gov (United States)

    Rizvi, Saliha; Raza, Syed Tasleem; Mahdi, Farzana

    2014-12-15

    Diabetic nephropathy accounts for the most serious microvascular complication of diabetes mellitus. It is suggested that the prevalence of diabetic nephropathy will continue to increase in future posing a major challenge to the healthcare system resulting in increased morbidity and mortality. It occurs as a result of interaction between both genetic and environmental factors in individuals with both type 1 and type 2 diabetes. Genetic susceptibility has been proposed as an important factor for the development and progression of diabetic nephropathy, and various research efforts are being executed worldwide to identify the susceptibility gene for diabetic nephropathy. Numerous single nucleotide polymorphisms have been found in various genes giving rise to various gene variants which have been found to play a major role in genetic susceptibility to diabetic nephropathy. The risk of developing diabetic nephropathy is increased several times by inheriting risk alleles at susceptibility loci of various genes like ACE, IL, TNF-α, COL4A1, eNOS, SOD2, APOE, GLUT, etc. The identification of these genetic variants at a biomarker level could thus, allow the detection of those individuals at high risk for diabetic nephropathy which could thus help in the treatment, diagnosis and early prevention of the disease. The present review discusses about the various gene variants found till date to be associated with diabetic nephropathy.

  10. Genetic variants associated with Crohn's disease

    Directory of Open Access Journals (Sweden)

    Michail S

    2013-07-01

    Full Text Available Sonia Michail,1 Gilberto Bultron,1 R William DePaolo2 1The University of Southern California, Children's Hospital of Los Angeles, Los Angeles, CA, USA; 2Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA Abstract: Crohn's disease is an immune-related disorder characterized by inflammation of the gastrointestinal mucosa, which can occur in any area throughout the digestive tract. This life-long disease commonly presents with abdominal pain, diarrhea, vomiting, and weight loss. While the exact etiology of this disease is largely unknown, it is thought to arise from an interaction between microbial, immunological, and environmental factors in a genetically susceptible host, whereby the immune system attacks the intestine as it cross reacts against gut microbial antigens. The study of genetic variants associated with Crohn's disease has shed light on our understanding of disease pathophysiology. A large number of genetic variants identified in Crohn's disease are related to genes targeting microbial recognition and bacterial wall sensing, the most common being NOD2/CARD15 gene. This review will discuss the recent advance in our knowledge of genetic variants of this disease and how they influence the disease course and prognosis. Keywords: Crohn's disease, genetics, autophagy

  11. 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

    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...... 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...... to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification...

  12. String Variant Alias Extraction Method using Ensemble Learner

    Directory of Open Access Journals (Sweden)

    P.Selvaperumal

    2016-02-01

    Full Text Available String variant alias names are surnames which are string variant form of the primary name. Extracting string variant aliases are important in tasks such as information retrieval, information extraction, and name resolution etc. String variant alias extraction involves candidate alias name extraction and string variant alias validation. In this paper, string variant aliases are first extracted from the web and then using seven different string similarity metrics as features, candidate aliases are validated using ensemble classifier random forest. Experiments were conducted using string variant name-alias dataset containing name-alias data for 15 persons containing 30 name-alias pairs. Experimental results show that the proposed method outperforms other similar methods in terms of accuracy.

  13. Physiological quality of rice seed submitted to gamma radiation; Qualidade fisiologica de sementes de arroz submetidas a radiacao gama

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, Helen Lucia da Cruz; Tillmann, Maria Angela Andre; Meneghello, Geri Eduardo, E-mail: helenllc@gmail.co [Universidade Federal de Pelotas (UFPel), RS (Brazil). Programa de Pos-graduacao em Ciencia e Tecnologia de Sementes; Bobrowski, Vera Lucia [Universidade Federal de Pelotas (UFPel), RS (Brazil). Dept. de Genetica; Dode, Luciana Bicca [Universidade Catolica de Pelotas (UCPel), RS (Brazil)

    2009-08-15

    The objective of this research was to evaluate the effects of the gamma radiation ({sup 60}Co) on the physiological quality of rice seeds. The research was carried out through three tests; in the first test rice seeds were irradiated at dosages of 0; 1; 2.5 and 5Gy, while for the second and third tests the seeds were subjected to accelerated aging before being irradiated. For the second test the seeds were divided into wet and dry and both groups subjected to accelerated aging previous to irradiation at dosages of 0; 1; 2.5 and 5Gy. For the third test the seeds were dried after being subjected to accelerated aging, and then irradiated at dosages of 0, 10, 25 and 50Gy. To assess the physiological effects of the gamma radiation, all seeds were tested for germination and their germination speed index recorded. Seedling growth was graded through the measurement of the lengths of the first leaf and seminal root system and total seedling dry weight, across all tests. The enzymatic activity of acid phosphatase and alpha-amylase was measured on dry seeds from the second test. The results from all tests indicate that the applied gamma radiation dosages did not cause any changes to the physiological quality of rice seeds. (author)

  14. VARIABILIDAD INTRA-POBLACIONAL EN LA UTILIZACION DEL NICHO TROFICO: FLEXIBILIDAD FISIOLOGICA Y ESPECIALIZACION INDIVIDUAL EN ZONOTRICHIA CAPENSIS

    OpenAIRE

    MALDONADO PACHECO, KARIN

    2009-01-01

    Debido a que el rango de distribución de las especies incluye diferentesambientes con características bióticas y abióticas generalmente contrastantes, laadecuación de los distintos genotipos de una misma especie a menudo difiereentre un hábitat y otro. De esta manera, la variabilidad en las característicasecológicas que experimentan las poblaciones podría promover diferencias interpoblacionales en la expresión y flexibilidad de los rasgos fisiológicos,morfológicos y conductuales, afectando fi...

  15. A new variant selection criterion for twin variants in titanium alloys. Pt. 2

    Energy Technology Data Exchange (ETDEWEB)

    Schuman, Christophe [Laboratoire d' Etude des Microstructures et de Mecanique des Materiaux, LEM3, CNRS 7239, Universite Paul Verlaine - Metz, Ile du Saulcy, Metz (France); Bao, Lei; Lecomte, Jean Sebastien; Zhang, Yudong; Raulot, Jean Marc; Philippe, Marie Jeanne; Esling, Claude [LEM3, CNRS 7239, Universite Paul Verlaine - Metz, Ile du Saulcy, Metz (France)

    2012-05-15

    A new selection criterion to explain the activation of the twinning variant is proposed. This criterion is based on the calculation of the deformation energy to create a primary twin. The calculation takes into account the effect of the grain size using a Hall-Petch type relation. This criterion allows to obtain a very good prediction for the twin family selection and twin variant selection. The calculations are compared with the experimental results obtained on T40 (ASTM grade 2) deformed by Channel Die compression. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Mutation Update: The Spectra of Nebulin Variants and Associated Myopathies

    Science.gov (United States)

    Lehtokari, Vilma-Lotta; Kiiski, Kirsi; Sandaradura, Sarah A.; Laporte, Jocelyn; Repo, Pauliina; Frey, Jennifer A.; Donner, Kati; Marttila, Minttu; Saunders, Carol; Barth, Peter G.; den Dunnen, Johan T.; Beggs, Alan H.; Clarke, Nigel F.; North, Kathryn N.; Laing, Nigel G.; Romero, Norma B.; Winder, Thomas L.; Pelin, Katarina; Wallgren-Pettersson, Carina

    2015-01-01

    A mutation update on the nebulin gene (NEB) is necessary because of recent developments in analysis methodology, the identification of increasing numbers and novel types of variants, and a widening in the spectrum of clinical and histological phenotypes associated with this gigantic, 183 exons containing gene. Recessive pathogenic variants in NEB are the major cause of nemaline myopathy (NM), one of the most common congenital myopathies. Moreover, pathogenic NEB variants have been identified in core-rod myopathy and in distal myopathies. In this update, we present the disease-causing variants in NEB in 159 families, 143 families with NM, and 16 families with NM-related myopathies. Eighty-eight families are presented here for the first time. We summarize 86 previously published and 126 unpublished variants identified in NEB. Furthermore, we have analyzed the NEB variants deposited in the Exome Variant Server (http://evs.gs.washington.edu/EVS/), identifying that pathogenic variants are a minor fraction of all coding variants (~7%). This indicates that nebulin tolerates substantial changes in its amino acid sequence, providing an explanation as to why variants in such a large gene result in relatively rare disorders. Lastly, we discuss the difficulties of drawing reliable genotype–phenotype correlations in NEB-associated disease. PMID:25205138

  17. XVCL: XML-based Variant Configuration Language

    DEFF Research Database (Denmark)

    Jarzabek, Stan; Basset, Paul; Zhang, Hongyu;

    2003-01-01

    XVCL (XML-based Variant Configuration Language) is a meta-programming technique and tool that provides effective reuse mechanisms. XVCL is an open source software developed at the National University of Singapore. Being a modern and versatile version of Bassett's frames, a technology that has...... achieved substantial gains in industry, the underlying principles of the XVCL have been thoroughly tested in practice. We envision many other applications in software and non-software domains, as we can apply XVCL to any domain that can be represented as a collection of textual documents....

  18. Clinical variants of idiopathic torsion dystonia.

    Science.gov (United States)

    Fahn, S

    1989-06-01

    Some patients with dystonic movements and postures not known to be caused by environmental or degenerative disorders can be segregated from classical-appearing idiopathic torsion dystonia on the basis of distinctive clinical and pharmacologic features. Many of them should be considered within the family of dystonia, as clinical variants of idiopathic torsion dystonia, while others are better classified as being part of other families of dyskinesias. In the former group are paradoxical dystonia, myoclonic dystonia, diurnal dystonia, and dopa-responsive dystonia. The latter group consists of dystonic tics and the various entities comprising paroxysmal dystonia, namely kinesigenic, nonkinesigenic and hypnogenic dystonia.

  19. Space-variant polarized Airy beam

    CERN Document Server

    Chen, Hao

    2015-01-01

    We experimentally generate an Airy beam with polarization structure while keeping its original amplitude and phase profile intact. This class of Airy beam preserves the acceleration properties. By monitoring their initial polarization structure we have provided insight concerning the self-healing mechanism of Airy beams. We investigate both theoretically and experimentally the self-healing polarization properties of the space-variant polarized Airy beams. Amplitude as well as the polarization structure tends to reform during propagation in spite of the severe truncation of the beam by finite apertures.

  20. Pitfalls and variants in pediatric chest imaging.

    Science.gov (United States)

    García Asensio, D; Fernández Martín, M

    2016-05-01

    Most pitfalls in the interpretation of pediatric chest imaging are closely related with the technique used and the characteristics of pediatric patients. To obtain a quality image that will enable the correct diagnosis, it is very important to use an appropriate technique. It is important to know how technical factors influence the image and to be aware of the possible artifacts that can result from poor patient cooperation. Moreover, radiologists need to be familiar with the normal anatomy in children, with the classic radiologic findings, and with the anatomic and developmental variants to avoid misinterpreting normal findings as pathological.

  1. Variant position of the medial plantar nerve

    Directory of Open Access Journals (Sweden)

    Astik RB

    2011-01-01

    Full Text Available Knowledge of variation of position of the medial plantar nerve is important for the forefoot surgeon for plantar reconstruction, local injection therapy and an excision of interdigital neuroma. During routine dissection of 50-year-old female cadaver, we found the medial plantar nerve and vessels variably located between plantar aponeurosis and the muscles of the first layer of the sole of the right foot. Due to this variant position, the medial plantar nerve and vessels lose their protection from the muscles of the first layer of the sole of the foot and became vulnerable for compression.

  2. Performance comparison of various time variant filters

    Energy Technology Data Exchange (ETDEWEB)

    Kuwata, M. [JEOL Engineering Co. Ltd., Akishima, Tokyo (Japan); Husimi, K.

    1996-07-01

    This paper describes the advantage of the trapezoidal filter used in semiconductor detector system comparing with the other time variant filters. The trapezoidal filter is the compose of a rectangular pre-filter and a gated integrator. We indicate that the best performance is obtained by the differential-integral summing type rectangular pre-filter. This filter is not only superior in performance, but also has the useful feature that the rising edge of the output waveform is linear. We introduce an example of this feature used in a high-energy experiment. (author)

  3. [Necrobiosis lipoidica. Variants on a theme].

    Science.gov (United States)

    Geissler, E; Laaff, H; Technau, K; Bruckner-Tuderman, L; Nashan, D

    2011-08-01

    A 69-year-old patient presented with different skin lesions all of which belonged to group of necrobiosis lipoidica. The initial histologic diagnosis was actinic granuloma O'Brien. A subsequent biopsy was interpreted as granulomatous necrobiosis lipoidica. The history of these necrobiotic variants is reviewed and exemplarily depicted with this case. Necrobiosis lipoidica is part of the spectrum of granulomatous skin disorders. Although its etiology is unclear, an association with diabetes mellitus is often discussed. Multiple therapeutic options exist, but standardized guidelines for treatment are missing.

  4. Oral fibrolipoma: A rare histological variant

    Directory of Open Access Journals (Sweden)

    Treville Pereira

    2014-01-01

    Full Text Available Lipomas are benign soft tissue mesenchymal neoplasms. Fibrolipoma is a histological variant of lipoma that mostly affects the buccal mucosa and causes functional and cosmetic disabilities. The diagnosis and differentiation of fibrolipoma with clinically similar lesions such as fibroma and pleomorphic adenoma is very essential for a correct treatment plan and complete follow-up. This article presents a case of a 35-year-old female with a fibrolipoma on the lingual marginal gingiva of the mandibular left third molar.

  5. Research progress of behavioral variant frontotemporal dementia

    Directory of Open Access Journals (Sweden)

    Xiao-hua GU

    2015-07-01

    Full Text Available There is no epidemiological data of frontotemporal dementia (FTD in China. The application of updated diagnostic criteria, publishing of frontotemporal lobar degeneration (FTLD consensus in China, development of multimodal imaging and biomarkers promote the clinical understanding on behavioral variant frontotemporal dementia (bvFTD. There is still no drugs treating FTD approved by U.S. Food and Drug Administration (FDA. Multidisciplinary intervention may delay the progression of bvFTD. DOI: 10.3969/j.issn.1672-6731.2015.07.006

  6. Immunogenic variants obtained by mutagenesis of mouse mastocytoma P815. V. H-2 associativity of variant-specific antigens.

    Science.gov (United States)

    Van Snick, J; Maryanski, J; Van Pel, A; Parmiani, G; Boon, T

    1982-11-01

    By in vitro mutagenesis of mastocytoma P815, it is possible to obtain tumor cell variants that are rejected by syngeneic mice (tum-). Most of these variants carry new individual antigens and stimulate a specific cytolytic T cell (CTL) response in mixed leukocyte tumor cell culture (MLTC). The H-2 associativity of this response was examined for six different variants by measuring the inhibition of cell-mediated cytolysis by antibodies directed against products of the K or the D end of the H-2d complex. The lysis was either not inhibited (variants P91 and P116) or inhibited selectively by anti-Kd (variants P21, P32 and P198) or anti-Dd antibodies (variant P35). All these tum- variants expressed Kd and Dd antigens as measured by absorption of H-2 alloantisera. Long-term CTL clones can be obtained that are specific for individual tum- antigens. The pattern of H-2 associativity obtained with MLTC-derived CTL against four tum- variants was verified with CTL clones directed against the specific antigens of these variants. Concordant results were observed in all cases. In addition to CTL clones specific for tum- antigens, it is possible to isolate clones against a P815 tumor-associated antigen found on all P815 tum- variants. For these clones no clear associativity with either Kd or Dd products was found.

  7. Schizophrenia copy number variants and associative learning

    Science.gov (United States)

    Clifton, N E; Pocklington, A J; Scholz, B; Rees, E; Walters, J T R; Kirov, G; O'Donovan, M C; Owen, M J; Wilkinson, L S; Thomas, K L; Hall, J

    2017-01-01

    Large-scale genomic studies have made major progress in identifying genetic risk variants for schizophrenia. A key finding from these studies is that there is an increased burden of genomic copy number variants (CNVs) in schizophrenia cases compared with controls. The mechanism through which these CNVs confer risk for the symptoms of schizophrenia, however, remains unclear. One possibility is that schizophrenia risk CNVs impact basic associative learning processes, abnormalities of which have long been associated with the disorder. To investigate whether genes in schizophrenia CNVs impact on specific phases of associative learning we combined human genetics with experimental gene expression studies in animals. In a sample of 11 917 schizophrenia cases and 16 416 controls, we investigated whether CNVs from patients with schizophrenia are enriched for genes expressed during the consolidation, retrieval or extinction of associative memories. We show that CNVs from cases are enriched for genes expressed during fear extinction in the hippocampus, but not genes expressed following consolidation or retrieval. These results suggest that CNVs act to impair inhibitory learning in schizophrenia, potentially contributing to the development of core symptoms of the disorder. PMID:27956746

  8. [Variant phenotype of Lesch-Nyhan syndrome].

    Science.gov (United States)

    Torres Jiménez, Rosa; García García, Marta; García Puig, Juan

    2011-01-29

    Lesch-Nyhan syndrome (LNS) and LNS variants are due to mutations in the HPRT1 gene causing HPRT enzymatic activity deficiency. We report a patient presenting a variant phenotype and a major genetic defect. The mutation has been previously reported as always associated with complete Lesch-Nyhan phenotype. We analyzed the presence of complete HPRT mRNA in this patient, in two patients with the complete Lesch Nyhan syndrome phenotype, and in control subjects. We found a minor amount of normal HPRT mRNA in the present patient but also in the two patients with splice mutation and the complete Lesch Nyhan syndrome phenotype. To our knowledge, this patient is the first report of a major genetic defect, with no detectable enzymatic activity, and a partial HPRT deficiency phenotype. Our results question the hypothesis of a normally spliced HPRT cDNA as the sole cause of the patient partial phenotype. Copyright © 2010 Elsevier España, S.L. All rights reserved.

  9. Clinical relevance of hepatitis B virus variants

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    The hepatitis B virus (HBV) is a global public health problem with more than 240 million people chronicallyinfected worldwide, who are at risk for end-stage liverdisease and hepatocellular carcinoma. There are anestimated 600000 deaths annually from complications ofHBV-related liver disease. Antiviral therapy with nucleos/tide analogs (NA) targeting the HBV polymerase (P) caninhibit disease progression by long-term suppression ofHBV replication. However, treatment may fail with firstgeneration NA therapy due to the emergence of drugresistantmutants, as well as incomplete medicationadherence. The HBV replicates via an error-prone reversetranscriptase leading to quasispecies. Due to overlappingopen reading frames mutations within the HBV P cancause concomitant changes in the HBV surface gene (S )and vice versa. HBV quasispecies diversity is associatedwith response to antiviral therapy, disease severity andlong-term clinical outcomes. Specific mutants havebeen associated with antiviral drug resistance, immuneescape, liver fibrosis development and tumorgenesis.An understanding of HBV variants and their clinicalrelevance may be important for monitoring chronichepatitis B disease progression and treatment response.In this review, we will discuss HBV molecular virology,mechanism of variant development, and their potentialclinical impact.

  10. Canonical and variant histones of protozoan parasites.

    Science.gov (United States)

    Dalmasso, Maria Carolina; Sullivan, William Joseph; Angel, Sergio Oscar

    2011-06-01

    Protozoan parasites have tremendously diverse lifestyles that require adaptation to a remarkable assortment of different environmental conditions. In order to complete their life cycles, protozoan parasites rely on fine-tuning gene expression. In general, protozoa use novel regulatory elements, transcription factors, and epigenetic mechanisms to regulate their transcriptomes. One of the most surprising findings includes the nature of their histones--these primitive eukaryotes lack some histones yet harbor novel histone variants of unknown function. In this review, we describe the histone components of different protozoan parasites based on literature and database searching. We summarize the key discoveries regarding histones and histone variants and their impact on chromatin regulation in protozoan parasites. In addition, we list histone genes IDs, sequences, and genomic localization of several protozoan parasites and Microsporidia histones, obtained from a thorough search of genome databases. We then compare these findings with those observed in higher eukaryotes, allowing us to highlight some novel aspects of epigenetic regulation in protists and to propose questions to be addressed in the upcoming years.

  11. Flavonoids as Inhibitors of Human Butyrylcholinesterase Variants

    Directory of Open Access Journals (Sweden)

    Maja Katalinić

    2014-01-01

    Full Text Available The inhibition of butyrylcholinesterase (BChE, EC 3.1.1.8 appears to be of interest in treating diseases with symptoms of reduced neurotransmitter levels, such as Alzheimer’s disease. However, BCHE gene polymorphism should not be neglected in research since it could have an effect on the expected outcome. Several well-known cholinergic drugs (e.g. galantamine, huperzine and rivastigmine originating from plants, or synthesised as derivatives of plant compounds, have shown that herbs could serve as a source of novel target-directed compounds. We focused our research on flavonoids, biologically active polyphenolic compounds found in many plants and plant-derived products, as BChE inhibitors. All of the tested flavonoids: galangin, quercetin, fisetin and luteolin reversibly inhibited usual, atypical, and fluoride-resistant variants of human BChE. The inhibition potency increased in the following order, identically for all three BChE variants: luteolin

  12. Kenny-Caffey syndrome: an Arab variant?

    Science.gov (United States)

    Sabry, M A; Farag, T I; Shaltout, A A; Zaki, M; Al-Mazidi, Z; Abulhassan, S J; Al-Torki, N; Quishawi, A; Al Awadi, S A

    1999-01-01

    We describe 2 unrelated Bedouin girls who met the criteria for the diagnosis of Kenny-Caffey syndrome. The girls had some unusual features--microcephaly and psychomotor retardation--that distinguish the Kenny-Caffey syndrome profile in Arab children from the classical Kenny-Caffey syndrome phenotype characterized by macrocephaly and normal intelligence. The 2 girls did not harbor the 22q11 microdeletion (the hallmark of the DiGeorge cluster of diseases) that we previously reported in another Bedouin family with the Kenny-Caffey syndrome (Sabry et al. J Med Genet 1998: 35(1): 31-36). This indicates considerable genetic heterogeneity for this syndrome. We also review previously reported 44 Arab/Bedouin patients with the same profile of hypoparathyroidism, short stature, seizures, mental retardation and microcephaly. Our results suggest that these patients represent an Arab variant of Kenny-Caffey syndrome with characteristic microcephaly and psychomotor retardation. We suggest that all patients with Kenny-Caffey syndrome should be investigated for the 22q11 microdeletion. Other possible genetic causes for the Kenny-Caffey syndrome or its Arab variant include chromosome 10p abnormalities.

  13. Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease

    OpenAIRE

    Pfeiffer Ronald F; Rudolph Alice; Halter Cheryl A; Pauciulo Michael W; Kissell Diane K; Pankratz Nathan; Simon David K; Nichols William C; Foroud Tatiana

    2010-01-01

    Abstract Background Mitochondrial function is impaired in Parkinson's disease (PD) and may contribute to the pathogenesis of PD, but the causes of mitochondrial impairment in PD are unknown. Mitochondrial dysfunction is recapitulated in cell lines expressing mitochondrial DNA (mtDNA) from PD patients, implicating mtDNA variants or mutations, though the role of mtDNA variants or mutations in PD risk remains unclear. We investigated the potential contribution of mtDNA variants or mutations to t...

  14. Rare variant detection using family-based sequencing analysis.

    Science.gov (United States)

    Peng, Gang; Fan, Yu; Palculict, Timothy B; Shen, Peidong; Ruteshouser, E Cristy; Chi, Aung-Kyaw; Davis, Ronald W; Huff, Vicki; Scharfe, Curt; Wang, Wenyi

    2013-03-05

    Next-generation sequencing is revolutionizing genomic analysis, but this analysis can be compromised by high rates of missing true variants. To develop a robust statistical method capable of identifying variants that would otherwise not be called, we conducted sequence data simulations and both whole-genome and targeted sequencing data analysis of 28 families. Our method (Family-Based Sequencing Program, FamSeq) integrates Mendelian transmission information and raw sequencing reads. Sequence analysis using FamSeq reduced the number of false negative variants by 14-33% as assessed by HapMap sample genotype confirmation. In a large family affected with Wilms tumor, 84% of variants uniquely identified by FamSeq were confirmed by Sanger sequencing. In children with early-onset neurodevelopmental disorders from 26 families, de novo variant calls in disease candidate genes were corrected by FamSeq as mendelian variants, and the number of uniquely identified variants in affected individuals increased proportionally as additional family members were included in the analysis. To gain insight into maximizing variant detection, we studied factors impacting actual improvements of family-based calling, including pedigree structure, allele frequency (common vs. rare variants), prior settings of minor allele frequency, sequence signal-to-noise ratio, and coverage depth (∼20× to >200×). These data will help guide the design, analysis, and interpretation of family-based sequencing studies to improve the ability to identify new disease-associated genes.

  15. Behavioral variant frontotemporal dementia with dominant gait disturbances - case report.

    Directory of Open Access Journals (Sweden)

    Wojciech Guenter

    2016-04-01

    Presented case emphasises the significance of accurately gathered anamnesis with patient and his family. Behavioural variant frontotemporal dementia should be considered in cases of unexplained gait abnormalities.

  16. A unified phylogeny-based nomenclature for histone variants

    Directory of Open Access Journals (Sweden)

    Talbert Paul B

    2012-06-01

    Full Text Available Abstract Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.

  17. Phenotypic and Enzymatic Comparative Analysis of the KPC Variants, KPC-2 and Its Recently Discovered Variant KPC-15

    OpenAIRE

    Dongguo Wang; Jiayu Chen; Linjun Yang; Yonghua Mou; Yijun Yang

    2014-01-01

    Sixteen different variants (KPC-2 to KPC-17) in the KPC family have been reported, and most current studies are focusing on KPC-2 and KPC-3. The KPC-15 variant, which isolated from Klebsiella pneumoniae in a Chinese hospital, was a recently discovered KPC enzyme. To compare the characteristics of KPC-15 and KPC-2, the variants were determined by susceptibility testing, PCR amplification and sequencing, and study of kinetic parameters. The strain harboring the KPC-15 showed resistance to 18 co...

  18. Current conveyors variants, applications and hardware implementations

    CERN Document Server

    Senani, Raj; Singh, A K

    2015-01-01

    This book serves as a single-source reference to Current Conveyors and their use in modern Analog Circuit Design. The authors describe the various types of current conveyors discovered over the past 45 years, details of all currently available, off-the-shelf integrated circuit current conveyors, and implementations of current conveyors using other, off-the-shelf IC building blocks. Coverage includes prominent bipolar/CMOS/Bi-CMOS architectures of current conveyors, as well as all varieties of starting from third generation current conveyors to universal current conveyors, their implementations and applications. •Describes all commercially available off-the-shelf IC current conveyors, as well as hardware implementations of current conveyors using other off-the-shelf ICs; • Describes numerous variants of current conveyors evolved over the past forty five years; • Describes a number of Bipolar/CMOS/Bi-CMOS architectures of current conveyors, along with their characteristic features; • Includes a comprehe...

  19. Genetic variants in periodontal health and disease

    Energy Technology Data Exchange (ETDEWEB)

    Dumitrescu, Alexandrina L. [Tromsoe Univ. (Norway). Inst. of Clinical Dentistry; Kobayashi, Junya [Kyoto Univ. (Japan). Dept. of Genome Repair Dynamics

    2010-07-01

    Periodontitis is a complex, multifactorial disease and its susceptibility is genetically determined. The present book systematically reviews the evidence of the association between the genetic variants and periodontitis progression and/or treatment outcomes. Genetic syndromes known to be associated with periodontal disease, the candidate gene polymorphisms investigated in relation to periodontitis, the heritability of chronic and aggressive periodontitis, as well as common guidelines for association studies are described. This growing understanding of the role of genetic variation in inflammation and periodontal chronic disease presents opportunities to identify healthy persons who are at increased risk of disease and to potentially modify the trajectory of disease to prolong healthy aging. The book represents a new concept in periodontology with its pronounced focus on understanding through knowledge rather than presenting the presently valid answers. Connections between genetics and periodontology are systematically reviewed and covered in detail. (orig.)

  20. A look-ahead variant of TFQMR

    Energy Technology Data Exchange (ETDEWEB)

    Freund, R.W. [AT& T Bell Labs., Murray Hill, NJ (United States); Nachtigal, N.M. [Oak Ridge National Lab., TN (United States)

    1994-12-31

    Recently, Freund proposed a Krylov subspace iteration, the transpose-free quasi-minimal residual method (TFQMR), for solving general nonsingular non-Hermitian linear systems. The algorithm relies on a version of the squared Lanczos process to generate the basis vectors for the underlying Krylov subspace. It then constructs iterates defined by a quasi-minimization property, which leads to a smooth and nearly monotone convergence behavior. The authors investigate a variant of TFQMR that uses look-ahead to avoid some of the problems associated with breakdowns in the underlying squared Lanczos procedure. They also present some numerical examples that illustrate the properties of the new method, as compared to the original TFQMR algorithm.

  1. Genetic variants associated with lung function

    DEFF Research Database (Denmark)

    Thyagarajan, Bharat; Wojczynski, Mary; Minster, Ryan L

    2014-01-01

    BACKGROUND: Reduced forced expiratory volume in 1 second (FEV1) and the ratio of FEV1 to forced vital capacity (FVC) are strong predictors of mortality and lung function is higher among individuals with exceptional longevity. However, genetic factors associated with lung function in individuals...... with exceptional longevity have not been identified. METHOD: We conducted a genome wide association study (GWAS) to identify novel genetic variants associated with lung function in the Long Life Family Study (LLFS) (n = 3,899). Replication was performed using data from the CHARGE/SpiroMeta consortia...... used the residuals of the FEV1 and FEV1/FVC, adjusted for age, sex, height, ancestry principal components (PCs), smoking status, pack-years, and field center. RESULTS: We identified nine SNPs in strong linkage disequilibrium in the CYP2U1 gene to be associated with FEV1 and a novel SNP (rs889574...

  2. Some variants of SAT and their properties

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new model for the well-known problem, the satisfiablility problem of boolean formula (SAT), is introduced. Based on this model, some variants of SAT and their properties are presented. Denote by NP the class of all languages which can be decided by a non-deterministic polynomial Turing machine and by P the class of all languages which can be decided by a deterministic polynomial-time Turing machine. This model also allows us to give another candidate for the natural problems in ((NP-NPC)-P), denoted as NPI, under the assumption P≠NP, where NPC represents NP-complete. It is proven that this candidate is not in NPC under P≠NP. While, it is indeed in NPI under some stronger but reasonable assumption, specifically, under the Exponential-Time Hypothesis (ETH). Thus we can partially solve this long standing important open problem.

  3. Sturge -Weber Syndrome - Three Classic variants

    Directory of Open Access Journals (Sweden)

    R S Sathawane

    2006-01-01

    Full Text Available Sturge-Weber syndrome (SWS, also known as encephalotrigeminal angiomatosis, a sporadic, non-familial, congenital disorder consists of congenital hamartomatous malformations that may affect the eye, skin and central nervous system at different times. Sturge-Weber syndrome is classified as 1 Complete trisymptomatic: - when all three organ systems i.e. eye, skin and CNS are involved 2 Incomplete bisymptomatic:- when the involvement is either oculocutaneous or neurocutaneous, and 3 Incomplete monosymptomatic: when there is only neural or cutaneous involvement. Failure of proper vascular development is believed to be the most likely cause of this condition. The malformed blood vessels or hemangiomas may lead to port-wine stain, epilepsy and glaucoma depending on its location. Three classic variants with typical findings are discussed.

  4. Development of industrial variant specification systems

    DEFF Research Database (Denmark)

    Hansen, Benjamin Loer

    With globalisation and increased competition industrial companies must be prepared to satisfy individual customer needs and still stay competitive with regards to lead times, quality, and prices. These factors require companies to be better prepared to handle specification activities during order...... acquisition and order fulfilment, i.e. the creation of drawings, bill-of-materials, routings, product descriptions, quote letters etc. The present thesis is rooted in the assumption that variant specification systems supporting the cross-functional processes of order acquisition and order fulfilment must...... 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...

  5. Lipoleiomyoma: A rare variant of uterine leiomyoma

    Directory of Open Access Journals (Sweden)

    D Manimaran

    2014-01-01

    Full Text Available Uterine fatty tumors are rare variants of benign leiomyoma. Lipoleiomyoma, lipomyoma, fibromyolipoma are various synonyms for this lesion. They usually occur in the obese perimenopausal and postmenopausal females in the age group 50-70 years and 90% cases occur in patients older than 40 years. There were only few cases reported in the literature. These lesions are interesting due to the occasional diagnostic confusion with sarcomas and the curiosity regarding its histogenesis. We are presenting three cases of lipoleiomyoma whose age ranged from 40 to 50 years with clinical, radiologic and pathologic correlation. All three cases came with complaints of abnormal vaginal bleeding and found to have intramural heteroechoic nodule in the ultrasonogram.

  6. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  7. Nuclear variants of bone morphogenetic proteins

    Directory of Open Access Journals (Sweden)

    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.

  8. New Variants of Ant Colony Optimization for Network Routing

    Directory of Open Access Journals (Sweden)

    Debasmita Mukherjee

    2012-12-01

    Full Text Available This paper suggests new variants of Ant Colony Optimization(ACOTechniques for Network Routing. There are three existing variants of ACO based on pheromone deposit calculation. In our earlier work we suggested three different heuristics for selecting the next node at each step of iteration. Incorporation of these heuristics in each of the above three variants result into nine variations. In this paper the performance of these nine variations has been studied. Moreover, we have modified the pheromone deposit calculation considering the transmission time of each successful packet(ant and incorporated this new pheromone update formula in each of the nine variants. As a result, we have obtained nine new variants of ACO. The performance of these new nine variants has been compared with previous ones with respect to the speed of execution, throughput and the number of successful packets. The experiments have been performed over two different network topologies. In one of the variant a tabu list has been incorporated. The length of the tabu list plays a vital role in improving the performance of the routing algorithm. In this paper it has been observed that the new variations of ACO have outperformed the previous ones. These new variants can perform efficient network routing in an environment having variable transmission time along the paths due to congestion or poor link quality.

  9. Managing Process Variants in the Process Life Cycle

    NARCIS (Netherlands)

    Hallerbach, A.; Bauer, Th.; Reichert, M.U.

    2007-01-01

    When designing process-aware information systems, often variants of the same process have to be specified. Each variant then constitutes an adjustment of a particular process to specific requirements building the process context. Current Business Process Management (BPM) tools do not adequately supp

  10. 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 exte

  11. 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.

  12. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis

    NARCIS (Netherlands)

    van Es, M.A.; Schelhaas, H.J.; van Vught, P.W.; Ticozzi, N.; Andersen, P.M.; Groen, E.J.; Schulte, C.; Blauw, H.M.; Koppers, M.; Diekstra, F.P.; Fumoto, K.; Leclerc, A.L.; Keagle, P.; Bloem, B.R.; Scheffer, H.; van Nuenen, B.F.; van Blitterswijk, M.; van Rheenen, W.; Wills, A.M.; Lowe, P.P.; Hu, G.F.; Yu, W.; Kishikawa, H.; Wu, D.; Folkerth, R.D.; Mariani, C.; Goldwurm, S.; Pezzoli, G.; van Damme, P.A.; Lemmens, R.; Dahlberg, C.; Birve, A.; Fernandez-Santiago, R.; Waibel, S.; Klein, C.; Weber, M.; van der Kooi, A.J.; de Visser, M.; Verbaan, D.; van Hilten, J.J.; Heutink, P.; Hennekam, E.A.; Cuppen, E.; Berg, D.; Brown Jr., R.H.; Silani, V.; Gasser, T.; Ludolph, A.C.; Robberecht, W.; Ophoff, R.A.; Veldink, J.H.; Pasterkamp, R.J.; Bakker, P.A.H.M.; Landers, J.E.; van de Warrenburg, B.P.; van den Berg, L.

    2011-01-01

    OBJECTIVE: Several studies have suggested an increased frequency of variants in the gene encoding angiogenin (ANG) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS

  13. Rare variants in PLXNA4 and Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Eva C Schulte

    Full Text Available Approximately 20% of individuals with Parkinson's disease (PD report a positive family history. Yet, a large portion of causal and disease-modifying variants is still unknown. We used exome sequencing in two affected individuals from a family with late-onset familial PD followed by frequency assessment in 975 PD cases and 1014 ethnically-matched controls and linkage analysis to identify potentially causal variants. Based on the predicted penetrance and the frequencies, a variant in PLXNA4 proved to be the best candidate and PLXNA4 was screened for additional variants in 862 PD cases and 940 controls, revealing an excess of rare non-synonymous coding variants in PLXNA4 in individuals with PD. Although we cannot conclude that the variant in PLXNA4 is indeed the causative variant, these findings are interesting in the light of a surfacing role of axonal guidance mechanisms in neurodegenerative disorders but, at the same time, highlight the difficulties encountered in the study of rare variants identified by next-generation sequencing in diseases with autosomal dominant or complex patterns of inheritance.

  14. The Structural Determinants behind the Epigenetic Role of Histone Variants

    Directory of Open Access Journals (Sweden)

    Manjinder S. Cheema

    2015-07-01

    Full Text Available Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.

  15. 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.

  16. 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...

  17. Two new variants of the manifold-mapping technique

    NARCIS (Netherlands)

    Echeverria, D.

    2006-01-01

    Manifold-mapping is an efficient surrogate-based optimization technique aimed at the acceleration of very time-consuming design problems. In this paper we present two new variants of the original algorithm that make it applicable to a broader range of optimization scenarios. The first variant is use

  18. denovo-db: a compendium of human de novo variants.

    Science.gov (United States)

    Turner, Tychele N; Yi, Qian; Krumm, Niklas; Huddleston, John; Hoekzema, Kendra; F Stessman, Holly A; Doebley, Anna-Lisa; Bernier, Raphael A; Nickerson, Deborah A; Eichler, Evan E

    2017-01-04

    Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db.gs.washington.edu), a database for human de novo variants. As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant. We included a feature on our browsable website to download any query result, including a downloadable file of the full database with additional variant details. denovo-db provides necessary information for researchers to compare their data to other individuals with the same phenotype and also to controls allowing for a better understanding of the biology of de novo variants and their contribution to disease. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Rare variants in XRCC2 as breast cancer susceptibility alleles

    NARCIS (Netherlands)

    Hilbers, F.S.; Wijnen, J.T.; Hoogerbrugge-van der Linden, N.; Oosterwijk, J.C.; Collee, M.J.; Peterlongo, P.; Radice, P.; Manoukian, S.; Feroce, I.; Capra, F.; Couch, F.J.; Wang, X.; Guidugli, L.; Offit, K.; Shah, S.; Campbell, I.G.; Thompson, E.R.; James, P.A.; Trainer, A.H.; Gracia, J.; Benitez, J.; Asperen, C.J. van; Devilee, P.

    2012-01-01

    BACKGROUND: Recently, rare germline variants in XRCC2 were detected in non-BRCA1/2 familial breast cancer cases, and a significant association with breast cancer was reported. However, the breast cancer risk associated with these variants needs further evaluation. METHODS: The coding regions and exo

  20. Isolation and characterization of human rhinovirus antigenic variants

    Energy Technology Data Exchange (ETDEWEB)

    Watson, D.G.

    1985-01-01

    Isolation of antigenic variants of human rhinovirus types 2, 14, and 17 was attempted by plaquing untreated virus (P-isolates), selecting variants in the presence of homologous antiserum (C-isolates), and by selecting variants in the presence of antibody following 5-fluorouracil mutagenesis (M-isolates). All viruses were triple-plaque purified and purity neutralization tested prior to isolate selection. Based on a fourfold reduction in neutralizing antibody titer to homologous antiserum, no antigenic variation was found in P-isolates from the three serotypes examined. Antigenic variants of all three serotypes could be isolated by the antiserum selection method (C-isolates). However, antigenic variants of RV17 were isolated at a much higher frequency and showed a larger degree of variation than those of RV2 and RV14. At least two of the variants selected, RV17 (C301) and RV2 (M803), failed to be neutralized by the known 89 rhinovirus antiserum. SDS-polyacrylamide gel electrophoresis of (/sup 35/S) methionine-labelled virion polypeptides revealed that each serotype had a characteristic pattern and that selected RV2 and RV17 isolates had patterns identical to those of the prototype strains. By isoelectric focusing an antigenic variant of RV2 was shown to contain altered virion polypeptides VP1 and VP2 whereas two RV17 antigenic variants demonstrated alterations only in the VP1 polypeptide.

  1. ADULT VARIANT BARTTER’S SYNDROME- A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Ishwar Sidappa Hasabi

    2017-02-01

    Full Text Available BACKGROUND Bartter syndrome is a group of channelopathies with different genetic origins and molecular pathophysiologies, but sharing common feature of decreased tubular transport of sodium chloride in thick ascending loop of Henle (TAL, 1 although more common in antenatal group. Classic adult variant of Bartter syndrome is a rare entity. We hereby present a rare adult variant of classic Bartter syndrome.

  2. 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 b...

  3. Pathological assessment of mismatch repair gene variants in Lynch syndrome

    DEFF Research Database (Denmark)

    Rasmussen, Lene Juel; Heinen, Christopher D; Royer-Pokora, Brigitte;

    2012-01-01

    . Also, identifying family members that do not carry the variant is important so they can be released from the intensive surveillance. Determining which genetic variants are pathogenic and which are neutral is a major challenge in clinical genetics. The profound mechanistic knowledge on the genetics...

  4. 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.

  5. Variante oncocítica del carcinoma mucoepidermoide Oncocyte variant of mucoepidermoid carcinoma

    Directory of Open Access Journals (Sweden)

    Sirced Salazar Rodríguez

    2011-03-01

    Full Text Available El carcinoma mucoepidermoide es el más común de todos los tumores malignos de glándulas salivales, constituye el 30 % de ellos. Aproximadamente la mitad de los casos (53 % ocurre en las glándulas salivales mayores. El 45 % predomina en glándula parótida, el 7 % en la submandibular y el 1 % en la glándula sublingual. Este tumor se presenta con más frecuencia en el sexo femenino (3:2 y en la quinta década de la vida. Múltiples variantes, con diferentes rangos de diferenciación han sido descritas, se incluyen: la oncocítica, esclerosante, uniquística, sebácea, de células claras, células globosas de alto grado, células fusocelular y psamomatosa. El carcinoma mucoepidermoide variante oncocítica es un subtipo raro que puede mostrar prominentes cambios oncocíticos. Se reporta un caso de carcinoma mucoepidermoide variante oncocítica de alto grado histológico. El índice de Ki 67 fue del 5 %, el tumor fue negativo para C-erb2 y presentó inmunorreactividad para E-caderina y Syndecan-1.The mucoepidermoid carcinoma is the commonest of all malignant tumors of salivary glands, accounting for the 30 % of them. Approximately the half of cases (53 % occurs in the major salivary glands. The 45 % has predominance in parotid gland, the 7 % in the submandibular one, and the 1 % in the sublingual gland one. This type of tumor is more frequent in female sex (3-2 and at fifth decade of life. Multiple variants with different ranks have been described including the oncocyte, sclerosant, unicystic, sebaceous, of clear cells, high degree spherical cells, fusocellular and psammomatous. The mucoepidermoid carcinoma, oncocyte variant, is an unusual subtype that may to shows significant oncocyte changes. Authors report a case of histological high degree mucoepidermoid carcinoma. The rate of Ki 67 was of 5 %, the negative tumor for C-erb2 and had immunoreaction to E-caderine and Syndecan-1.

  6. Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics

    NARCIS (Netherlands)

    Hu, Y.J.; Berndt, S.I.; Gustafsson, S.; Ganna, A.; Hirschhorn, J.; North, K.E.; Ingelsson, E.; Lin, D.Y.; Kiemeney, L.A.L.M.; Vermeulen, S.

    2013-01-01

    Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rar

  7. αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia

    Science.gov (United States)

    Buitrago, Lorena; Rendon, Augusto; Liang, Yupu; Simeoni, Ilenia; Negri, Ana; Filizola, Marta; Ouwehand, Willem H.; Coller, Barry S.; Alessi, Marie-Christine; Ballmaier, Matthias; Bariana, Tadbir; Bellissimo, Daniel; Bertoli, Marta; Bray, Paul; Bury, Loredana; Carrell, Robin; Cattaneo, Marco; Collins, Peter; French, Deborah; Favier, Remi; Freson, Kathleen; Furie, Bruce; Germeshausen, Manuela; Ghevaert, Cedric; Gomez, Keith; Goodeve, Anne; Gresele, Paolo; Guerrero, Jose; Hampshire, Dan J.; Hadinnapola, Charaka; Heemskerk, Johan; Henskens, Yvonne; Hill, Marian; Hogg, Nancy; Johnsen, Jill; Kahr, Walter; Kerr, Ron; Kunishima, Shinji; Laffan, Michael; Natwani, Amit; Neerman-Arbez, Marguerite; Nurden, Paquita; Nurden, Alan; Ormiston, Mark; Othman, Maha; Ouwehand, Willem; Perry, David; Vilk, Shoshana Ravel; Reitsma, Pieter; Rondina, Matthew; Simeoni, Ilenia; Smethurst, Peter; Stephens, Jonathan; Stevenson, William; Szkotak, Artur; Turro, Ernest; Van Geet, Christel; Vries, Minka; Ward, June; Waye, John; Westbury, Sarah; Whiteheart, Sidney; Wilcox, David; Zhang, Bi

    2015-01-01

    Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin αIIbβ3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the ThromboGenomics project, comprising ∼32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting ∼11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting ∼9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of αIIbβ3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. αIIb P176H and β3 C547G severely reduced αIIbβ3 expression, whereas αIIb P943A partially reduced αIIbβ3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69–98% sensitivity in detecting GT mutations, between 27% and 71% of the novel αIIb or β3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on αIIbβ3 and highlight the challenges in predicting the clinical significance of novel missense variants. PMID:25827233

  8. Rare variant analysis for family-based design.

    Directory of Open Access Journals (Sweden)

    Gourab De

    Full Text Available Genome-wide association studies have been able to identify disease associations with many common variants; however most of the estimated genetic contribution explained by these variants appears to be very modest. Rare variants are thought to have larger effect sizes compared to common SNPs but effects of rare variants cannot be tested in the GWAS setting. Here we propose a novel method to test for association of rare variants obtained by sequencing in family-based samples by collapsing the standard family-based association test (FBAT statistic over a region of interest. We also propose a suitable weighting scheme so that low frequency SNPs that may be enriched in functional variants can be upweighted compared to common variants. Using simulations we show that the family-based methods perform at par with the population-based methods under no population stratification. By construction, family-based tests are completely robust to population stratification; we show that our proposed methods remain valid even when population stratification is present.

  9. Private mitochondrial DNA variants in danish patients with hypertrophic cardiomyopathy.

    Directory of Open Access Journals (Sweden)

    Christian M Hagen

    Full Text Available Hypertrophic cardiomyopathy (HCM is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA haplogroups are susceptibility factors for HCM. Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446 variants. After elimination of 312 (69.9% non-coding and synonymous variants, a further 109 (24.4% with a global prevalence > 0.1%, three (0.7% haplogroup associated and 19 (2.0% variants with a low predicted in silico likelihood of pathogenicity, three variants: MT-TC: m.5772G>A, MT-TF: m.644A>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM.

  10. Sialyloligosaccharide receptors of binding variants of polyoma virus.

    Science.gov (United States)

    Cahan, L D; Singh, R; Paulson, J C

    1983-10-30

    Hemagglutination and lytic infection of host cells by polyoma virus has been shown to require specific sialyloligosaccharide structures. The nature of the sialyloligosaccharide sequence recognized by three binding variants of polyoma virus, the large plaque (LP), small plaque (SP), and Py235 variants, was examined. Hemagglutination of native erythrocytes and erythrocytes derivatized with highly specific sialyltransferases to contain cell surface sialyloligosaccharides of defined sequence was compared for the three variants. In addition, soluble glycoprotein inhibitors of known sialyloligosaccharide structure were used to further elucidate the specificities of the three variants. There are important differences in the receptors for these variants. While all three appear to bind the structure NeuAc alpha 2,3Gal beta 1,3GalNAc the LP and Py235 variant bind the disialyl structure NeuAc alpha 2,3Gal beta 1,3(NeuAc alpha 2,6)GalNAc with much lower affinity than does the SP virus. It is suggested that polyoma virus adsorption to cells may depend on the cell surface content of at least three different sialyloligosaccharide sequences and the relative abilities of the virus variant to utilize them as receptor determinants.

  11. How important are rare variants in common disease?

    Science.gov (United States)

    Saint Pierre, Aude; Génin, Emmanuelle

    2014-09-01

    Genome-wide association studies have uncovered hundreds of common genetic variants involved in complex diseases. However, for most complex diseases, these common genetic variants only marginally contribute to disease susceptibility. It is now argued that rare variants located in different genes could in fact play a more important role in disease susceptibility than common variants. These rare genetic variants were not captured by genome-wide association studies using single nucleotide polymorphism-chips but with the advent of next-generation sequencing technologies, they have become detectable. It is now possible to study their contribution to common disease by resequencing samples of cases and controls or by using new genotyping exome arrays that cover rare alleles. In this review, we address the question of the contribution of rare variants in common disease by taking the examples of different diseases for which some resequencing studies have already been performed, and by summarizing the results of simulation studies conducted so far to investigate the genetic architecture of complex traits in human. So far, empirical data have not allowed the exclusion of many models except the most extreme ones involving only a small number of rare variants with large effects contributing to complex disease. To unravel the genetic architecture of complex disease, case-control data will not be sufficient, and alternative study designs need to be proposed together with methodological developments.

  12. The Clinical Significance of Unknown Sequence Variants in BRCA Genes

    Energy Technology Data Exchange (ETDEWEB)

    Calò, Valentina; Bruno, Loredana; Paglia, Laura La; Perez, Marco; Margarese, Naomi [Department of Surgery and Oncology, Regional Reference Center for the Biomolecular Characterization and Genetic Screening of Hereditary Tumors, University of Palermo, Via del Vespro 127, 90127 Palermo (Italy); Gaudio, Francesca Di [Department of Medical Biotechnologies and Legal Medicine, University of Palermo, Palermo (Italy); Russo, Antonio, E-mail: lab-oncobiologia@usa.net [Department of Surgery and Oncology, Regional Reference Center for the Biomolecular Characterization and Genetic Screening of Hereditary Tumors, University of Palermo, Via del Vespro 127, 90127 Palermo (Italy)

    2010-09-10

    Germline mutations in BRCA1/2 genes are responsible for a large proportion of hereditary breast and/or ovarian cancers. Many highly penetrant predisposition alleles have been identified and include frameshift or nonsense mutations that lead to the translation of a truncated protein. Other alleles contain missense mutations, which result in amino acid substitution and intronic variants with splicing effect. The discovery of variants of uncertain/unclassified significance (VUS) is a result that can complicate rather than improve the risk assessment process. VUSs are mainly missense mutations, but also include a number of intronic variants and in-frame deletions and insertions. Over 2,000 unique BRCA1 and BRCA2 missense variants have been identified, located throughout the whole gene (Breast Cancer Information Core Database (BIC database)). Up to 10–20% of the BRCA tests report the identification of a variant of uncertain significance. There are many methods to discriminate deleterious/high-risk from neutral/low-risk unclassified variants (i.e., analysis of the cosegregation in families of the VUS, measure of the influence of the VUSs on the wild-type protein activity, comparison of sequence conservation across multiple species), but only an integrated analysis of these methods can contribute to a real interpretation of the functional and clinical role of the discussed variants. The aim of our manuscript is to review the studies on BRCA VUS in order to clarify their clinical relevance.

  13. Identification of copy number variants in horses

    KAUST Repository

    Doan, R.

    2012-03-01

    Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.

  14. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how the resul......The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how...... the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  15. CRY2 genetic variants associate with dysthymia.

    Directory of Open Access Journals (Sweden)

    Leena Kovanen

    Full Text Available People with mood disorders often have disruptions in their circadian rhythms. Recent molecular genetics has linked circadian clock genes to mood disorders. Our objective was to study two core circadian clock genes, CRY1 and CRY2 as well as TTC1 that interacts with CRY2, in relation to depressive and anxiety disorders. Of these three genes, 48 single-nucleotide polymorphisms (SNPs whose selection was based on the linkage disequilibrium and potential functionality were genotyped in 5910 individuals from a nationwide population-based sample. The diagnoses of major depressive disorder, dysthymia and anxiety disorders were assessed with a structured interview (M-CIDI. In addition, the participants filled in self-report questionnaires on depressive and anxiety symptoms. Logistic and linear regression models were used to analyze the associations of the SNPs with the phenotypes. Four CRY2 genetic variants (rs10838524, rs7121611, rs7945565, rs1401419 associated significantly with dysthymia (false discovery rate q<0.05. This finding together with earlier CRY2 associations with winter depression and with bipolar type 1 disorder supports the view that CRY2 gene has a role in mood disorders.

  16. 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.

  17. Migraine variants--occurrence in pediatric neurology practice.

    Science.gov (United States)

    Pacheva, Iliyana H; Ivanov, Ivan S

    2013-09-01

    Migraine is common in pediatric neurology practice, while migraine variants are rare and pose diagnostic problems. The aim was to establish the occurrence of migraine variants in pediatric neurology practice and among migraine, and to discuss their presentation. The files of 2509 newly diagnosed patients, aged 0-18 years, treated as in- and out-patients in the Neuropediatric Ward at the Plovdiv Medical University Hospital between 2002 and 2006 were examined retrospectively. Migraine forms were diagnosed according to ICHD-II. Benign paroxysmal torticolis and alternating hemiplegia of childhood were also accepted as migraine variants according to proposed diagnostic criteria in the appendix of ICHD-II. Some specific forms like acute confusional migraine (ACM), Alice in wonderland syndrome (AWS), ophthalmoplegic migraine were also diagnosed although not included as migraine variants in the ICHD-II classification. 111 patients met diagnostic criteria for migraine. Patients with migraine variants comprised 24.3% of migrainous cases. Basilar type migraine was the most common (6.3% of all migrainous patients), followed by benign paroxysmal vertigo (5.4%), hemiplegic migraine (3.6%), ACM (2.7%), benign paroxysmal torticolis (2.7%), typical aura without headache (1.8%), abdominal migraine (1.8%), AWS (0.9%), ophthalmoplegic migraine (0.9%) and cyclical vomiting (0.9%). Alternating hemiplegia of childhood and retinal migraine was not found. Some patients either presented or were classified as different migraine variants. Basilar type migraine was the most common migraine variant. ACM and AWS should be regarded as distinct entities in the ICHD as migraine with complex aura. Benign paroxysmal torticollis also deserves its place as a migraine variant. Cases of ophthalmoplegic migraine with spontaneous remission and no cranial nerve enhancement on MRI should be considered as migraine form. Analyzing migraine variants will contribute to better awareness and adequate diagnosis

  18. Geometric Structures of Stable Time-Variant State Feedback Systems

    Institute of Scientific and Technical Information of China (English)

    ZHONG Feng-wei; SUN Hua-fei; ZHANG Zhen-ning

    2007-01-01

    A new technique for considering the stabilizing time-variant state feedback gains is proposed from the viewpoint of information geometry. First, parametrization of the set of all stabilizing time-variant state feedback gains is given. Moreover, a diffeomorphic structure between the set of stabilizing time-variant state feedback gains and the Cartesian product of positive definite matrix and skew symmetric matrix satisfying certain algebraic conditions is constructed. Furth ermore, an immersion and some results about the eigenvalue locations of stable state feedback systems are derived.

  19. De Novo Coding Variants Are Strongly Associated with Tourette Disorder

    DEFF Research Database (Denmark)

    Willsey, A Jeremy; Fernandez, Thomas V; Yu, Dongmei

    2017-01-01

    Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186...... trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably...

  20. The role of common genetic variants in atrial fibrillation

    DEFF Research Database (Denmark)

    Paludan-Muller, Christian; Svendsen, Jesper H.; Olesen, Morten S.

    2016-01-01

    this approach. Highly penetrant variants in lone AF have also been described in a number of cases. Furthermore, familial AF, although rare, have been recognized for many years. Variants associated with AF have been identified in more than 40 genes, including cardiac gap junction proteins, ion channels and beta......This review focuses on the genetic basis of atrial fibrillation (AF) and the role of variants in the susceptibility of developing the disease. AF is the most common cardiac arrhythmia affecting 1-2% of the general population. Studies in the last decade have demonstrated that AF, and in particular...... and non-cardiac diseases....

  1. Variante de Dandy Walker: relato de caso = Dandy Walker variant: a case report

    Directory of Open Access Journals (Sweden)

    Khan, Richard Lester et al.

    2009-01-01

    Full Text Available Objetivos: relatar o caso de um paciente com variante de Dandy Walker, chamando atenção para a importância da suspeita, investigação e manejo das repercussões clínicas. Descrição do caso: é relatado o caso de um paciente do sexo masculino, com quadro clínico e radiológico típico da Variante de Dandy Walker. Durante o pré-natal, através de ecografia obstétrica com 23 semanas e 3 dias, apresentou alterações sugestivas de Síndrome de Dandy Walker. Ao nascimento apresentou exame físico com fenda palatina, criptorquidia à direita, hexodactilia em ambos os pés. Apresentava ainda ecocardiograma com forame oval patente e persistência do canal arterial. O diagnóstico foi estabelecido através da ressonância magnética realizada após o nascimento, que evidenciava hipoplasia do vermis cerebelar, alargamento da fossa posterior e leve dilatação ventricular. Conclusões: este artigo procura caracterizar a variante de Dandy Walker, que é uma malformação congênita do sistema nervoso central e é o tipo mais comum da Síndrome de Dandy Walker. Seu fenótipo é variável, devendo-se sempre pesquisar malformações tanto intra quanto extracranianas, visto que o risco de mortalidade pós-natal aumenta quando existe esta associação. O tratamento envolve equipe multidisciplinar e o prognóstico é reservado, variando conforme o fenótipo.

  2. Variant Boussinesq方程组的精确解%Exact Solutions for Variant Boussinesq Equations

    Institute of Scientific and Technical Information of China (English)

    吴世旭

    2009-01-01

    F-展开法是近年提出的求非线性偏微分方程的精确解的一种简单而有效的方法.本文运用改进的F-展开法寻求Variant Boussinesq方程组的行波解,得到了该方程组多种类型的精确解,包括Jacobi椭圆函数解、孤立波解、三角函数解和有理函数解.

  3. Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects.

    Directory of Open Access Journals (Sweden)

    Nengjun Yi

    2011-12-01

    Full Text Available Complex diseases and traits are likely influenced by many common and rare genetic variants and environmental factors. Detecting disease susceptibility variants is a challenging task, especially when their frequencies are low and/or their effects are small or moderate. We propose here a comprehensive hierarchical generalized linear model framework for simultaneously analyzing multiple groups of rare and common variants and relevant covariates. The proposed hierarchical generalized linear models introduce a group effect and a genetic score (i.e., a linear combination of main-effect predictors for genetic variants for each group of variants, and jointly they estimate the group effects and the weights of the genetic scores. This framework includes various previous methods as special cases, and it can effectively deal with both risk and protective variants in a group and can simultaneously estimate the cumulative contribution of multiple variants and their relative importance. Our computational strategy is based on extending the standard procedure for fitting generalized linear models in the statistical software R to the proposed hierarchical models, leading to the development of stable and flexible tools. The methods are illustrated with sequence data in gene ANGPTL4 from the Dallas Heart Study. The performance of the proposed procedures is further assessed via simulation studies. The methods are implemented in a freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/.

  4. Hierarchical Generalized Linear Models for Multiple Groups of Rare and Common Variants: Jointly Estimating Group and Individual-Variant Effects

    Science.gov (United States)

    Yi, Nengjun; Liu, Nianjun; Zhi, Degui; Li, Jun

    2011-01-01

    Complex diseases and traits are likely influenced by many common and rare genetic variants and environmental factors. Detecting disease susceptibility variants is a challenging task, especially when their frequencies are low and/or their effects are small or moderate. We propose here a comprehensive hierarchical generalized linear model framework for simultaneously analyzing multiple groups of rare and common variants and relevant covariates. The proposed hierarchical generalized linear models introduce a group effect and a genetic score (i.e., a linear combination of main-effect predictors for genetic variants) for each group of variants, and jointly they estimate the group effects and the weights of the genetic scores. This framework includes various previous methods as special cases, and it can effectively deal with both risk and protective variants in a group and can simultaneously estimate the cumulative contribution of multiple variants and their relative importance. Our computational strategy is based on extending the standard procedure for fitting generalized linear models in the statistical software R to the proposed hierarchical models, leading to the development of stable and flexible tools. The methods are illustrated with sequence data in gene ANGPTL4 from the Dallas Heart Study. The performance of the proposed procedures is further assessed via simulation studies. The methods are implemented in a freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/). PMID:22144906

  5. Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

    Science.gov (United States)

    Hu, Yi-Juan; Berndt, Sonja I; Gustafsson, Stefan; Ganna, Andrea; Hirschhorn, Joel; North, Kari E; Ingelsson, Erik; Lin, Dan-Yu

    2013-08-08

    Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.

  6. Myostatin: genetic variants, therapy and gene doping

    Directory of Open Access Journals (Sweden)

    André Katayama Yamada

    2012-09-01

    Full Text Available Since its discovery, myostatin (MSTN has been at the forefront of muscle therapy research because intrinsic mutations or inhibition of this protein, by either pharmacological or genetic means, result in muscle hypertrophy and hyperplasia. In addition to muscle growth, MSTN inhibition potentially disturbs connective tissue, leads to strength modulation, facilitates myoblast transplantation, promotes tissue regeneration, induces adipose tissue thermogenesis and increases muscle oxidative phenotype. It is also known that current advances in gene therapy have an impact on sports because of the illicit use of such methods. However, the adverse effects of these methods, their impact on athletic performance in humans and the means of detecting gene doping are as yet unknown. The aim of the present review is to discuss biosynthesis, genetic variants, pharmacological/genetic manipulation, doping and athletic performance in relation to the MSTN pathway. As will be concluded from the manuscript, MSTN emerges as a promising molecule for combating muscle wasting diseases and for triggering wide-ranging discussion in view of its possible use in gene doping.Desde sua descoberta, a miostatina (MSTN entrou na linha de frente em pesquisas relacionadas às terapias musculares porque mutações intrínsecas ou inibição desta proteína tanto por abordagens farmacológicas como genéticas resultam em hipertrofia muscular e hiperplasia. Além do aumento da massa muscular, a inibição de MSTN potencialmente prejudica o tecido conectivo, modula a força muscular, facilita o transplante de mioblastos, promove regeneração tecidual, induz termogênese no tecido adiposo e aumenta a oxidação na musculatura esquelética. É também sabido que os atuais avanços em terapia gênica têm uma relação com o esporte devido ao uso ilícito de tal método. Os efeitos adversos de tal abordagem, seus efeitos no desempenho de atletas e métodos para detectar doping genético s

  7. Study on Variant Anatomy of Sciatic Nerve

    Science.gov (United States)

    V, Sangeetha

    2014-01-01

    Introduction: Sciatic Nerve (SN) is the nerve of the posterior compartment of thigh formed in the pelvis from the ventral rami of the L4 to S3 spinal nerves. It leaves the pelvis via the greater sciatic foramen below piriformis and divides into Common Peroneal Nerve (CPN) and Tibial Nerve (TN) at the level of the upper angle of the popliteal fossa. Higher division of the sciatic nerve is the most common variation where the TN and CPN may leave the pelvis through different routes. Such variation may lead to compression of the nerve and lead to Non-discogenic sciatica. Materials and Methods: Fifty lower limbs were used for the study from Department of Anatomy, J.J.M.M.C Davangere, Karnataka, India. Observation and Results: In our study on 25 cadavers (50 lower limbs), we have observed 4 (8 %) lower limbs high division of sciatic nerve was noted. High division of sciatic nerve in the back of thigh was noted in one specimen (2%), while high division within the pelvis was noted in 3 specimens (6%), while in 46 (92%) it occurred outside the pelvis. Conclusion: Knowledge regarding such variation and differences in the course of SN is important for the surgeons to plan for various surgical interventions pertaining to the gluteal region. The variant anatomy of SN may cause piriformis syndrome and failure of SN block. Hence present study is undertaken to know the level of division, exit, course, relationship to piriformis and variations in the branching pattern of SN. PMID:25302181

  8. Common Gene Variants Account for Most Genetic Risk for Autism

    Science.gov (United States)

    ... July 20, 2014 Common gene variants account for most genetic risk for autism Roles of heritability, mutations, ... factors. Population-Based Autism Genetics and Environment Study Most of the genetic risk for autism comes from ...

  9. Variant Plasmodium ovale isolated from a patient infected in Ghana

    Directory of Open Access Journals (Sweden)

    Petersen Eskild

    2011-01-01

    Full Text Available Abstract Recent data have found that Plasmodium ovale can be separated in two distinct species: classic and variant P. ovale based on multilocus typing of different genes. This study presents a P. ovale isolate from a patient infected in Ghana together with an analysis of the small subunit RNA, cytochrome b, cytochrome c oxidase I, cysteine protease and lactate dehydrogenase genes, which show that the sample is a variant P. ovale and identical or highly similar to variant P. ovale isolated from humans in South-East Asia and Africa, and from a chimpanzee in Cameroon. The split between the variant and classic P. ovale is estimated to have occurred 1.7 million years ago.

  10. Differential protein expression in phenotypic variants of Streptococcus pneumoniae

    NARCIS (Netherlands)

    K. Overweg (Karin); C.D. Pericone; G.G. Verhoef; J.N. Weiser; H.D. Meiring; A.P. de Jong; R. de Groot (Ronald); P.W.M. Hermans (Peter)

    2000-01-01

    textabstractStreptococcus pneumoniae undergoes spontaneous phase variation resulting in opaque and transparent colony forms. Differences in colony opacity correlate with differences in virulence: the transparent variants are more capable of colonizing the nasopharynx, w

  11. Neuropathology in classical and variant ataxia-telangiectasia.

    NARCIS (Netherlands)

    Verhagen, M.M.M.; Martin, J.J.; Deuren, M. van; Ceuterick-de Groote, C.; Weemaes, C.M.R.; Kremer, B.; Taylor, M.A.; Willemsen, M.A.A.P.; Lammens, M.M.Y.

    2012-01-01

    Ataxia-telangiectasia (A-T) is classically characterized by progressive neurodegeneration, oculocutaneous telangiectasia, immunodeficiency and elevated alpha-fetoprotein levels. Some patients, classified as variant A-T, exhibit a milder clinical course. In the latter patients extrapyramidal symptoms

  12. 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.

  13. Behavioral variant of frontotemporal dementia mimicking Huntington's disease

    DEFF Research Database (Denmark)

    Nielsen, T Rune; Bruhn, Peter; Nielsen, Jørgen E

    2010-01-01

    Behavioral changes and cognitive decline are the core clinical manifestations in the behavioral variant of frontotemporal dementia (bv-FTD). The behavioral changes may include characteristic stereotypic movements. These movements, although without clear purpose, are not involuntary. Involuntary m...

  14. Lipoprotein lipase gene variants: Association with acute myocardial ...

    African Journals Online (AJOL)

    Lipoprotein lipase gene variants: Association with acute myocardial infarction and lipid profiles. ... Therefore, genes involved in lipid and lipoprotein metabolism pathways such as lipoprotein lipase (LPL), are proper candidates ... Article Metrics.

  15. Genetic variant as a marker for bladder cancer therapy

    Science.gov (United States)

    Patients who have inherited a specific common genetic variant develop bladder cancer tumors that strongly express a protein known as prostate stem cell antigen (PSCA), which is also expressed in many pancreatic and prostate tumors, according to research a

  16. Influenza A (H3N2) Variant Virus

    Science.gov (United States)

    ... Error processing SSI file Influenza A (H3N2) Variant Virus Language: English Español Recommend on Facebook Tweet Share Compartir Influenza viruses that normally circulate in pigs are called “ ...

  17. Variant Timekeeping Patterns and Their Effects in Jazz Drumming

    National Research Council Canada - National Science Library

    Butterfield, Matthew W

    2010-01-01

    ...." This essay shows how one modern jazz drummer employs variants of common timekeeping patterns in a more "liquid" way to generate motional energy through the strategic production of metric dissonance...

  18. Leapfrog variants of iterative methods for linear algebra equations

    Science.gov (United States)

    Saylor, Paul E.

    1988-01-01

    Two iterative methods are considered, Richardson's method and a general second order method. For both methods, a variant of the method is derived for which only even numbered iterates are computed. The variant is called a leapfrog method. Comparisons between the conventional form of the methods and the leapfrog form are made under the assumption that the number of unknowns is large. In the case of Richardson's method, it is possible to express the final iterate in terms of only the initial approximation, a variant of the iteration called the grand-leap method. In the case of the grand-leap variant, a set of parameters is required. An algorithm is presented to compute these parameters that is related to algorithms to compute the weights and abscissas for Gaussian quadrature. General algorithms to implement the leapfrog and grand-leap methods are presented. Algorithms for the important special case of the Chebyshev method are also given.

  19. Anorectal agenesis with rectovaginal fistula: A rare/regional variant

    Directory of Open Access Journals (Sweden)

    Subhasis Roy Choudhury

    2017-01-01

    Conclusion: RVF with anorectal agenesis is a rare/regional variant of female ARMs. Clinical examination along with distal colostogram, EUA, and endoscopy clinches the diagnosis. Anorectal reconstruction by posterior sagittal anorectoplasty results in a satisfactory outcome.

  20. Vitiligo, con énfasis en su variante inflamatoria Vitiligo, with emphasis in its inflammatory variant

    Directory of Open Access Journals (Sweden)

    C I Vera

    2009-03-01

    Full Text Available El vitiligo inflamatorio es un trastorno melanocitopénico adquirido, de baja frecuencia con características clínicas e histológicas propias. Ocurre en ambos sexos, a cualquier edad. Su fisiopatogenia parece involucrar mecanismos autoinmunes. En su evolución es frecuente la desaparición del componente inflamatorio que resulta en una mácula hipopigmentada clásica; a ello debe anticiparse también nuestra elección terapéutica. Se describe un paciente con vitiligo inflamatorio de resolución espontánea, junto a una revisión crítica de la bibliografía. Se discute si representa una variante de vitiligo vulgar o una entidad independiente.Inflammatory vitiligo is a low frequency melanocytopenic acquired entity with clinical and histological features of it 's own. It occurs in both sexes at any age. Fisiopathogenesis may involve autoimmune mechanisms. It's evolution most commonly ends up in a classic hypopigmented maculae, therefore our therapeutic choice has to be oriented to this outcome. A patient with inflammatory vitiligo is described along a critical review of the literature. It is discussed if it represents a variant of common vitiligo or an independent entity.

  1. Histone variant innovation in a rapidly evolving chordate lineage

    Directory of Open Access Journals (Sweden)

    Jansen Pascal WTC

    2011-07-01

    Full Text Available Abstract Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.

  2. BIFURCATIONS OF TRAVELLING WAVE SOLUTIONS IN VARIANT BOUSSINESQ EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    YUAN Yu-bo; PU Dong-mei; LI Shu-min

    2006-01-01

    The bifurcations of solitary waves and kink waves for variant Boussinesq equations are studied by using the bifurcation theory of planar dynamical systems. The bifurcation sets and the numbers of solitary waves and kink waves for the variant Boussinesq equations are presented. Several types explicit formulas of solitary waves solutions and kink waves solutions are obtained. In the end, several formulas of periodic wave solutions are presented.

  3. Generalization of Rare Variant Association Tests for Longitudinal Family Studies.

    Science.gov (United States)

    Chien, Li-Chu; Hsu, Fang-Chi; Bowden, Donald W; Chiu, Yen-Feng

    2016-02-01

    Given the functional relevance of many rare variants, their identification is frequently critical for dissecting disease etiology. Functional variants are likely to be aggregated in family studies enriched with affected members, and this aggregation increases the statistical power to detect rare variants associated with a trait of interest. Longitudinal family studies provide additional information for identifying genetic and environmental factors associated with disease over time. However, methods to analyze rare variants in longitudinal family data remain fairly limited. These methods should be capable of accounting for different sources of correlations and handling large amounts of sequencing data efficiently. To identify rare variants associated with a phenotype in longitudinal family studies, we extended pedigree-based burden (BT) and kernel (KS) association tests to genetic longitudinal studies. Generalized estimating equation (GEE) approaches were used to generalize the pedigree-based BT and KS to multiple correlated phenotypes under the generalized linear model framework, adjusting for fixed effects of confounding factors. These tests accounted for complex correlations between repeated measures of the same phenotype (serial correlations) and between individuals in the same family (familial correlations). We conducted comprehensive simulation studies to compare the proposed tests with mixed-effects models and marginal models, using GEEs under various configurations. When the proposed tests were applied to data from the Diabetes Heart Study, we found exome variants of POMGNT1 and JAK1 genes were associated with type 2 diabetes.

  4. Five Rare β Globin Chain Hemoglobin Variants in India.

    Science.gov (United States)

    Colah, Roshan B; Nadkarni, Anita; Gorakshakar, Ajit; Sawant, Pratibha; Gorivale, Manju; Mehta, Pallavi; Sawant, Madhavi; Ghosh, Kanjaksha

    2016-06-01

    Thalassemias as well as structural hemoglobin (Hb) variants are common monogenic inherited disorders of Hb in India. In this paper we describe 5 rare β-chain Hb variants identified in the Indian population on the basis of high performance liquid chromatography (HPLC). Of these 3 were identified during antenatal screening of β-thalassemia while the other 2 cases were referred to us for a diagnostic work up. These 5 Hb variants were Hb British Columbia (β CD 101 GAG → AAG), Hb Saint Louis (β CD28 CTG → CAG), Hb G Coushatta (β CD 22 GAA → GCA), Hb Pyrgos (β CD 83 GGC → GAC) and Hb Agenogi (β CD 90 GAG → AAG). Hb Saint Louis and Hb G Coushatta eluted in the HbA2 window, Hb British Columbia and Hb Agenogi eluted in the Hb C window while Hb Pyrgos eluted in an unknown window on HPLC. They were all identified by DNA sequencing. The child having Hb St. Louis had hepatosplenomegaly and anemia while the individuals with the other 4 variants were asymptomatic. Rare Hb variants are diagnostic curiosities that may be encountered by laboratories. Correct identification requires the application of more than one technique to avoid misdiagnosing them as more common variants (e.g. St. Louis and G Coushatta as E or D Iran on HPLC. Some, like G Coushatta may interfere with HPLC-based HbA1c estimation).

  5. Common susceptibility variants examined for association with dilated cardiomyopathy.

    Science.gov (United States)

    Rampersaud, Evadnie; Kinnamon, Daniel D; Hamilton, Kara; Khuri, Sawsan; Hershberger, Ray E; Martin, Eden R

    2010-03-01

    Rare mutations in more than 20 genes have been suggested to cause dilated cardiomyopathy (DCM), but explain only a small percentage of cases, mainly in familial forms. We hypothesised that more common variants may also play a role in increasing genetic susceptibility to DCM, similar to that observed in other common complex disorders. To test this hypothesis, we performed case-control analyses on all DNA polymorphic variation identified in a resequencing study of six candidate DCM genes (CSRP3, LDB3, MYH7, SCN5A, TCAP, and TNNT2) conducted in 289 unrelated white probands with DCM of unknown cause and 188 unrelated white controls. In univariate analyses, we identified associated common variants at LDB3 site 10779, LDB3 site 57877, MYH7 sites 16384 and 17404, and TCAP sites 140 and 1735. Multivariate analyses to examine the joint effects of multiple gene variants confirmed univariate results for MYH7 and TCAP and identified a block of nine variants in MYH7 that was strongly associated with DCM. Common variants in genes known to be causative of DCM may play a role in genetic susceptibility to DCM. Our results suggest that examination of common genetic variants may be warranted in future studies of DCM and other Mendelian-like disorders.

  6. Update on lichen planus and its clinical variants

    Directory of Open Access Journals (Sweden)

    Gillian Weston, MSIII

    2015-08-01

    Full Text Available Lichen planus (LP is an inflammatory skin condition with characteristic clinical and histopathological findings. Classic LP typically presents as pruritic, polygonal, violaceous flat-topped papules and plaques; many variants in morphology and location also exist, including oral, nail, linear, annular, atrophic, hypertrophic, inverse, eruptive, bullous, ulcerative, lichen planus pigmentosus, lichen planopilaris, vulvovaginal, actinic, lichen planus-lupus erythematosus overlap syndrome, and lichen planus pemphigoides. Clinical presentation of the rarer variant lesions may be largely dissimilar to classic LP and therefore difficult to diagnose based solely on clinical examination. However, histopathological examination of LP and LP-variant lesions reveal similar features, aiding in the proper diagnosis of the disease. Management of LP and LP variants aims to control symptoms and to decrease time from onset to resolution; it often involves topical corticosteroids, but varies depending on the severity and location of the lesion. The literature contains an array of reports on the variations in presentation and successful management of LP and its variants. A familiarity with LP and its variants is important in achieving timely recognition and management of the disease.

  7. Sonographic and cytopathologic correlation of papillary thyroid carcinoma variants.

    Science.gov (United States)

    Lee, Ji Hyun; Shin, Jung Hee; Lee, Hyun-Woo; Oh, Young Lyun; Hahn, Soo Yeon; Ko, Eun Young

    2015-01-01

    Papillary thyroid carcinoma (PTC) is the most common thyroid cancer and constitutes more than 70% of thyroid malignancies. Although TNM staging is the most widely used parameter for determination of therapeutic plans, recent studies have suggested that different histopathologic variants of PTC can also have different clinical courses and patient prognoses. Sonographic criteria for PTC are well established and include a taller-than-wide shape, an irregular margin, microcalcifications, and marked hypoechogenicity. The role of sonography has expanded to enable the characterization of PTC variants based on their sonographic features. Tall cell and diffuse sclerosing variants appear to have more aggressive clinical courses with unfavorable prognoses, whereas the more recently described cribriform-morular and Warthin-like variants have relatively indolent clinical courses. The prognoses of patients with follicular, solid, columnar cell, and oncocytic variants are still controversial and may be similar to the prognosis of conventional PTC. Understanding the sonographic characteristics of PTC variants with clinicopathologic correlation may be helpful for suggesting an appropriate treatment plan.

  8. Mouse tissues express multiple splice variants of prominin-1.

    Directory of Open Access Journals (Sweden)

    Kristel Kemper

    Full Text Available Prominin-1, a heavily glycosylated pentaspan membrane protein, is mainly known for its function as a marker for (cancer stem cells, although it can also be detected on differentiated cells. Mouse prominin-1 expression is heavily regulated by splicing in eight different variants. The function or the expression pattern of prominin-1 and its splice variants (SVs is thus far unknown. In this study, we analyzed the expression of the prominin-1 splice variants on mRNA level in several mouse tissues and found a broad tissue expression of the majority of SVs, but a specific set of SVs had a much more restricted expression profile. For instance, the testis expressed only SV3 and SV7. Moreover, SV8 was solely detected in the eye. Intriguingly, prominin-1 knockout mice do not suffer from gross abnormalities, but do show signs of blindness, which suggest that SV8 has a specific function in this tissue. In addition, databases searches for putative promoter regions in the mouse prominin-1 gene revealed three potential promoter regions that could be linked to specific SVs. Interestingly, for both SV7 and SV8, a specific potential promoter region could be identified. To conclude, the majority of mouse prominin-1 splice variants are widely expressed in mouse tissues. However, specific expression of a few variants, likely driven by specific promoters, suggests distinct regulation and a potential important function for these variants in certain tissues.

  9. Variants affecting exon skipping contribute to complex traits.

    Directory of Open Access Journals (Sweden)

    Younghee Lee

    Full Text Available DNA variants that affect alternative splicing and the relative quantities of different gene transcripts have been shown to be risk alleles for some Mendelian diseases. However, for complex traits characterized by a low odds ratio for any single contributing variant, very few studies have investigated the contribution of splicing variants. The overarching goal of this study is to discover and characterize the role that variants affecting alternative splicing may play in the genetic etiology of complex traits, which include a significant number of the common human diseases. Specifically, we hypothesize that single nucleotide polymorphisms (SNPs in splicing regulatory elements can be characterized in silico to identify variants affecting splicing, and that these variants may contribute to the etiology of complex diseases as well as the inter-individual variability in the ratios of alternative transcripts. We leverage high-throughput expression profiling to 1 experimentally validate our in silico predictions of skipped exons and 2 characterize the molecular role of intronic genetic variations in alternative splicing events in the context of complex human traits and diseases. We propose that intronic SNPs play a role as genetic regulators within splicing regulatory elements and show that their associated exon skipping events can affect protein domains and structure. We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits.

  10. BRCA Share: A Collection of Clinical BRCA Gene Variants.

    Science.gov (United States)

    Béroud, Christophe; Letovsky, Stanley I; Braastad, Corey D; Caputo, Sandrine M; Beaudoux, Olivia; Bignon, Yves Jean; Bressac-De Paillerets, Brigitte; Bronner, Myriam; Buell, Crystal M; Collod-Béroud, Gwenaëlle; Coulet, Florence; Derive, Nicolas; Divincenzo, Christina; Elzinga, Christopher D; Garrec, Céline; Houdayer, Claude; Karbassi, Izabela; Lizard, Sarab; Love, Angela; Muller, Danièle; Nagan, Narasimhan; Nery, Camille R; Rai, Ghadi; Revillion, Françoise; Salgado, David; Sévenet, Nicolas; Sinilnikova, Olga; Sobol, Hagay; Stoppa-Lyonnet, Dominique; Toulas, Christine; Trautman, Edwin; Vaur, Dominique; Vilquin, Paul; Weymouth, Katelyn S; Willis, Alecia; Eisenberg, Marcia; Strom, Charles M

    2016-12-01

    As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance of variants becomes ever more acute. Germline variants in the BRCA1 and BRCA2 genes can confer substantial lifetime risk of breast and ovarian cancer. Assessment of variant pathogenicity is a vital part of clinical genetic testing for these genes. A database of clinical observations of BRCA variants is a critical resource in that process. This article describes BRCA Share™, a database created by a unique international alliance of academic centers and commercial testing laboratories. By integrating the content of the Universal Mutation Database generated by the French Unicancer Genetic Group with the testing results of two large commercial laboratories, Quest Diagnostics and Laboratory Corporation of America (LabCorp), BRCA Share™ has assembled one of the largest publicly accessible collections of BRCA variants currently available. Although access is available to academic researchers without charge, commercial participants in the project are required to pay a support fee and contribute their data. The fees fund the ongoing curation effort, as well as planned experiments to functionally characterize variants of uncertain significance. BRCA Share™ databases can therefore be considered as models of successful data sharing between private companies and the academic world.

  11. Prebiotic Competition between Information Variants, With Low Error Catastrophe Risks

    Directory of Open Access Journals (Sweden)

    Radu Popa

    2015-07-01

    Full Text Available During competition for resources in primitive networks increased fitness of an information variant does not necessarily equate with successful elimination of its competitors. If variability is added fast to a system, speedy replacement of pre-existing and less-efficient forms of order is required as novel information variants arrive. Otherwise, the information capacity of the system fills up with information variants (an effect referred as “error catastrophe”. As the cost for managing the system’s exceeding complexity increases, the correlation between performance capabilities of information variants and their competitive success decreases, and evolution of such systems toward increased efficiency slows down. This impasse impedes the understanding of evolution in prebiotic networks. We used the simulation platform Biotic Abstract Dual Automata (BiADA to analyze how information variants compete in a resource-limited space. We analyzed the effect of energy-related features (differences in autocatalytic efficiency, energy cost of order, energy availability, transformation rates and stability of order on this competition. We discuss circumstances and controllers allowing primitive networks acquire novel information with minimal “error catastrophe” risks. We present a primitive mechanism for maximization of energy flux in dynamic networks. This work helps evaluate controllers of evolution in prebiotic networks and other systems where information variants compete.

  12. Homolog-specific PCR primer design for profiling splice variants.

    Science.gov (United States)

    Srivastava, Gyan Prakash; Hanumappa, Mamatha; Kushwaha, Garima; Nguyen, Henry T; Xu, Dong

    2011-05-01

    To study functional diversity of proteins encoded from a single gene, it is important to distinguish the expression levels among the alternatively spliced variants. A variant-specific primer pair is required to amplify each alternatively spliced variant individually. For this purpose, we developed a new feature, homolog-specific primer design (HSPD), in our high-throughput primer and probe design software tool, PRIMEGENS-v2. The algorithm uses a de novo approach to design primers without any prior information of splice variants or close homologs for an input query sequence. It not only designs primer pairs but also finds potential isoforms and homologs of the input sequence. Efficiency of this algorithm was tested for several gene families in soybean. A total of 187 primer pairs were tested under five different abiotic stress conditions with three replications at three time points. Results indicate a high success rate of primer design. Some primer pairs designed were able to amplify all splice variants of a gene. Furthermore, by utilizing combinations within the same multiplex pool, we were able to uniquely amplify a specific variant or duplicate gene. Our method can also be used to design PCR primers to specifically amplify homologs in the same gene family. PRIMEGENS-v2 is available at: http://primegens.org.

  13. Alternative Technical Summary Report: Electrometallurgical Treatment Variant

    Energy Technology Data Exchange (ETDEWEB)

    Gray, L.W.

    1995-11-30

    Immobilization is the fixation of the surplus fissile materials in an acceptable matrix such as glass or ceramics to create an environmentally benign form for disposal in a repository. In addition to the traditional characteristics required of an immobilization form to achieve isolation of the fissile material from the biosphere over geologic times, the immobilization form for the Fissile Materials Disposition Program (FMDP) must also possess the property that it is inherently as unattractive and inaccessible as the fissile material from commercial spent fuel. This latter requirement is similar to the wording of the ''spent fuel standard'' invoked in the National Academy of Sciences (NAS) study on plutonium disposition. High-level wastes (HLW) or separated cesium ({sup 137}Cs), can be added with the fissile material into the waste form to create a radiation field that increases the proliferation resistance and decreases reuse by the host nation in the following ways: (1) Plutonium will be diluted with elements that must be removed by extensive chemical processing to return it to weapons-usable purity; (2) The immobilized plutonium canisters will contain approximately 2 tonnes (2000 kg; 2.2 tons) of mass, thereby forcing the use of heavy equipment to move the canisters; (3) A gamma radiation barrier will be added to the immobilized plutonium canisters; the present concept is to add a radiation barrier that is greater than 1 Gy (100 rad) per hour at 1 m (3 ft) 30 years after fabrication; (4) These canisters will then be sealed in casks and emplaced into drifts in a federal repository where they will be monitored for 100 years before the repository is sealed. This immobilization process is shown conceptually in Figure 1. In the electrometallurgical treatment (ET) variant, plutonium-rich residues are shipped to existing Argonne National Laboratory-West (ANL-W) facilities where the plutonium is converted to plutonium chloride, dissolved in a molten

  14. Genetic risk variants for social anxiety.

    Science.gov (United States)

    Stein, Murray B; Chen, Chia-Yen; Jain, Sonia; Jensen, Kevin P; He, Feng; Heeringa, Steven G; Kessler, Ronald C; Maihofer, Adam; Nock, Matthew K; Ripke, Stephan; Sun, Xiaoying; Thomas, Michael L; Ursano, Robert J; Smoller, Jordan W; Gelernter, Joel

    2017-03-01

    Social anxiety is a neurobehavioral trait characterized by fear and reticence in social situations. Twin studies have shown that social anxiety has a heritable basis, shared with neuroticism and extraversion, but genetic studies have yet to demonstrate robust risk variants. We conducted genomewide association analysis (GWAS) of subjects within the Army Study To Assess Risk and Resilience in Servicemembers (Army STARRS) to (i) determine SNP-based heritability of social anxiety; (ii) discern genetic risk loci for social anxiety; and (iii) determine shared genetic risk with neuroticism and extraversion. GWAS were conducted within ancestral groups (EUR, AFR, LAT) using linear regression models for each of the three component studies in Army STARRS, and then meta-analyzed across studies. SNP-based heritability for social anxiety was significant (h(2)g  = 0.12, P = 2.17 × 10(-4) in EUR). One meta-analytically genomewide significant locus was seen in each of EUR (rs708012, Chr 6: BP 36965970, P = 1.55 × 10(-8) ; beta = 0.073) and AFR (rs78924501, Chr 1: BP 88406905, P = 3.58 × 10(-8) ; beta = 0.265) samples. Social anxiety in Army STARRS was significantly genetically correlated (negatively) with extraversion (rg  = -0.52, se = 0.22, P = 0.02) but not with neuroticism (rg  = 0.05, se = 0.22, P = 0.81) or with an anxiety disorder factor score (rg  = 0.02, se = 0.32, P = 0.94) from external GWAS meta-analyses. This first GWAS of social anxiety confirms a genetic basis for social anxiety, shared with extraversion but possibly less so with neuroticism. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. Two insular regions are differentially involved in behavioral variant FTD and nonfluent/agrammatic variant PPA.

    Science.gov (United States)

    Mandelli, Maria Luisa; Vitali, Paolo; Santos, Miguel; Henry, Maya; Gola, Kelly; Rosenberg, Lynne; Dronkers, Nina; Miller, Bruce; Seeley, William W; Gorno-Tempini, Maria Luisa

    2016-01-01

    The non-fluent/agrammatic variant of primary progressive aphasia (nfvPPA) and the behavioral variant frontotemporal dementia (bvFTD) are focal neurodegenerative disorders belonging to the FTD-spectrum clinical syndromes. NfvPPA is characterized by effortful speech and/or agrammatism and left frontal atrophy, while bvFTD is characterized by social-emotional dysfunction often accompanied by right-lateralized frontal damage. Despite their contrasting clinical presentations, both disorders show prominent left anterior insula atrophy. We investigated differential patterns of insular sub-region atrophy in nfvPPA and bvFTD. Based on knowledge of insular connectivity and physiology, we hypothesized that the left superior precentral region of the dorsal anterior insula (SPGI) would be more atrophic in nvfPPA due to its critical role in motor speech, whereas the ventral anterior region would be more atrophied in bvFTD reflecting its known role in social-emotional-autonomic functions. Early stage nfvPPA and bvFTD patients matched for disease severity, age, gender and education and healthy controls participated in the study. Detailed clinical history, neurological examination, neuropsychological screening evaluation, and high-resolution T1-weighted brain magnetic resonance imaging (MRI) were collected. Voxel-based morphometry (VBM) was applied to perform group comparisons across the whole brain and in bilateral insula region of interest (ROI). Correlation analyses between insular sub-region atrophy and relevant clinical features were performed. Whole brain group comparisons between nfvPPA and bvFTD showed the expected predominantly left or right anterior insular atrophy pattern. ROI analysis of bilateral insula showed that the left SPGI was significantly more atrophied in nfvPPA compared to bvFTD, while the bilateral ventral anterior and right dorsal anterior insula sub-regions were more atrophied in bvFTD than nfvPPA. Only left SPGI volume correlated with speech production

  16. Further Evidence That the CFTR Variant c.2620-6T>C Is Benign.

    Science.gov (United States)

    Wallerstein, Violet I; Wallerstein, Robert

    2017-01-01

    The c.2620-6T>C variant in the CFTR gene is a rare variant about which little is known. We present an asymptomatic adult who has this variant as well as the well described delta F508 pathogenic variant in transpresentation. This patient provides additional evidence that this is a benign polymorphism.

  17. Further Evidence That the CFTR Variant c.2620-6T>C Is Benign

    Science.gov (United States)

    Wallerstein, Violet I.

    2017-01-01

    The c.2620-6T>C variant in the CFTR gene is a rare variant about which little is known. We present an asymptomatic adult who has this variant as well as the well described delta F508 pathogenic variant in transpresentation. This patient provides additional evidence that this is a benign polymorphism. PMID:28163942

  18. 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.

  19. Further Evidence That the CFTR Variant c.2620-6T>C Is Benign

    Directory of Open Access Journals (Sweden)

    Violet I. Wallerstein

    2017-01-01

    Full Text Available The c.2620-6T>C variant in the CFTR gene is a rare variant about which little is known. We present an asymptomatic adult who has this variant as well as the well described delta F508 pathogenic variant in transpresentation. This patient provides additional evidence that this is a benign polymorphism.

  20. Combined effects of thrombosis pathway gene variants predict cardiovascular events.

    Directory of Open Access Journals (Sweden)

    Kirsi Auro

    2007-07-01

    Full Text Available The genetic background of complex diseases is proposed to consist of several low-penetrance risk loci. Addressing this complexity likely requires both large sample size and simultaneous analysis of different predisposing variants. We investigated the role of four thrombosis genes: coagulation factor V (F5, intercellular adhesion molecule 1 (ICAM1, protein C (PROC, and thrombomodulin (THBD in cardiovascular diseases. Single allelic gene variants and their pair-wise combinations were analyzed in two independently sampled population cohorts from Finland. From among 14,140 FINRISK participants (FINRISK-92, n = 5,999 and FINRISK-97, n = 8,141, we selected for genotyping a sample of 2,222, including 528 incident cardiovascular disease (CVD cases and random subcohorts totaling 786. To cover all known common haplotypes (>10%, 54 single nucleotide polymorphisms (SNPs were genotyped. Classification-tree analysis identified 11 SNPs that were further analyzed in Cox's proportional hazard model as single variants and pair-wise combinations. Multiple testing was controlled by use of two independent cohorts and with false-discovery rate. Several CVD risk variants were identified: In women, the combination of F5 rs7542281 x THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events. Our strategy to combine the classification-tree analysis with more traditional genetic models was successful in identifying SNPs-acting either in combination or as single variants--predisposing to CVD, and produced consistent results in two independent cohorts. These results suggest that variants in these four thrombosis genes contribute to arterial cardiovascular events at population level.

  1. Functionally significant, rare transcription factor variants in tetralogy of Fallot.

    Directory of Open Access Journals (Sweden)

    Ana Töpf

    Full Text Available Rare variants in certain transcription factors involved in cardiac development cause Mendelian forms of congenital heart disease. The purpose of this study was to systematically assess the frequency of rare transcription factor variants in sporadic patients with the cardiac outflow tract malformation tetralogy of Fallot (TOF.We sequenced the coding, 5'UTR, and 3'UTR regions of twelve transcription factor genes implicated in cardiac outflow tract development (NKX2.5, GATA4, ISL1, TBX20, MEF2C, BOP/SMYD1, HAND2, FOXC1, FOXC2, FOXH, FOXA2 and TBX1 in 93 non-syndromic, non-Mendelian TOF cases. We also analysed Illumina Human 660W-Quad SNP Array data for copy number variants in these genes; none were detected. Four of the rare variants detected have previously been shown to affect transactivation in in vitro reporter assays: FOXC1 p.P297S, FOXC2 p.Q444R, FOXH1 p.S113T and TBX1 p.P43_G61del PPPPRYDPCAAAAPGAPGP. Two further rare variants, HAND2 p.A25_A26insAA and FOXC1 p.G378_G380delGGG, A488_491delAAAA, affected transactivation in in vitro reporter assays. Each of these six functionally significant variants was present in a single patient in the heterozygous state; each of the four for which parental samples were available were maternally inherited. Thus in the 93 TOF cases we identified six functionally significant mutations in the secondary heart field transcriptional network.This study indicates that rare genetic variants in the secondary heart field transcriptional network with functional effects on protein function occur in 3-13% of patients with TOF. This is the first report of a functionally significant HAND2 mutation in a patient with congenital heart disease.

  2. MEFV Variants in Patients with PFAPA Syndrome in Japan.

    Science.gov (United States)

    Taniuchi, Shoichiro; Nishikomori, Ryuta; Iharada, Anna; Tuji, Shoji; Heike, Toshio; Kaneko, Kazunari

    2013-01-01

    The pathogenesis of PFAPA (periodic fever, aphthous stomatitis, pharyngitis, adenitis) syndrome is unknown as yet. In order to understand whether genes implicated in other auto-inflammatory diseases might be involved in the pathogenesis of PFAPA, all variants in the genes causing familial Mediterranean fever (FMF), tumor necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS), and Hyper IgD syndrome were analyzed in children with PFAPA. All variants in MEFV, TNFRSF1A, and MVK were analyzed in 20 patients with PFAPA. PFAPA were diagnosed by previous published criteria. The findings of all analyses in PFAPA patients were compared with those of unaffected normal subjects (n=62). In the 13 children of 20 with PFAPA, the heterozygous variants of MEFV (5 patients: E148Q-L110P, 2 patients: E148Q, 1 patient: E148Q-L110P/E148Q, 1 patient: E148Q-P369S-R408Q-E84K, 1 patient: E148Q-L110P-P369S-A408G, 1 patient: R202Q, 1 patient: P115R) were found. No variants belonging to TNFRSF1A or MVK were detected in children with PFAPA. The frequency of the E148Q-L110P variants in children with PFAPA was significantly higher than that observed in unaffected normal subjects (7/20 versus 8/62). The duration of the episodes of illness in PFAPA children with MEFV variants was shorter than that of patients without variants. Genes involved in the development and progression of MEFV may affect the incidence and the phenotype of PFAPA in children.

  3. Mendelian randomization analysis with multiple genetic variants using summarized data.

    Science.gov (United States)

    Burgess, Stephen; Butterworth, Adam; Thompson, Simon G

    2013-11-01

    Genome-wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual-level data in simulation studies. We investigate the impact of gene-gene interactions, linkage disequilibrium, and 'weak instruments' on these estimates. Both an inverse-variance weighted average of variant-specific associations and a likelihood-based approach for summarized data give similar estimates and precision to the two-stage least squares method for individual-level data, even when there are gene-gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P-value in a linear regression of the risk factor for each variant is less than 1×10⁻⁵, then weak instrument bias will be small. We use these methods to estimate the causal association of low-density lipoprotein cholesterol (LDL-C) on coronary artery disease using published data on five genetic variants. A 30% reduction in LDL-C is estimated to reduce coronary artery disease risk by 67% (95% CI: 54% to 76%). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual-level data, although the necessary assumptions cannot be so fully assessed. © 2013 WILEY PERIODICALS, INC.

  4. Functionally significant, rare transcription factor variants in tetralogy of Fallot.

    Science.gov (United States)

    Töpf, Ana; Griffin, Helen R; Glen, Elise; Soemedi, Rachel; Brown, Danielle L; Hall, Darroch; Rahman, Thahira J; Eloranta, Jyrki J; Jüngst, Christoph; Stuart, A Graham; O'Sullivan, John; Keavney, Bernard D; Goodship, Judith A

    2014-01-01

    Rare variants in certain transcription factors involved in cardiac development cause Mendelian forms of congenital heart disease. The purpose of this study was to systematically assess the frequency of rare transcription factor variants in sporadic patients with the cardiac outflow tract malformation tetralogy of Fallot (TOF). We sequenced the coding, 5'UTR, and 3'UTR regions of twelve transcription factor genes implicated in cardiac outflow tract development (NKX2.5, GATA4, ISL1, TBX20, MEF2C, BOP/SMYD1, HAND2, FOXC1, FOXC2, FOXH, FOXA2 and TBX1) in 93 non-syndromic, non-Mendelian TOF cases. We also analysed Illumina Human 660W-Quad SNP Array data for copy number variants in these genes; none were detected. Four of the rare variants detected have previously been shown to affect transactivation in in vitro reporter assays: FOXC1 p.P297S, FOXC2 p.Q444R, FOXH1 p.S113T and TBX1 p.P43_G61del PPPPRYDPCAAAAPGAPGP. Two further rare variants, HAND2 p.A25_A26insAA and FOXC1 p.G378_G380delGGG, A488_491delAAAA, affected transactivation in in vitro reporter assays. Each of these six functionally significant variants was present in a single patient in the heterozygous state; each of the four for which parental samples were available were maternally inherited. Thus in the 93 TOF cases we identified six functionally significant mutations in the secondary heart field transcriptional network. This study indicates that rare genetic variants in the secondary heart field transcriptional network with functional effects on protein function occur in 3-13% of patients with TOF. This is the first report of a functionally significant HAND2 mutation in a patient with congenital heart disease.

  5. HABP2 G534E Variant in Papillary Thyroid Carcinoma.

    Science.gov (United States)

    Tomsic, Jerneja; Fultz, Rebecca; Liyanarachchi, Sandya; He, Huiling; Senter, Leigha; de la Chapelle, Albert

    2016-01-01

    The main nonmedullary form of thyroid cancer is papillary thyroid carcinoma (PTC) that accounts for 80-90% of all thyroid malignancies. Only 3-10% of PTC patients have a positive family history of PTC yet the familiality is one of the highest of all cancers as measured by case control studies. A handful of genes have been implicated accounting for a small fraction of this genetic predisposition. It was therefore of considerable interest that a mutation in the HABP2 gene was recently implicated in familial PTC. The present work was undertaken to examine the extent of HABP2 variant involvement in PTC. The HABP2 G534E variant (rs7080536) was genotyped in blood DNA from 179 PTC families (one affected individual per family), 1160 sporadic PTC cases and 1395 controls. RNA expression of HABP2 was tested by qPCR in RNA extracted from tumor and normal thyroid tissue from individuals that are homozygous wild-type or heterozygous for the variant. The variant was found to be present in 6.1% familial cases, 8.0% sporadic cases (2 individuals were homozygous for the variant) and 8.7% controls. The variant did not segregate with PTC in one large and 6 smaller families in which it occurred. In keeping with data from the literature and databases the expression of HABP2 was highest in the liver, much lower in 3 other tested tissues (breast, kidney, brain) but not found in thyroid. Given these results showing lack of any involvement we suggest that the putative role of variant HABP2 in PTC should be carefully scrutinized.

  6. HABP2 G534E Variant in Papillary Thyroid Carcinoma.

    Directory of Open Access Journals (Sweden)

    Jerneja Tomsic

    Full Text Available The main nonmedullary form of thyroid cancer is papillary thyroid carcinoma (PTC that accounts for 80-90% of all thyroid malignancies. Only 3-10% of PTC patients have a positive family history of PTC yet the familiality is one of the highest of all cancers as measured by case control studies. A handful of genes have been implicated accounting for a small fraction of this genetic predisposition. It was therefore of considerable interest that a mutation in the HABP2 gene was recently implicated in familial PTC. The present work was undertaken to examine the extent of HABP2 variant involvement in PTC. The HABP2 G534E variant (rs7080536 was genotyped in blood DNA from 179 PTC families (one affected individual per family, 1160 sporadic PTC cases and 1395 controls. RNA expression of HABP2 was tested by qPCR in RNA extracted from tumor and normal thyroid tissue from individuals that are homozygous wild-type or heterozygous for the variant. The variant was found to be present in 6.1% familial cases, 8.0% sporadic cases (2 individuals were homozygous for the variant and 8.7% controls. The variant did not segregate with PTC in one large and 6 smaller families in which it occurred. In keeping with data from the literature and databases the expression of HABP2 was highest in the liver, much lower in 3 other tested tissues (breast, kidney, brain but not found in thyroid. Given these results showing lack of any involvement we suggest that the putative role of variant HABP2 in PTC should be carefully scrutinized.

  7. Connected speech production in three variants of primary progressive aphasia.

    Science.gov (United States)

    Wilson, Stephen M; Henry, Maya L; Besbris, Max; Ogar, Jennifer M; Dronkers, Nina F; Jarrold, William; Miller, Bruce L; Gorno-Tempini, Maria Luisa

    2010-07-01

    Primary progressive aphasia is a clinical syndrome defined by progressive deficits isolated to speech and/or language, and can be classified into non-fluent, semantic and logopenic variants based on motor speech, linguistic and cognitive features. The connected speech of patients with primary progressive aphasia has often been dichotomized simply as 'fluent' or 'non-fluent', however fluency is a multidimensional construct that encompasses features such as speech rate, phrase length, articulatory agility and syntactic structure, which are not always impacted in parallel. In this study, our first objective was to improve the characterization of connected speech production in each variant of primary progressive aphasia, by quantifying speech output along a number of motor speech and linguistic dimensions simultaneously. Secondly, we aimed to determine the neuroanatomical correlates of changes along these different dimensions. We recorded, transcribed and analysed speech samples for 50 patients with primary progressive aphasia, along with neurodegenerative and normal control groups. Patients were scanned with magnetic resonance imaging, and voxel-based morphometry was used to identify regions where atrophy correlated significantly with motor speech and linguistic features. Speech samples in patients with the non-fluent variant were characterized by slow rate, distortions, syntactic errors and reduced complexity. In contrast, patients with the semantic variant exhibited normal rate and very few speech or syntactic errors, but showed increased proportions of closed class words, pronouns and verbs, and higher frequency nouns, reflecting lexical retrieval deficits. In patients with the logopenic variant, speech rate (a common proxy for fluency) was intermediate between the other two variants, but distortions and syntactic errors were less common than in the non-fluent variant, while lexical access was less impaired than in the semantic variant. Reduced speech rate was

  8. 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

    2015-04-01

    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.

  9. CooVar: Co-occurring variant analyzer

    Directory of Open Access Journals (Sweden)

    Vergara Ismael A

    2012-11-01

    Full Text Available Abstract Background Evaluating the impact of genomic variations (GV on protein-coding transcripts is an important step in identifying variants of functional significance. Currently available programs for variant annotation depend on external databases or annotate multiple variants affecting the same transcript independently, which limits program use to organisms available in these databases or results in potentially incorrect or incomplete annotations. Findings We have developed CooVar (Co-occurring Variant Analyzer, a database-independent program for assessing the impact of GVs on protein-coding transcripts. CooVar takes GVs, reference genome sequence, and protein-coding exons as input and provides annotated GVs and transcripts as output. Other than similar programs, CooVar considers the combined impact of all GVs affecting the same transcript, generating biologically more accurate annotations. CooVar is operated from the command-line and supports standard file formats VCF, GFF/GTF, and GVF, which makes it easy to integrate into existing computational pipelines. We have extensively tested CooVar on worm and human data sets and demonstrate that it generates correct annotations in only a short amount of time. Conclusions CooVar is an easy-to-use and lightweight variant annotation tool that considers the combined impact of GVs on protein-coding transcripts. CooVar is freely available at http://genome.sfu.ca/projects/coovar/.

  10. Epidemiological and functional implications of molecular variants of human papillomavirus

    Directory of Open Access Journals (Sweden)

    Sichero L.

    2006-01-01

    Full Text Available Human papillomavirus genomes are classified into molecular variants when they present more than 98% of similarity to the prototype sequence within the L1 gene. Comparative nucleotide sequence analyses of these viruses have elucidated some features of their phylogenetic relationship. In addition, human papillomavirus intratype variability has also been used as an important tool in epidemiological studies of viral transmission, persistence and progression to clinically relevant cervical lesions. Until the present, little has been published concerning the functional significance of molecular variants. It has been shown that nucleotide variability within the long control region leads to differences in the binding affinity of some cellular transcriptional factors and to the enhancement of the expression of E6 and E7 oncogenes. Furthermore, in vivo and in vitro studies revealed differences in E6 and E7 biochemical and biological properties among molecular variants. Nevertheless, further correlation with additional functional information is needed to evaluate the significance of genome intratypic variability. These results are also important for the development of vaccines and to determine the extent to which immunization with L1 virus-like particles of one variant could induce antibodies that cross-neutralize other variants.

  11. Targeted quantitative mass spectrometric immunoassay for human protein variants

    Directory of Open Access Journals (Sweden)

    Nedelkov Dobrin

    2011-04-01

    Full Text Available Abstract Background Post-translational modifications and genetic variations give rise to protein variants that significantly increase the complexity of the human proteome. Modified proteins also play an important role in biological processes. While sandwich immunoassays are routinely used to determine protein concentrations, they are oblivious to protein variants that may serve as biomarkers with better sensitivity and specificity than their wild-type proteins. Mass spectrometry, coupled to immunoaffinity separations, can provide an efficient mean for simultaneous detection and quantification of protein variants. Results Presented here is a mass spectrometric immunoassay method for targeted quantitative proteomics analysis of protein modifications. Cystatin C, a cysteine proteinase inhibitor and a potential marker for several pathological processes, was used as a target analyte. An internal reference standard was incorporated into the assay, serving as a normalization point for cystatin C quantification. The precision, linearity, and recovery characteristics of the assay were established. The new assay was also benchmarked against existing cystatin C ELISA. In application, the assay was utilized to determine the individual concentration of several cystatin C variants across a cohort of samples, demonstrating the ability to fully quantify individual forms of post-translationally modified proteins. Conclusions The mass spectrometric immunoassays can find use in quantifying specific protein modifications, either as a part of a specific protein biomarker discovery/rediscovery effort to delineate the role of these variants in the onset of the disease, progression, and response to therapy, or in a more systematic study to delineate and understand human protein diversity.

  12. [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.

  13. Breast cancer susceptibility variants alter risk in familial ovarian cancer.

    Science.gov (United States)

    Latif, A; McBurney, H J; Roberts, S A; Lalloo, F; Howell, A; Evans, D G; Newman, W G

    2010-12-01

    Recent candidate gene and genome wide association studies have revealed novel loci associated with an increased risk of breast cancer. We evaluated the effect of these breast cancer associated variants on ovarian cancer risk in individuals with familial ovarian cancer both with and without BRCA1 or BRCA2 mutations. A total of 158 unrelated white British women (54 BRCA1/2 mutation positive and 104 BRCA1/2 mutation negative) with familial ovarian cancer were genotyped for FGFR2, TNRC9/TOX3 and CASP8 variants. The p.Asp302His CASP8 variant was associated with reduced ovarian cancer risk in the familial BRCA1/2 mutation negative ovarian cancer cases (P = 0.016). The synonymous TNRC9/TOX3 (Ser51) variant was present at a significantly lower frequency than in patients with familial BRCA1/2 positive breast cancer (P = 0.0002). Our results indicate that variants in CASP8 and TNRC9/TOX3 alter the risk of disease in individuals affected with familial ovarian cancer.

  14. Identification and characterization of variant alleles at CODIS STR loci.

    Science.gov (United States)

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  15. De Novo Coding Variants Are Strongly Associated with Tourette Disorder.

    Science.gov (United States)

    Willsey, A Jeremy; Fernandez, Thomas V; Yu, Dongmei; King, Robert A; Dietrich, Andrea; Xing, Jinchuan; Sanders, Stephan J; Mandell, Jeffrey D; Huang, Alden Y; Richer, Petra; Smith, Louw; Dong, Shan; Samocha, Kaitlin E; Neale, Benjamin M; Coppola, Giovanni; Mathews, Carol A; Tischfield, Jay A; Scharf, Jeremiah M; State, Matthew W; Heiman, Gary A

    2017-05-03

    Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186 trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably damaging missense) are overrepresented in probands (RR 1.37, p = 0.003). We identify four likely risk genes with multiple de novo damaging variants in unrelated probands: WWC1 (WW and C2 domain containing 1), CELSR3 (Cadherin EGF LAG seven-pass G-type receptor 3), NIPBL (Nipped-B-like), and FN1 (fibronectin 1). Overall, we estimate that de novo damaging variants in approximately 400 genes contribute risk in 12% of clinical cases. VIDEO ABSTRACT. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. 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

  17. Spatially variant morphological image processing: theory and applications

    Science.gov (United States)

    Bouaynaya, N.; Schonfeld, D.

    2006-01-01

    Originally, mathematical morphology was a theory of signal transformations which are invariant under Euclidean translations. An interest in the extension of mathematical morphology to spatially-variant (SV) operators has emerged due to the requirements imposed by numerous applications in adaptive signal (image) processing. This paper presents a general theory of spatially-variant mathematical morphology in the Euclidean space. We define the binary and gray-level spatially-variant basic morphological operators (i.e., erosion, dilation, opening and closing) and study their properties. We subsequently derive kernel representations for a large class of binary and gray-level SV operators in terms of the basic SV morphological operators. The theory of SV mathematical morphology is used to extend and analyze two important image processing applications: morphological image restoration and skeleton representation of binary images. For morphological image restoration, we obtain new realizations of adaptive median filters in terms of the basic SV morphological operators. For skeleton representation, we develop an algorithm to construct the optimal structuring elements, in the sense of minimizing the cardinality of the spatially-variant morphological skeleton representation. Experimental results show the power of the proposed theory of spatially-variant mathematical morphology in practical image processing applications.

  18. Unclassified sequence variants (UVS and genetic predisposition to cancer

    Directory of Open Access Journals (Sweden)

    Yves-Jean Bignon

    2011-06-01

    Full Text Available Hereditary breast and ovarian cancers are mainly attributable to predisposition genes whose germinal mutations are responsible for the disease. The most common genes associated with breast/ovarian cancer are BRCA1 and BRCA2 but at least 20 other genes of medium of high penetrance have been associated with these types of cancer. Lifetime risk of breast cancer for BRCA mutations carriers approaches 90%. Appropriate medical follow-up is therefore essential for women carrying mutations in these genes. BRCA mutational spectrum has not been entirely characterized but not all sequence variants are pathogenic. These are classified as benign polymorphisms or unclassified variants (UV with unknown pathological potential. To date, 43,5% of over 3500 genetic variants BRCA1 and BRCA2 are reported as having uncertain clinical significance. Whether one sequence variant has or not a pathogenicity implication is often a hard decision to take, involving important consequences for diagnosis and medical follow-up. Here we present several cases of unclassified sequence variants detection and interpretation by in-silico analysis.

  19. [Genetic variants associated to male infertility in Mexican patients].

    Science.gov (United States)

    Piña-Aguilar, Raúl Eduardo; Chima-Galán, María del Carmen; Yerena-de-vega, María de la Concepción A; Regalado-Hernández, Miguel Angel; Sánchez-Guerrero, Cecilia; García-Ortiz, Liliana; Santillán-Hernández, Yuritzi; Moreno-García, Jesús Daniel

    2013-05-01

    Recently Mexican Federation of Obstetrics and Gynecology Colleges (Federación Mexicana de Colegios de Obstetricia y Ginecologia, FEMECOG) published the Mexican guideline forthe management of male infertility, which suggests performing genetic laboratory tests as part of diagnosis and management of infertile patients and states that these should receive genetic counseling. This paper reviews the genetic approach proposed by Mexican guideline. A systematic review of medical literature was performed in Pubmed and Web of Knowledge from 1980 to 2012 in order to find reports of genetic variants associated to male infertility in Mexican patients. Also it is discussed the current knowledge of these variants, their clinical implications and finally the guidelines and recommendations for their molecular diagnosis. Most genetic variants in Mexican infertile patients are chromosome abnormalities. In relation to other variants there is only a report of Y chromosome microdeletions, repeated CAG in androgen receptor and more common mutations in CFTR, and other article reporting mutations in CFTR in patients with congenital absence of vas deferens. Little is known about the genetics of Mexican infertile patients apart from chromosome abnormalities. However, the contribution of genetics as etiology of male infertility is taking more relevance and currently the consensual management of infertile male should include the screening of genetic background. This review pretends to be a quick guide for clinicians who want to know about reports of genetic variants related to male infertility in Mexican population and how to approach their diagnosis.

  20. VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.

    Science.gov (United States)

    Hart, Steven N; Duffy, Patrick; Quest, Daniel J; Hossain, Asif; Meiners, Mike A; Kocher, Jean-Pierre

    2016-03-01

    Next-generation sequencing platforms are widely used to discover variants associated with disease. The processing of sequencing data involves read alignment, variant calling, variant annotation and variant filtering. The standard file format to hold variant calls is the variant call format (VCF) file. According to the format specifications, any arbitrary annotation can be added to the VCF file for downstream processing. However, most downstream analysis programs disregard annotations already present in the VCF and re-annotate variants using the annotation provided by that particular program. This precludes investigators who have collected information on variants from literature or other sources from including these annotations in the filtering and mining of variants. We have developed VCF-Miner, a graphical user interface-based stand-alone tool, to mine variants and annotation stored in the VCF. Powered by a MongoDB database engine, VCF-Miner enables the stepwise trimming of non-relevant variants. The grouping feature implemented in VCF-Miner can be used to identify somatic variants by contrasting variants in tumor and in normal samples or to identify recessive/dominant variants in family studies. It is not limited to human data, but can also be extended to include non-diploid organisms. It also supports copy number or any other variant type supported by the VCF specification. VCF-Miner can be used on a personal computer or large institutional servers and is freely available for download from http://bioinformaticstools.mayo.edu/research/vcf-miner/.

  1. Variant of partially mapped crossover for the Travelling Salesman problems

    Directory of Open Access Journals (Sweden)

    Kusum Deep

    2012-01-01

    Full Text Available In this paper a variant of partially mapped crossover (VPMX is designed using cut point positions and is tested for its performance with the existing partially mapped crossover (PMX.In order to test the performance ,two mutation operators are used. These mutation operators are inverted displacement and inversion mutations. Partially mapped crossover (PMX with inversion and with inverted displacement and a variant of partially mapped crossover (VPMX with inversion and with inverted displacement are programmed in C++ and implemented on a set of ten benchmark problems taken from the Travelling salesman problem library (TSPLIB. The results indicate that the designed variant of PMX is superior by showing a better performance in eight instances in combination with the inverted displacement mutation. In two instances PMX has obtained a better result. One is PMX with inversion mutation and the other is PMX with inverted displacement mutation.

  2. Arrhythmogenic KCNE gene variants: current knowledge and future challenges

    Directory of Open Access Journals (Sweden)

    Shawn M Crump

    2014-01-01

    Full Text Available There are twenty-five known inherited cardiac arrhythmia susceptibility genes, all of which encode either ion channel pore-forming subunits or proteins that regulate aspects of ion channel biology such as function, trafficking and localization. The human KCNE gene family comprises five potassium channel regulatory subunits, sequence variants in each of which are associated with cardiac arrhythmias. KCNE gene products exhibit promiscuous partnering and in some cases ubiquitous expression, hampering efforts to unequivocally correlate each gene to specific native potassium currents. Likewise, deducing the molecular etiology of cardiac arrhythmias in individuals harboring rare KCNE gene variants, or more common KCNE polymorphisms, can be challenging. In this review we provide an update on putative arrhythmia-causing KCNE gene variants, and discuss current thinking and future challenges in the study of molecular mechanisms of KCNE-associated cardiac rhythm disturbances.

  3. PCSK9 genetic variants and risk of type 2 diabetes

    DEFF Research Database (Denmark)

    Schmidt, Amand F; Swerdlow, Daniel I; Holmes, Michael V;

    2016-01-01

    a standardised analysis plan, meta-analyses, and weighted gene-centric scores. FINDINGS: Data were available for more than 550 000 individuals and 51 623 cases of type 2 diabetes. Combined analyses of four independent PCSK9 variants (rs11583680, rs11591147, rs2479409, and rs11206510) scaled to 1 mmol/L lower LDL......BACKGROUND: Statin treatment and variants in the gene encoding HMG-CoA reductase are associated with reductions in both the concentration of LDL cholesterol and the risk of coronary heart disease, but also with modest hyperglycaemia, increased bodyweight, and modestly increased risk of type 2...... diabetes, which in no way offsets their substantial benefits. We sought to investigate the associations of LDL cholesterol-lowering PCSK9 variants with type 2 diabetes and related biomarkers to gauge the likely effects of PCSK9 inhibitors on diabetes risk. METHODS: In this mendelian randomisation study, we...

  4. Pediatric cervical spine: normal anatomy, variants, and trauma.

    Science.gov (United States)

    Lustrin, Elizabeth Susan; Karakas, Sabiha Pinar; Ortiz, A Orlando; Cinnamon, Jay; Castillo, Mauricio; Vaheesan, Kirubahara; Brown, James H; Diamond, Alan S; Black, Karen; Singh, Sudha

    2003-01-01

    Emergency radiologic evaluation of the pediatric cervical spine can be challenging because of the confusing appearance of synchondroses, normal anatomic variants, and injuries that are unique to children. Cervical spine injuries in children are usually seen in the upper cervical region owing to the unique biomechanics and anatomy of the pediatric cervical spine. Knowledge of the normal embryologic development and anatomy of the cervical spine is important to avoid mistaking synchondroses for fractures in the setting of trauma. Familiarity with anatomic variants is also important for correct image interpretation. These variants include pseudosubluxation, absence of cervical lordosis, wedging of the C3 vertebra, widening of the predental space, prevertebral soft-tissue widening, intervertebral widening, and "pseudo-Jefferson fracture." In addition, familiarity with mechanisms of injury and appropriate imaging modalities will aid in the correct interpretation of radiologic images of the pediatric cervical spine.

  5. Genetically complex epilepsies, copy number variants and syndrome constellations.

    Science.gov (United States)

    Mefford, Heather C; Mulley, John C

    2010-10-05

    Epilepsy is one of the most common neurological disorders, with a prevalence of 1% and lifetime incidence of 3%. There are numerous epilepsy syndromes, most of which are considered to be genetic epilepsies. Despite the discovery of more than 20 genes for epilepsy to date, much of the genetic contribution to epilepsy is not yet known. Copy number variants have been established as an important source of mutation in other complex brain disorders, including intellectual disability, autism and schizophrenia. Recent advances in technology now facilitate genome-wide searches for copy number variants and are beginning to be applied to epilepsy. Here, we discuss what is currently known about the contribution of copy number variants to epilepsy, and how that knowledge is redefining classification of clinical and genetic syndromes.

  6. Private mitochondrial DNA variants in danish patients with hypertrophic cardiomyopathy

    DEFF Research Database (Denmark)

    Hagen, Christian M; Aidt, Frederik H; Havndrup, Ole;

    2015-01-01

    Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA) haplogroups are susceptibility factors for HCM....... Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446......>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM....

  7. Genetic variants associated with warfarin dosage in Kuwaiti population.

    Science.gov (United States)

    John, Sumi Elsa; Antony, Dinu; Eaaswarkhanth, Muthukrishnan; Hebbar, Prashantha; Alkayal, Fadi; Tuomilehto, Jaakko; Alsmadi, Osama; Thanaraj, Thangavel Alphonse

    2017-06-01

    Assessing the distinct prevalence or absence of genetic variants associated with differential response to the anticoagulant medication of warfarin in different population groups is actively pursued by pharmacogenomics community. Populations from Arabian Peninsula are underrepresented in such studies. By way of examining exome- and genome-wide genotype data from 1395 Arab individuals in Kuwait, we report distinct occurrence of warfarin response-related variants rs12460590_A/CYP2A7, rs2108622_T/CYP4F2, rs2884737_C/VKORC1 and distinct absence of rs11150606_C/PRSS53 in Kuwaiti population. The presented results in conjunction with similar literature reports on Qatari population enhance the worldwide understanding on population-specific distributions of genetic variants associated with warfarin drug dosage.

  8. KD4v: Comprehensible Knowledge Discovery System for Missense Variant.

    Science.gov (United States)

    Luu, Tien-Dao; Rusu, Alin; Walter, Vincent; Linard, Benjamin; Poidevin, Laetitia; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Raffelsberger, Wolfgang; Wicker, Nicolas; Lecompte, Odile; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-07-01

    A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at http://decrypthon.igbmc.fr/kd4v.

  9. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver.

    Directory of Open Access Journals (Sweden)

    Phillip H Pham

    Full Text Available Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease--without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER.

  10. CEACAM6 gene variants in inflammatory bowel disease.

    Directory of Open Access Journals (Sweden)

    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.

  11. Analysis of Plasminogen Genetic Variants in Multiple Sclerosis Patients

    Science.gov (United States)

    Sadovnick, A. Dessa; Traboulsee, Anthony L.; Bernales, Cecily Q.; Ross, Jay P.; Forwell, Amanda L.; Yee, Irene M.; Guillot-Noel, Lena; Fontaine, Bertrand; Cournu-Rebeix, Isabelle; Alcina, Antonio; Fedetz, Maria; Izquierdo, Guillermo; Matesanz, Fuencisla; Hilven, Kelly; Dubois, Bénédicte; Goris, An; Astobiza, Ianire; Alloza, Iraide; Antigüedad, Alfredo; Vandenbroeck, Koen; Akkad, Denis A.; Aktas, Orhan; Blaschke, Paul; Buttmann, Mathias; Chan, Andrew; Epplen, Joerg T.; Gerdes, Lisa-Ann; Kroner, Antje; Kubisch, Christian; Kümpfel, Tania; Lohse, Peter; Rieckmann, Peter; Zettl, Uwe K.; Zipp, Frauke; Bertram, Lars; Lill, Christina M; Fernandez, Oscar; Urbaneja, Patricia; Leyva, Laura; Alvarez-Cermeño, Jose Carlos; Arroyo, Rafael; Garagorri, Aroa M.; García-Martínez, Angel; Villar, Luisa M.; Urcelay, Elena; Malhotra, Sunny; Montalban, Xavier; Comabella, Manuel; Berger, Thomas; Fazekas, Franz; Reindl, Markus; Schmied, Mascha C.; Zimprich, Alexander; Vilariño-Güell, Carles

    2016-01-01

    Multiple sclerosis (MS) is a prevalent neurological disease of complex etiology. Here, we describe the characterization of a multi-incident MS family that nominated a rare missense variant (p.G420D) in plasminogen (PLG) as a putative genetic risk factor for MS. Genotyping of PLG p.G420D (rs139071351) in 2160 MS patients, and 886 controls from Canada, identified 10 additional probands, two sporadic patients and one control with the variant. Segregation in families harboring the rs139071351 variant, identified p.G420D in 26 out of 30 family members diagnosed with MS, 14 unaffected parents, and 12 out of 30 family members not diagnosed with disease. Despite considerably reduced penetrance, linkage analysis supports cosegregation of PLG p.G420D and disease. Genotyping of PLG p.G420D in 14446 patients, and 8797 controls from Canada, France, Spain, Germany, Belgium, and Austria failed to identify significant association with disease (P = 0.117), despite an overall higher prevalence in patients (OR = 1.32; 95% CI = 0.93–1.87). To assess whether additional rare variants have an effect on MS risk, we sequenced PLG in 293 probands, and genotyped all rare variants in cases and controls. This analysis identified nine rare missense variants, and although three of them were exclusively observed in MS patients, segregation does not support pathogenicity. PLG is a plausible biological candidate for MS owing to its involvement in immune system response, blood-brain barrier permeability, and myelin degradation. Moreover, components of its activation cascade have been shown to present increased activity or expression in MS patients compared to controls; further studies are needed to clarify whether PLG is involved in MS susceptibility. PMID:27194806

  12. Variants associated with Gaucher disease in multiple system atrophy

    Science.gov (United States)

    Mitsui, Jun; Matsukawa, Takashi; Sasaki, Hidenao; Yabe, Ichiro; Matsushima, Masaaki; Dürr, Alexandra; Brice, Alexis; Takashima, Hiroshi; Kikuchi, Akio; Aoki, Masashi; Ishiura, Hiroyuki; Yasuda, Tsutomu; Date, Hidetoshi; Ahsan, Budrul; Iwata, Atsushi; Goto, Jun; Ichikawa, Yaeko; Nakahara, Yasuo; Momose, Yoshio; Takahashi, Yuji; Hara, Kenju; Kakita, Akiyoshi; Yamada, Mitsunori; Takahashi, Hitoshi; Onodera, Osamu; Nishizawa, Masatoyo; Watanabe, Hirohisa; Ito, Mizuki; Sobue, Gen; Ishikawa, Kinya; Mizusawa, Hidehiro; Kanai, Kazuaki; Hattori, Takamichi; Kuwabara, Satoshi; Arai, Kimihito; Koyano, Shigeru; Kuroiwa, Yoshiyuki; Hasegawa, Kazuko; Yuasa, Tatsuhiko; Yasui, Kenichi; Nakashima, Kenji; Ito, Hijiri; Izumi, Yuishin; Kaji, Ryuji; Kato, Takeo; Kusunoki, Susumu; Osaki, Yasushi; Horiuchi, Masahiro; Kondo, Tomoyoshi; Murayama, Shigeo; Hattori, Nobutaka; Yamamoto, Mitsutoshi; Murata, Miho; Satake, Wataru; Toda, Tatsushi; Filla, Alessandro; Klockgether, Thomas; Wüllner, Ullrich; Nicholson, Garth; Gilman, Sid; Tanner, Caroline M; Kukull, Walter A; Stern, Mathew B; Lee, Virginia M-Y; Trojanowski, John Q; Masliah, Eliezer; Low, Phillip A; Sandroni, Paola; Ozelius, Laurie J; Foroud, Tatiana; Tsuji, Shoji

    2015-01-01

    Objective Glucocerebrosidase gene (GBA) variants that cause Gaucher disease are associated with Parkinson disease (PD) and dementia with Lewy bodies (DLB). To investigate the role of GBA variants in multiple system atrophy (MSA), we analyzed GBA variants in a large case–control series. Methods We sequenced coding regions and flanking splice sites of GBA in 969 MSA patients (574 Japanese, 223 European, and 172 North American) and 1509 control subjects (900 Japanese, 315 European, and 294 North American). We focused solely on Gaucher-disease-causing GBA variants. Results In the Japanese series, we found nine carriers among the MSA patients (1.65%) and eight carriers among the control subjects (0.89%). In the European series, we found three carriers among the MSA patients (1.35%) and two carriers among the control subjects (0.63%). In the North American series, we found five carriers among the MSA patients (2.91%) and one carrier among the control subjects (0.34%). Subjecting each series to a Mantel–Haenszel analysis yielded a pooled odds ratio (OR) of 2.44 (95% confidence interval [CI], 1.14–5.21) and a P-value of 0.029 without evidence of significant heterogeneity. Logistic regression analysis yielded similar results, with an adjusted OR of 2.43 (95% CI 1.15–5.37) and a P-value of 0.022. Subtype analysis showed that Gaucher-disease-causing GBA variants are significantly associated with MSA cerebellar subtype (MSA-C) patients (P = 7.3 × 10−3). Interpretation The findings indicate that, as in PD and DLB, Gaucher-disease-causing GBA variants are associated with MSA. PMID:25909086

  13. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis.

    Science.gov (United States)

    van Es, Michael A; Schelhaas, Helenius J; van Vught, Paul W J; Ticozzi, Nicola; Andersen, Peter M; Groen, Ewout J N; Schulte, Claudia; Blauw, Hylke M; Koppers, Max; Diekstra, Frank P; Fumoto, Katsumi; LeClerc, Ashley Lyn; Keagle, Pamela; Bloem, Bastiaan R; Scheffer, Hans; van Nuenen, Bart F L; van Blitterswijk, Marka; van Rheenen, Wouter; Wills, Anne-Marie; Lowe, Patrick P; Hu, Guo-fu; Yu, Wenhao; Kishikawa, Hiroko; Wu, David; Folkerth, Rebecca D; Mariani, Claudio; Goldwurm, Stefano; Pezzoli, Gianni; Van Damme, Philip; Lemmens, Robin; Dahlberg, Caroline; Birve, Anna; Fernández-Santiago, Rubén; Waibel, Stefan; Klein, Christine; Weber, Markus; van der Kooi, Anneke J; de Visser, Marianne; Verbaan, Dagmar; van Hilten, Jacobus J; Heutink, Peter; Hennekam, Eric A M; Cuppen, Edwin; Berg, Daniela; Brown, Robert H; Silani, Vincenzo; Gasser, Thomas; Ludolph, Albert C; Robberecht, Wim; Ophoff, Roel A; Veldink, Jan H; Pasterkamp, R Jeroen; de Bakker, Paul I W; Landers, John E; van de Warrenburg, Bart P; van den Berg, Leonard H

    2011-12-01

    Several studies have suggested an increased frequency of variants in the gene encoding angiogenin (ANG) in patients with amyotrophic lateral sclerosis (ALS). Interestingly, a few ALS patients carrying ANG variants also showed signs of Parkinson disease (PD). Furthermore, relatives of ALS patients have an increased risk to develop PD, and the prevalence of concomitant motor neuron disease in PD is higher than expected based on chance occurrence. We therefore investigated whether ANG variants could predispose to both ALS and PD. We reviewed all previous studies on ANG in ALS and performed sequence experiments on additional samples, which allowed us to analyze data from 6,471 ALS patients and 7,668 controls from 15 centers (13 from Europe and 2 from the USA). We sequenced DNA samples from 3,146 PD patients from 6 centers (5 from Europe and 1 from the USA). Statistical analysis was performed using the variable threshold test, and the Mantel-Haenszel procedure was used to estimate odds ratios. Analysis of sequence data from 17,258 individuals demonstrated a significantly higher frequency of ANG variants in both ALS and PD patients compared to control subjects (p = 9.3 × 10(-6) for ALS and p = 4.3 × 10(-5) for PD). The odds ratio for any ANG variant in patients versus controls was 9.2 for ALS and 6.7 for PD. The data from this multicenter study demonstrate that there is a strong association between PD, ALS, and ANG variants. ANG is a genetic link between ALS and PD. Copyright © 2011 American Neurological Association.

  14. Analysis of Plasminogen Genetic Variants in Multiple Sclerosis Patients

    Directory of Open Access Journals (Sweden)

    A. Dessa Sadovnick

    2016-07-01

    Full Text Available Multiple sclerosis (MS is a prevalent neurological disease of complex etiology. Here, we describe the characterization of a multi-incident MS family that nominated a rare missense variant (p.G420D in plasminogen (PLG as a putative genetic risk factor for MS. Genotyping of PLG p.G420D (rs139071351 in 2160 MS patients, and 886 controls from Canada, identified 10 additional probands, two sporadic patients and one control with the variant. Segregation in families harboring the rs139071351 variant, identified p.G420D in 26 out of 30 family members diagnosed with MS, 14 unaffected parents, and 12 out of 30 family members not diagnosed with disease. Despite considerably reduced penetrance, linkage analysis supports cosegregation of PLG p.G420D and disease. Genotyping of PLG p.G420D in 14446 patients, and 8797 controls from Canada, France, Spain, Germany, Belgium, and Austria failed to identify significant association with disease (P = 0.117, despite an overall higher prevalence in patients (OR = 1.32; 95% CI = 0.93–1.87. To assess whether additional rare variants have an effect on MS risk, we sequenced PLG in 293 probands, and genotyped all rare variants in cases and controls. This analysis identified nine rare missense variants, and although three of them were exclusively observed in MS patients, segregation does not support pathogenicity. PLG is a plausible biological candidate for MS owing to its involvement in immune system response, blood-brain barrier permeability, and myelin degradation. Moreover, components of its activation cascade have been shown to present increased activity or expression in MS patients compared to controls; further studies are needed to clarify whether PLG is involved in MS susceptibility.

  15. Adenosine and Preexcitation Variants: Reappraisal of Electrocardiographic Changes.

    Science.gov (United States)

    Ali, Hussam; Lupo, Pierpaolo; Foresti, Sara; De Ambroggi, Guido; Epicoco, Gianluca; Fundaliotis, Angelica; Cappato, Riccardo

    2016-07-01

    Intravenous adenosine is a short-acting blocker of the atrioventricular node that has been used to unmask subtle or latent preexcitation, and also to enable catheter ablation in selected patients with absent or intermittent preexcitation. Depending on the accessory pathway characteristics, intravenous adenosine may produce specific electrocardiographic changes highly suggestive of the preexcitation variant. Herein, we view different ECG responses to this pharmacological test in various preexcitation patterns that were confirmed by electrophysiological studies. Careful analysis of electrocardiographic changes during adenosine test, with emphasis on P-delta interval, preexcitation degree, and atrioventricular block, can be helpful to diagnose the preexcitation variant/pattern.

  16. Complexity on Acute Myeloid Leukemia mRNA Transcript Variant

    Directory of Open Access Journals (Sweden)

    Carlo Cattani

    2011-01-01

    Full Text Available This paper deals with the sequence analysis of acute myeloid leukemia mRNA. Six transcript variants of mlf1 mRNA, with more than 2000 bps, are analyzed by focusing on the autocorrelation of each distribution. Through the correlation matrix, some patches and similarities are singled out and commented, with respect to similar distributions. The comparison of Kolmogorov fractal dimension will be also given in order to classify the six variants. The existence of a fractal shape, patterns, and symmetries are discussed as well.

  17. Cribriform-Morular Variant of Papillary Thyroid Carcinoma

    Directory of Open Access Journals (Sweden)

    Bahar AKKAYA

    2009-09-01

    Full Text Available Cribriform-morular variant of papillary thyroid carcinoma is a rare histological subtype of papillary thyroid carcinoma. This subtype is commonly reported in patients with familial adenomatous polyposis. However, cases not associated with polyposis have also been reported. The differential diagnosis of this entity from other aggressive thyroid neoplasms is important. A 29-year old man presented with a solitary mass in the left thyroid lobe underwent total thyroidectomy. Pathologic examination of the specimen revealed cribriform-morular variant of papillary thyroid carcinoma. After diagnosis, colonoscopy revealed a normal colon without polyposis. Herein, we report a case not associated with polyposis and discuss with the literature.

  18. Processing morphological variants in searches of Latin text

    OpenAIRE

    Mark Greengrass; Alexander M. Robertson; Robyn Schinke; Peter Willett

    1996-01-01

    A characteristic of natural-language text databases is that a user must be able to specify all of the variant forms of each query word if high recall is to be achieved. The most common type of word variants are those arising from morphology and thus most retrieval systems provide facilities for user-controlled right-hand (and occasionally left-hand) truncation to allow the retrieval of all words with the same root. A stemming algorithm, or stemmer, is a computational procedure that reduces al...

  19. Structure of chymotrypsin variant B from Atlantic cod, Gadus morhua

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Asgeirsson, B; Thórólfsson, M

    1996-01-01

    The amino-acid sequence of chymotrypsin variant B isolated from the pyloric caeca of Atlantic cod has been elucidated. The characterization of the primary structure is based on N-terminal Edman degradation and mass spectrometry of the native protein and enzymatically derived peptides. Chymotrypsin...... side-chains may contribute to the maintenance of flexibility at low temperatures. Several amino-acid sequence differences adjacent to the catalytic site are observed in the two cod chymotrypsin variants which also differ in kinetic properties. Unlike the mammalian chymotrypsins, which contain several...

  20. Diffuse sclerosing variant of papillary thyroid carcinoma: case report

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Chan; Kim, Dong Wook [Masan Samsung Hospital, Sungkyunkwan University, School of Medicine, Masan (Korea, Republic of)

    2006-07-15

    Diffuse sclerosing papillary carcinoma (DSPC) is a variant of papillary thyroid carcinoma (PTC), but it shows more aggressive clinical course and a poorer prognosis than the other types of PTC. Most PTCs show a focal nodular pattern in the thyroid on the imaging modalities, but DSPC reveals a diffuse infiltrating configuration in the thyroid without any focal nodular lesion. To our knowledge, there are scant radiological reports of diffuse sclerosing variant of papillary thyroid carcinoma. In this report, we present the case of a patient with DSPC who showed the characteristic findings on sonography and computed tomography.

  1. Variants in Pharmacokinetic Transporters and Glycaemic Response to Metformin

    DEFF Research Database (Denmark)

    Dujic, Tanja; Zhou, Kaixin; Yee, Sook Wah

    2017-01-01

    Therapeutic response to metformin, a first-line drug for type 2 diabetes (T2D), is highly variable, in part likely due to genetic factors. To date, metformin pharmacogenetic studies have mainly focused on the impact of variants in metformin transporters genes, with inconsistent results. To clarify....... None of the variants showed a significant effect on metformin response in the primary analysis, or in the exploratory secondary analyses, when patients were stratified according to possible confounding genotypes or prescribed metformin daily dose. Our results suggest that candidate transporters genes...

  2. GPI Mount Scopus--a variant of glucosephosphate isomerase deficiency.

    Science.gov (United States)

    Shalev, O; Shalev, R S; Forman, L; Beutler, E

    1993-10-01

    Glucosephosphate isomerase (GPI) deficiency is an unusual cause of hereditary nonspherocytic hemolytic anemia. The disease, inherited as an autosomal recessive disorder, is most often manifested by symptoms and signs of chronic hemolysis, ameliorated by splenectomy. We recently diagnosed GPI deficiency in a 23-year-old Ashkenazi Jewish man who displayed the typical clinical course of this disorder. The biophysical characteristics of the GPI variant are slow electrophoretic mobility, presence of only one of the two bands normally present, and extreme thermolability. To the best of our knowledge, this is the first report of GPI deficiency in a patient of Jewish descent, and we propose to designate this enzyme variant "GPI Mount Scopus".

  3. The Association between Pediatric NAFLD and Common Genetic Variants

    Directory of Open Access Journals (Sweden)

    Giuseppina Rosaria Umano

    2017-06-01

    Full Text Available Non-alcoholic fatty liver disease (NAFLD is one of the most common complications of obesity. Several studies have shown that genetic predisposition probably plays an important role in its pathogenesis. In fact, in the last few years a large number of genetic studies have provided compelling evidence that some gene variants, especially those in genes encoding proteins regulating lipid metabolism, are associated with intra-hepatic fat accumulation. Here we provide a comprehensive review of the gene variants that have affected the natural history of the disease.

  4. The influence of genomic context on mutation patterns in the human genome inferred from rare variants.

    Science.gov (United States)

    Schaibley, Valerie M; Zawistowski, Matthew; Wegmann, Daniel; Ehm, Margaret G; Nelson, Matthew R; St Jean, Pamela L; Abecasis, Gonçalo R; Novembre, John; Zöllner, Sebastian; Li, Jun Z

    2013-12-01

    Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to common variants in humans and human-chimpanzee fixed differences (substitutions), rare variants, on average, arose more recently in the human lineage and are less affected by the potentially confounding effects of natural selection, population demographic history, and biased gene conversion. We analyzed variants obtained from a population-based sequencing study of 202 genes in >14,000 individuals. We observed considerable variability in the per-gene mutation rate, which was correlated with local GC content, but not recombination rate. Using >20,000 variants with a derived allele frequency ≤ 10(-4), we examined the effect of local GC content and recombination rate on individual variant subtypes and performed comparisons with common variants and substitutions. The influence of local GC content on rare variants differed from that on common variants or substitutions, and the differences varied by variant subtype. Furthermore, recombination rate and recombination hotspots have little effect on rare variants of any subtype, yet both have a relatively strong impact on multiple variant subtypes in common variants and substitutions. This observation is consistent with the effect of biased gene conversion or selection-dependent processes. Our results highlight the distinct biases inherent in the initial mutation patterns and subsequent evolutionary processes that affect segregating variants.

  5. 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.

  6. From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS.

    Science.gov (United States)

    Mueller, Sabine C; Sommer, Björn; Backes, Christina; Haas, Jan; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2016-01-22

    Understanding the role of genetics in disease has become a central part of medical research. Non-synonymous single nucleotide variants (nsSNVs) in coding regions of human genes frequently lead to pathological phenotypes. Beyond single variations, the individual combination of nsSNVs may add to pathogenic processes. We developed a multiscale pipeline to systematically analyze the existence of quantitative effects of multiple nsSNVs and gene combinations in single individuals on pathogenicity. Based on this pipeline, we detected in a data set of 842 nsSNVs discovered in 76 genes related to cardiomyopathies, associated nsSNV combinations in seven genes present in at least 70% of all 639 patient samples, but not in a control cohort of healthy humans. Structural analyses of these revealed primarily an influence on the protein stability. For amino acid substitutions located at the protein surface, we generally observed a proximity to putative binding pockets. To computationally analyze cumulative effects and their impact, pathogenicity methods are currently being developed. Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer.

  7. Comparison of locus-specific databases for BRCA1 and BRCA2 variants reveals disparity in variant classification within and among databases.

    Science.gov (United States)

    Vail, Paris J; Morris, Brian; van Kan, Aric; Burdett, Brianna C; Moyes, Kelsey; Theisen, Aaron; Kerr, Iain D; Wenstrup, Richard J; Eggington, Julie M

    2015-10-01

    Genetic variants of uncertain clinical significance (VUSs) are a common outcome of clinical genetic testing. Locus-specific variant databases (LSDBs) have been established for numerous disease-associated genes as a research tool for the interpretation of genetic sequence variants to facilitate variant interpretation via aggregated data. If LSDBs are to be used for clinical practice, consistent and transparent criteria regarding the deposition and interpretation of variants are vital, as variant classifications are often used to make important and irreversible clinical decisions. In this study, we performed a retrospective analysis of 2017 consecutive BRCA1 and BRCA2 genetic variants identified from 24,650 consecutive patient samples referred to our laboratory to establish an unbiased dataset representative of the types of variants seen in the US patient population, submitted by clinicians and researchers for BRCA1 and BRCA2 testing. We compared the clinical classifications of these variants among five publicly accessible BRCA1 and BRCA2 variant databases: BIC, ClinVar, HGMD (paid version), LOVD, and the UMD databases. Our results show substantial disparity of variant classifications among publicly accessible databases. Furthermore, it appears that discrepant classifications are not the result of a single outlier but widespread disagreement among databases. This study also shows that databases sometimes favor a clinical classification when current best practice guidelines (ACMG/AMP/CAP) would suggest an uncertain classification. Although LSDBs have been well established for research applications, our results suggest several challenges preclude their wider use in clinical practice.

  8. Variant of a Klippel-Trenaunay syndrome - Case report; Variante eines Klippel-Trenaunay-Syndroms - ein Fallbericht

    Energy Technology Data Exchange (ETDEWEB)

    Irlbacher, K.; Behse, F.; Roericht, S.; Meyer, B.U. [Charite-Campus Virchow Klinikum, Humboldt-Univ. Berlin (Germany); Hoffmann, K.T. [Charite-Campus Virchow Klinikum, Humboldt-Univ. Berlin (Germany). Radiologische Klinik

    2000-07-01

    We report a patient with a variant of this syndrome presenting with extensive varicose veins and arteriovenous shunts within the left arm, bony hypotrophy of the left hand, mucocutaneous melanin spots in the face and thrombocytopenia. Imaging techniques play a major role in making a diagnosis in angiophakomatoses. (orig.) [German] Hier wird eine Patientin mit einer Variante eines KT vorgestellt, bei der klinisch und mit bildgebenden Verfahren folgende Befunde erhoben wurden: Segmentale varikoese Venektasien und arteriovenoese Kurzschluesse im linken Arm und Hypotrophie von Handknochen, Phlebolithen, Venenektasien in der linken Wangenschleimhaut, Pigmentnaevi in der Gesichts-, Lippen-, und Wangenschleimhaut und Thrombozytopenie. Bildgebende Verfahren helfen hier eine diagnostische Einstufung vorzunehmen. (orig.)

  9. Generalidades sobre las partículas similares al Virus del Papiloma Humano

    Directory of Open Access Journals (Sweden)

    Jorge Félix Beltrán Lissabet

    2014-01-01

    Full Text Available El virus del papiloma humano provoca (VPH una de las enfermedades de transmisión sexual más frecuentes a nivel mundial que afecta aproximadamente a 500 000 mujeres cada año. La proteína L1 se encuentra m arcadamente conservada entre los diferentes tipos del VPH, y tiene la capacidad de autoensamblarse formando partículas similares a virus (PSV que presentan u na elevada inmunogenicidad. El uso de PSV recombinantes como inmunógenos, se ha incrementado en lo s últimos años. Las dos vacunas profilácticas actuales contra el VPH (Gardasil y Cervarix están basadas en PSV, las cuales han resultado muy eficac es. Existen disímiles estrategias encaminadas a la obtención de PSV, entre las que se destacan las modifica ciones genéticas, la selección idónea de un sistema de expresión y la optimización de los métodos de purificación. Pese a los resultados en las investigaciones en el campo del desarrollo de PSV del VPH, aún queda mucho por hacer, debido a la influencia de disímiles variables desconocidas que afectan la organización y la actividad biológica de este complejo macromolecular. La purificación de la proteína L1 constituye una etapa clave durante la obtención PSV del VPH, que depende de la estrategia de purificaci ón utilizada. El desarrollo de PSV quiméricas del VPH se ha convertido en una prometedora estrategia que permite el desarrollo de una repue sta humoral heterogénea contra las infecciones provocadas por los diferentes tipos del VPH. Aunque se ha avanzado en las investigaciones encaminadas al desarrollo de las PSV del VPH, aún existen muchas variables desconocidas que influyen de maner a desconocida en el ensamblaje macromolecular de estas estructuras.

  10. TEMA 1-2014: GENERALIDADES SOBRE SÍNDROME COMPARTIMENTAL EN EXTREMIDADES

    OpenAIRE

    2014-01-01

    El síndrome compartimental que no se reconoce y no se trata de manera inmediata puede llevar a la pérdida de la extremidad y en el peor de los casos amenaza la vida del paciente. El pronósticopara la recuperación depende del diagnóstico y tratamiento inmediato. El dar un diagnóstico tardío o equivocado aumenta el número de complicaciones y riesgos. Esta revisión de tema se basa en hacer énfasis en la clínica del paciente, sobre todo si el dolor en la extremidad es lo que predomina ante las me...

  11. Uso de glucocorticoides sistémicos en Pediatría: generalidades

    OpenAIRE

    Mónica Rodríguez González; Francisco Espinosa Rosales

    2016-01-01

    El cortisol y la corticosterona son hormonas sintetizadas y secretadas por la corteza (cortico) de las glándulas suprarrenales a partir del metabolismo del colesterol (esteroides). Debido a su papel en el metabolismo de carbohidratos se clasifican como glucocorticoides. Su regulación es dada por el eje hipotálamo– adenohipofisiario y tienen un papel pleiotrópico en homeostasis, metabolismo celular y regulación inmune.

  12. Generalidades sobre Rocas y Análisis Químicos de Suelos.

    Directory of Open Access Journals (Sweden)

    Orozco Aycardo

    1940-12-01

    Full Text Available Tomaré como base para estas anotaciones un análisis químico de suelo siguiendo el método de la fusión con carbonato de sodio, acentuando mis apuntes sobre los distintos métodos seguidos para la determinación de los elementos hierro, aluminio, calcio, magnesio, fósforo y potasio, partiendo de una solución clorhídrica. Al tratar Ia muestra con carbonato de sodio con una molécula, de agua o anhidro a la temperatura de la fusión se acusa una modificación de la molécula de silicatos complejos, haciéndolos pasar a la forma de silicatos alcalinos que es la operación que en química se conoce con los nombres de Disgragación o Desgregación. Los demás minerales presentes en la muestra se modifican. obteniéndolos así en forma de aluminatos y fosfatos. De esta manera se tienen silicatos, aluminatos y fosfatos de hierro, calcio, magnesio, manganeso, bario, etc., solubles en solución de ácido clorhídrico.

  13. GENERALIDADES DE LOS UREDINALES(Fungi: Basidiomycota Y DE SUS RELACIONES FILOGENÉTICAS

    Directory of Open Access Journals (Sweden)

    ZULUAGA CATALINA MARÍA

    2009-04-01

    Full Text Available

    RESUMEN

    Los hongos-roya (Uredinales, Basidiomycetes representan uno de los grupos de microorganismos fitoparásitos más diversos y con mayor importancia económica mundial en la producción agrícola y forestal. Se caracterizan por ser patógenos obligados y por presentar una estrecha coevolución con sus hospedantes vegetales. Su taxonomía se ha basado fundamentalmente en el estudio de caracteres morfológicos, resultando en muchos casos en la formación de taxones polifiléticos. Sin embargo, en los últimos años se han tratado de incorporar herramientas moleculares que conduzcan a la generación de sistemas de clasificación basados en afinidades evolutivas. En esta revisión se ofrece una mirada general a las características de los uredinales, enfatizando en el surgimiento reciente de estudios filogenéticos que plantean la necesidad de establecer una profunda revisión de la taxonomía de este grupo. Finalmente se alerta sobre la necesidad de que en dichos estudios taxonómicos se incluya un alto número de especies de royas neotropicales, pues esta zona es reconocida no sólo por su alta diversidad de hongos-royas, sino también por las características únicas de sus ciclos de vida.

    Palabras clave: filogenia, hongos-roya, Puccinia, secuenciación, teliosporas.


    ABSTRACT

    Rust fungi (Uredinales, Basidiomycetes are one of the most diverse and economically important plant pathogens of crops world-wide. They are obligated parasites and have a close evolutionary relationship with their plant hosts. Taxonomy of this group has been based on morphological treats, resulting in generation of polyphyletic taxa. Recently, different studies have incorporated molecular techniques addressed to establishing evolutionary affinities between these fungi. This review presents a general view of the biological characteristics of rust fungi, with a detailed discussion on the phylogenetic studies regarding the group. Finally, the review proposes the necessity to establish phylogenetic studies on rust fungi from the neotropics, where these fungi present a very high diversity and unique life cycles.

    Key words: phylogeny, Puccinia, rust fungi, sequencing, teliospores.

  14. El síndrome autista: un acercamiento a sus características y generalidades

    Directory of Open Access Journals (Sweden)

    Ronald Soto Calderón

    2002-01-01

    Full Text Available En este artículo se presentan aspectos generales sobre el Síndrome del Autismo, se mencionan algunas propuestas etiológicas, los aspectos clínicos relacionados con el Síndrome, entre los que se incluyen algunas definiciones y descripciones propuestas por investigadores y científicos, y manuales psiquiátricos, de los cuales se extraen los criterios propuestos para un diagnóstico del Síndrome. Por otro lado, se escribe un apartado sobre la planificación de la acción correctiva a partir de un diagnóstico, en donde se respeta la individualidad de la persona, se hace referencia a los aspectos familiares, los aspectos educativos, y a diferentes aspectos relacionados con el diagnóstico, los servicios, y los tratamientos en nuestro país. También se menciona la epidemiología del Síndrome y su pronóstico. Se presenta además un cuadro donde se resumen las características del Síndrome Autista. De esta manera se considera importante que las personas que interactúan con las personas portadoras del Síndrome de Autismo, conozcan sobre este síndrome y la forma en que pueden ser apoyadas en su proceso de desarrollo, desde una visión más interdisciplinaria

  15. Aditivos para hormigones, morteros y pastas: generalidades, clasificación y definiciones

    Directory of Open Access Journals (Sweden)

    Gaspar-Tebar, Demetrio

    1982-05-01

    Full Text Available Not available.El empleo de aditivos en la fabricación de hormigones, morteros y pastas, hechos a base de cemento, proporciona una serie de ventajas al mejorar al menos alguna de sus propiedades y, porque además, contribuye a conseguir una calidad constante. De este modo se obtienen productos más competitivos en los aspectos técnicos y económicos frente a otros materiales; de aquí, el incremento que ha experimentado el consumo de aditivos en los últimos años.

  16. Data mining : Generalidades y un enfoque al problema de reglas de asociación cuantitativas

    OpenAIRE

    1999-01-01

    Con el correr del tiempo, /as capacidades de generar y coleccionar datos se han incrementado con rapidez. El extenso uso de códigos de barras en al mayoría de los productos comerciales, la informatización de muchas actividades y de gestiones de gobierno, y los avances en herramientas de colección de datos; proveen enormes cantidades de ellos. La disponibilidad de poderosos sistemas de Bases de Datos y el crecimiento explosivo en los datos, generaron una urgente necesidad de algunas técnicas y...

  17. Stereotaxis: Its history, generalities and updating. Estereotaxia: Historia, generalidades y actualidades.

    Directory of Open Access Journals (Sweden)

    Osmany Morales Sabina

    Full Text Available The brain is considered the human being’s organ rector, it is characterized by its fragility, complexity and fineness, therefore any surgical intervention on him should be precise and sure. The present publication revises in way chronological aspects of national and international relevance related with the history of the stereotaxy, the medicals principles and technicians in that its operation is sustained approaches, and it summarizes the indications, complication and contraindications of the technique. The work conception is explained in team that they require these considerations, based on the experience of Service of Neurosurgery of Cienfuegos, current considerations of the present and future of the stereotaxy are emitted.

    El cerebro es considerado el órgano rector del ser humano, se caracteriza por su fragilidad, complejidad y delicadeza, por ende cualquier intervención quirúrgica sobre él debe ser precisa y certera. La presente publicación revisa de manera cronológica aspectos de relevancia nacional e internacional relacionados con la historia de la estereotaxia, aborda los principios médicos y técnicos en que se sustenta su funcionamiento, y resume las indicaciones, complicaciones y contraindicaciones de la técnica. Se explica la concepción de trabajo en equipo que requieren estos procederes, basado en la experiencia del Servicio de Neurocirugía de Cienfuegos, y se emiten consideraciones actuales del presente y futuro de la estereotaxia.

  18. La ley 100 de 1993, Generalidades, Alcances, Incidencia en las Instituciones de salud

    Directory of Open Access Journals (Sweden)

    Gustavo Malagón Londoño

    1994-09-01

    Full Text Available

    Foro llevado a cabo en la Academia Nacional de Medicina el día 23 de junio de 1994.

    Interviene en primer lugar el Académico Malagón Londoño, quien inicia su participación explicando que realizará una ojeada rápida en relación con las definiciones, las implicaciones y los objetivos de la Ley 100 de 1993 y las instituciones de salud y el cuerpo médico nacional.

    Antecedentes
    El tema de la seguridad social surge por primera vez en nuestra historia en el Congreso de Angostura en 1819.1,2 La siguiente mención a este tema aparece en la Constitución de 1886, donde se habla de la asistencia pública como obligatoria. M El presidente Alfonso López Pumarejo, en su Acto Legislativo N° 1 de 1936, 5,6 habla de la asistencia pública y de la obligación social del Gobierno. Agrega que el trabajo es una obligación del ciudadano y el Estado, a su vez, tiene la obligación de darle seguridad y salud al trabajador. En su segunda magistratura, su gobierno emite la Ley 6a de 1945 que trata, precisamente, sobre los mecanismos para llegar a una seguridad social, sin que se expliquen suficientemente bien.

    En 1946, la Ley 90 sobre seguridad social, logra una mejor definición de los conceptos básicos, que se constituyen en los preámbulos de la Constitución de 1991. Desde ese entonces se confunde la seguridad social con el Seguro Social. Viene mucho más tarde la Constitución de 1991, que sienta las bases fundamentales para crear un estado de derecho y seguridad social integral. Los constituyentes del 91 trabajaron con base en ese concepto de estado de derecho, determinando las obligaciones básicas e irrenunciables del Gobierno para con el bienestar social y la salud. En esa forma nace el esquema de la Ley 100. En los artículos 42, 43, 44, 45, 46 y 47 se prepara el terreno; ya en el artículo 48 se habla de la seguridad social y el artículo 49 demuestra la obligatoriedad del Estado para dar salud a todos los colombianos.

    Son estos los puntos de referencia fundamentales de la Ley 100, indispensables para definir el sistema de Seguridad Social Integral, el cual se dirige a afrontar la realidad, vista la inequidad en la atención de la salud, la baja cobertura, la ineficiencia y la desarticulación de los mecanismos asistenciales. El viejo modelo de asistencia pública se basaba en el concepto de la caridad, de la atención en hospitales vetustos, mal dotados y, con muchísima frecuencia, mal atendidos. Aparece entonces el modelo actual en la competencia -aspecto importantísimo en el estímulo para el progreso y la mejoría de los organismos de salud-lleva a la creación de servicios de salud calificados.

    La Ley 100 de Seguridad Social Integral significa un importante paso de avanzada; representa una nueva era en la asistencia en salud. El Gobierno, a partir de la Ley 10 de 1990, sienta políticas generales que llevan a una asistencia integral en salud. Recomienda métodos de control y de evaluación en factores de riesgo, con la participación de la comunidad y propende por una cobertura total, habida cuenta de la pobre cobertura existente, no más allá del 20% de la población. Se apoya dicha ley en estadísticas reales de déficit asistencial existente en la nación. Estos puntos han sido tenidos en cuenta dentro de la estructuración de la Ley 100...

  19. Abuso sexual en menores de edad: generalidades, consecuencias y prevención

    OpenAIRE

    2014-01-01

    Introducción: El abuso sexual en menores de edad es uno de los tipos de maltrato infantil con peores repercusiones en sus víctimas y que usualmente coexiste con otros tipos de violencia. Incluye tanto agravios que no involucran contacto físico como aquellos que sí lo hacen, lo que cubre una amplia gama de posibilidades. Objetivo: Debido a lo trascendental de esta problemática, se realizó está revisión bibliográfica con el fin de exponer la importancia del tema de abuso sexual en menores de ed...

  20. Generalidades sobre Rocas y Análisis Químicos de Suelos.

    Directory of Open Access Journals (Sweden)

    Facultad Nacional de Agronomía Universidad Nacional de Colombia Sede Medellín

    1940-09-01

    Full Text Available Como consecuencia de la guerra mundial de 1914 a 1918, surgieron modificaciones y criticas caracterizadas por una pluralidad singular, lo cual creó la necesidad de una nueva organización en estas cuestiones, que tuvo como resultado la reunión en Roma, en el año de 1924, de una Conferencia Internacional, la que decidió no modificar el sistema anterior y comisionar a un grupo de químicos para que estudiaran la proporción que debía existir entre la concentración de la solución clorhídrica y la cantidad de muestra; el tiempo de la ebullición y para que reunieran la mayor cantidad posible de conclusiones al respecto de esta interesante cuestión En seguida expondré un ligero comentario sobre algunos debates que han surgido en torno al disolvente más apropiado en los análisis químicos de los suelos. Aquí podrá verse la agobiadora anarquia que ha existido en torno a estas cuestiones, no obstante las intervenciones de congresos y academias.

  1. Abuso sexual en menores de edad: generalidades, consecuencias y prevención

    Directory of Open Access Journals (Sweden)

    María José Acuña Navas

    2014-03-01

    Full Text Available Introducción: El abuso sexual en menores de edad es uno de los tipos de maltrato infantil con peores repercusiones en sus víctimas y que usualmente coexiste con otros tipos de violencia. Incluye tanto agravios que no involucran contacto físico como aquellos que sí lo hacen, lo que cubre una amplia gama de posibilidades. Objetivo: Debido a lo trascendental de esta problemática, se realizó está revisión bibliográfica con el fin de exponer la importancia del tema de abuso sexual en menores de edad, sus aspectos generales, consecuencias y medida preventivas. Síntesis de datos: El abuso sexual es frecuente. Las víctimas suelen ser mujeres a pesar de que existen ciertos factores de riesgo que predisponen a ciertos niños a ser agredidos, y sus abusadores por lo general son personas cercanas a ellos. Las consecuencias tanto a corto como largo plazo abarcan todos los aspectos del ser humano y la magnitud de su gravedad dependerá de diversos factores. Existen métodos de prevención primaria y secundaria, que van desde programas educativos y campañas publicitarias hasta medidas judiciales. Conclusiones: Es necesaria más información relativa al abuso sexual en menores y es imprescindible liberarse de los estereotipos en torno a esta problemática para detectar a tiempo posibles casos de abuso. Toda víctima deberá obtener una atención individualizada posterior al suceso, dirigida a atenuar las secuelas. El abordaje del abuso sexual se deberá hacer desde diversas perspectivas y todos estamos a cargo de su combate.

  2. GENERALIDADES DE LOS UREDINALES (Fungi: Basidiomycota Y DE SUS RELACIONES FILOGENÉTICAS

    Directory of Open Access Journals (Sweden)

    CATALINA MARÍA ZULUAGA

    2009-01-01

    Full Text Available Los hongos-roya (Uredinales, Basidiomycetes representan uno de los grupos de microor- ganismos fitoparásitos más diversos y con mayor importancia económica mundial en la producción agrícola y forestal. Se caracterizan por ser patógenos obligados y por presentar una estrecha coevolución con sus hospedantes vegetales. Su taxonomía se ha basado fundamentalmente en el estudio de caracteres morfológicos, resultando en muchos casos en la formación de taxones polifiléticos. Sin embargo, en los últimos años se han tratado de incorporar herramientas moleculares que conduzcan a la generación de sistemas de clasificación basados en afinidades evolutivas. En esta revisión se ofrece una mirada general a las características de los uredinales, enfatizando en el surgimiento reciente de estudios filogenéticos que plantean la necesidad de establecer una profunda revisión de la taxonomía de este grupo. Finalmente se alerta sobre la necesidad de que en dichos estudios taxonómicos se incluya un alto número de especies de royas neo- tropicales, pues esta zona es reconocida no sólo por su alta diversidad de hongos-royas, sino también por las características únicas de sus ciclos de vida.

  3. Gimnasia artística. Generalidades y aspectos básicos

    OpenAIRE

    Ávalos Ramos, María Alejandra; Vega Ramírez, Lilyan

    2016-01-01

    Descripción del origen de la gimnasia y presentación de las características principales de los aparatos específicos utilizados tanto en la modalidad de la la gimnasia artística femenina como en la modalidad de la gimnasia artística masculina.

  4. GENERALIDADES DE LOS UREDINALES (Fungi: Basidiomycota) Y DE SUS RELACIONES FILOGENÉTICAS

    OpenAIRE

    CATALINA MARÍA ZULUAGA; PABLO BURITICÁ CÉSPEDES; MAURICIO MARÍN-MONTOYA

    2009-01-01

    Los hongos-roya (Uredinales, Basidiomycetes) representan uno de los grupos de microor- ganismos fitoparásitos más diversos y con mayor importancia económica mundial en la producción agrícola y forestal. Se caracterizan por ser patógenos obligados y por presentar una estrecha coevolución con sus hospedantes vegetales. Su taxonomía se ha basado fundamentalmente en el estudio de caracteres morfológicos, resultando en muchos casos en la formación de taxones polifiléticos. Sin embargo, en los últi...

  5. Turismo médico: generalidades para su comprensión integral

    OpenAIRE

    Daniel Martínez Chaves

    2016-01-01

    Se plantea un estudio sobre el desarrollo del turismo médico, con su enfoque teórico, epistemológico y crítico, y con un formato lógico y concreto, que permita al lector comprender la complejidad de modo mesurado y técnico. Posterior a esto, se aborda cómo implementar los conceptos y sus características al plano práctico (metodología), sus variables y las interrelaciones de estas en forma integral u holística. Se concluye con la propuesta de un método heurístico de diseño propio del investiga...

  6. Odontología en equinos: generalidades e importancia en medicina veterinaria

    Directory of Open Access Journals (Sweden)

    Lina Marcela Rodríguez Jiménez

    2011-12-01

    Full Text Available A través del tiempo, los equinos han evolucionado tanto anatómicamente como en sus hábitos alimenticios debido a su domesticación, por tanto, su dentición ha cambiado pero es la huella que permite conocer su edad. En la práctica de clínica veterinaria es necesario conocer la estructura y fisiología de la cavidad oral, y la manera como se manifiesta la presencia de alteraciones de orden dental que afectan a los equinos, y de qué forma se debe realizar un correcto examen clínico de dicha cavidad, facilitando el uso de tratamientos preventivos y, en el caso de que exista una afección, llegar a un diagnóstico acertado y posteriormente establecer el tratamiento adecuado. Es importante tener en cuenta que la odontología veterinaria se ha descuidado por parte de los profesionales dejando que sea invadida por empíricos u odontólogos humanos.

  7. Generalidades sobre Rocas y Análisis Químicos de Suelos.

    Directory of Open Access Journals (Sweden)

    Orozco R. Aycardo

    1940-03-01

    Full Text Available Desde el día en que inicie el presente trabajo, apoyado por la amable circular que me proporcionó el Rector de la Facultad Nacional de Agronomía, el Jorge Gutiérrez, para dirigirme a diversos lugares del país en solitud de material que me sirviera para poner en práctica los diversos métodos que me fuere dado ejecutar, no tuve otro objetivo que el de reunir el mayor número posible de métodos, para hacer un análisis químico del suelo. Tenía el pleno convencimiento de que nada nuevo iba a aportar a las ciencias químicas, pero en cambio, como me lo sugirió el que más tarde designé como Presidente de Tesis, doctor Antonio Durán A., si podría compilar una serie de métodos explicados en un lenguaje tan sencillo, como en texto alguno pudiera presentarse. Entonces nació en mí el deseo de proporcionar a los estudiantes venideros un texto elemental sobre principios de análisis de algunos elementos de importancia agronómica, el cual no lo dudo me ha quedado defectuoso, pero estoy seguro que, el ser corregido por el Profesor respectivo, tendrá el valor a que yo aspiro. Con gran delicadeza he practicado los sistemas de análisis que anoto, procurándome así una experiencia que si es corta en realidad de verdad, si me permite diferenciar los diversos métodos de determinaciones, basado en la bondad de resultados verificados en muchas ocasiones. No creyendo tanto en la influencia del factor personal cuanto es la bondad del método, he resuelto acogerme hasta el conocimiento de nuevos y más eficientes, a los siguientes para las determinaciones de elementos, partiendo de soluciones clorhídricas.

  8. Generalidades y potencialidad en biocontrol de las gregarinas entomoparásitas

    OpenAIRE

    REYES VILLANUEVA, FILIBERTO

    2004-01-01

    Se presenta una descripciU?n general de la taxonomI?a, ciclo biologico, rango de huespedes y patoge- nicidad de las gregarinas par·sitas de insectos. Se mencionan los factores responsables mas importan- tes que determinan su patogenicidad, usando ejemplos de especies con baja, moderada y alta patogenicidad sobre insectos plaga y vectores de patogenos al hombre. Finalmente, se recomiendan lI?neas de investigacion como una guI?a para estudios futuros orientados hacia el posible uso de estos ...

  9. Neuropathology in classical and variant ataxia-telangiectasia

    NARCIS (Netherlands)

    Verhagen, Mijke M. M.; Martin, Jean-Jacques; van Deuren, Marcel; Groote, Chantal Ceuterick-de; Weemaes, Corry M. R.; Kremer, Berry H. P. H.; Taylor, Malcolm A. R.; Willemsen, Michel A. A. P.; Lammens, Martin

    2012-01-01

    Ataxia-telangiectasia (A-T) is classically characterized by progressive neurodegeneration, oculocutaneous telangiectasia, immunodeficiency and elevated a-fetoprotein levels. Some patients, classified as variant A-T, exhibit a milder clinical course. In the latter patients extrapyramidal symptoms, in

  10. Clear Speech Variants: An Acoustic Study in Parkinson's Disease

    Science.gov (United States)

    Lam, Jennifer; Tjaden, Kris

    2016-01-01

    Purpose: The authors investigated how different variants of clear speech affect segmental and suprasegmental acoustic measures of speech in speakers with Parkinson's disease and a healthy control group. Method: A total of 14 participants with Parkinson's disease and 14 control participants served as speakers. Each speaker produced 18 different…

  11. Inferring causative variants in microRNA target sites.

    Science.gov (United States)

    Thomas, Laurent F; Saito, Takaya; Sætrom, Pål

    2011-09-01

    MicroRNAs (miRNAs) regulate genes post transcription by pairing with messenger RNA (mRNA). Variants such as single nucleotide polymorphisms (SNPs) in miRNA regulatory regions might result in altered protein levels and disease. Genome-wide association studies (GWAS) aim at identifying genomic regions that contain variants associated with disease, but lack tools for finding causative variants. We present a computational tool that can help identifying SNPs associated with diseases, by focusing on SNPs affecting miRNA-regulation of genes. The tool predicts the effects of SNPs in miRNA target sites and uses linkage disequilibrium to map these miRNA-related variants to SNPs of interest in GWAS. We compared our predicted SNP effects in miRNA target sites with measured SNP effects from allelic imbalance sequencing. Our predictions fit measured effects better than effects based on differences in free energy or differences of TargetScan context scores. We also used our tool to analyse data from published breast cancer and Parkinson's disease GWAS and significant trait-associated SNPs from the NHGRI GWAS Catalog. A database of predicted SNP effects is available at http://www.bigr.medisin.ntnu.no/mirsnpscore/. The database is based on haplotype data from the CEU HapMap population and miRNAs from miRBase 16.0.

  12. Two new splice variants in porcine PPARGC1A

    Directory of Open Access Journals (Sweden)

    Peelman Luc J

    2008-12-01

    Full Text Available Abstract Background Peroxisome proliferator-activated receptor γ coactivator 1α (PPARGC1A is a coactivator with a vital and central role in fat and energy metabolism. It is considered to be a candidate gene for meat quality in pigs and is involved in the development of obesity and diabetes in humans. How its many functions are regulated, is however still largely unclear. Therefore a transcription profile of PPARGC1A in 32 tissues and 4 embryonic developmental stages in the pig was constructed by screening its cDNA for possible splice variants with exon-spanning primers. Findings This led to the discovery of 2 new splice variants in the pig, which were subsequently also detected in human tissues. In these variants, exon 8 was either completely or partly (the last 66 bp were conserved spliced out, potentially coding for a much shorter protein of respectively 337 and 359 amino acids (aa, of which the first 291 aa would be the same compared to the complete protein (796 aa. Conclusion Considering the functional domains of the PPARGC1A protein, it is very likely these splice variants considerably affect the function of the protein and alternative splicing could be one of the mechanisms by which the diverse functions of PPARGC1A are regulated.

  13. Reliability and Validation Study of the Online Instinctual Variant Questionnaire

    Science.gov (United States)

    Andre, Sherry

    2014-01-01

    Leaders often manage both chaos and diversity. We can improve our leadership effectiveness by better understanding our motives and behaviors, and those of our followers. A potential tool for leadership development is the Instinctual Variant Questionnaire (IVQ). Based on Enneagram theory (pronounced "ANY-a-gram"), this online instrument…

  14. Status quo of annotation of human disease variants

    NARCIS (Netherlands)

    Venselaar, H.; Camilli, F.; Gholizadeh, S.; Snelleman, M.; Brunner, H.G.; Vriend, G.

    2013-01-01

    BACKGROUND: The ever on-going technical developments in Next Generation Sequencing have led to an increase in detected disease related mutations. Many bioinformatics approaches exist to analyse these variants, and of those the methods that use 3D structure information generally outperform those that

  15. Novel EYA1 variants causing Branchio-oto-renal syndrome.

    Science.gov (United States)

    Klingbeil, Kyle D; Greenland, Christopher M; Arslan, Selcuk; Llamos Paneque, Arianne; Gurkan, Hakan; Demir Ulusal, Selma; Maroofian, Reza; Carrera-Gonzalez, Andrea; Montufar-Armendariz, Stefany; Paredes, Rosario; Elcioglu, Nursel; Menendez, Ibis; Behnam, Mahdiyeh; Foster, Joseph; Guo, Shengru; Escarfuller, Sebastian; Cengiz, Filiz Basak; Duman, Duygu; Bademci, Guney; Tekin, Mustafa

    2017-07-01

    Branchio-oto-renal (BOR) syndrome is an autosomal dominant genetic disorder characterized by second branchial arch anomalies, hearing impairment, and renal malformations. Pathogenic mutations have been discovered in several genes such as EYA1, SIX5, and SIX1. However, nearly half of those affected reveal no pathogenic variant by traditional genetic testing. Whole Exome sequencing and/or Sanger sequencing performed in 10 unrelated families from Turkey, Iran, Ecuador, and USA with BOR syndrome in this study. We identified causative DNA variants in six families including novel c.525delT, c.979T > C, and c.1768delG and a previously reported c.1779A > T variants in EYA1. Two large heterozygous deletions involving EYA1 were detected in additional two families. Whole exome sequencing did not reveal a causative variant in the remaining four families. A variety of DNA changes including large deletions underlie BOR syndrome in different populations, which can be detected with comprehensive genetic testing. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Mutation Update for UBE3A variants in Angelman syndrome.

    Science.gov (United States)

    Sadikovic, Bekim; Fernandes, Priscilla; Zhang, Victor Wei; Ward, Patricia A; Miloslavskaya, Irene; Rhead, William; Rosenbaum, Richard; Gin, Robert; Roa, Benjamin; Fang, Ping

    2014-12-01

    Angelman syndrome is a neurodevelopmental disorder caused by a deficiency of the imprinted and maternally expressed UBE3A gene. Although de novo genetic and epigenetic imprinting defects of UBE3A genomic locus account for majority of Angelman diagnoses, approximately 10% of individuals affected with Angelman syndrome are a result of UBE3A loss-of-function mutations occurring on the expressed maternal chromosome. The variants described in this manuscript represent the analysis of 2,515 patients referred for UBE3A gene sequencing at our institution, along with a comprehensive review of the UBE3A mutation literature. Of these, 267 (10.62%) patients had a report issued for detection of a UBE3A gene nucleotide variant, which in many cases involved family studies resulting in reclassification of variants of unknown clinical significance (VUS). Overall, 111 (4.41%) probands had a nucleotide change classified as pathogenic or strongly favored to be pathogenic, 29 (1.15%) had a VUS, and 126 (5.0%) had a nucleotide change classified as benign or strongly favored to be benign. All variants and their clinical interpretations are submitted to NCBI ClinVar, a freely accessible human variation and phenotype database. © 2014 WILEY PERIODICALS, INC.

  17. A Galeazzi-variant type fracture-dislocation in adults

    National Research Council Canada - National Science Library

    Raju Vaishya Sundar Kumar Shrestha Abhishek Vaish

    2013-01-01

    ...) is not a common injury and is inherently unstable.Here we report a case series,with both-bone forearm fractures associated with dislocation of DRUJ,as a Galeazzi-variant type fracture-dislocation,and try to analyze this injury...

  18. A Variant of Young's Double Slit Experiment for Educational Purposes

    Science.gov (United States)

    Henault, Francois; Spang, Alain

    2011-01-01

    We describe a variant of the classical Young's double slit experiment that can be easily realized in any classroom, in order to evidence the wave nature of light. The proposed apparatus and its simplified theory are described and pictures of fringes, readily obtained using only cheap and off-the-shelf optical components, are reproduced. The…

  19. A PYY Q62P variant linked to human obesity

    Energy Technology Data Exchange (ETDEWEB)

    Ahituv, Nadav; Kavaslar, Nihan; Schackwitz, Wendy; Ustaszewska,Anna; Collier, John Michael; Hebert, Sybil; Doelle, Heather; Dent,Robert; Pennacchio, Len A.; McPherson, Ruth

    2005-06-27

    Members of the pancreatic polypeptide family and the irreceptors have been implicated in the control of food intake in rodents and humans. To investigate whether nucleotide changes in these candidate genes result in abnormal weight in humans, we sequenced the coding exons and splice sites of seven family members (NPY, PYY, PPY, NPY1R, NPY2R, NPY4R, and NPY5R) in a large cohort of extremely obese (n=379) and lean (n=378) individuals. In total we found eleven rare non-synonymous variants, four of which exhibited familial segregation, NPY1R L53P and PPY P63L with leanness and NPY2R D42G and PYY Q62P with obesity. Functional analysis of the obese variants revealed NPY2R D42G to have reduced cell surface expression, while previous cell culture based studies indicated variant PYY Q62P to have altered receptor binding selectivity and we show that it fails to reduce food intake through mouse peptide injection experiments. These results support that rare non-synonymous variants within these genes can alter susceptibility to human body mass index extremes.

  20. Oncogenic potential diverge among human papillomavirus type 16 natural variants

    Energy Technology Data Exchange (ETDEWEB)

    Sichero, Laura, E-mail: lsichero@gmail.com [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Simao Sobrinho, Joao [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Lina Villa, Luisa [Molecular Biology Laboratory, Center of Translational Oncology, Instituto do Cancer do Estado de Sao Paulo-ICESP, Sao Paulo 01246-000 (Brazil); Department of Virology, Ludwig Institute for Cancer Research, Sao Paulo 01323-903 (Brazil); Department of Radiology, School of Medicine, University of Sao Paulo (Brazil)

    2012-10-10

    We compared E6/E7 protein properties of three different HPV-16 variants: AA, E-P and E-350G. Primary human foreskin keratinocytes (PHFK) were transduced with HPV-16 E6 and E7 and evaluated for proliferation and ability to grow in soft agar. E-P infected keratinocytes presented the lowest efficiency in colony formation. AA and E-350G keratinocytes attained higher capacity for in vitro transformation. We observed similar degradation of TP53 among HPV-16 variants. Furthermore, we accessed the expression profile in early (p5) and late passage (p30) transduced cells of 84 genes commonly involved in carcinogenesis. Most differences could be attributed to HPV-16 E6/E7 expression. In particular, we detected different expression of ITGA2 and CHEK2 in keratinocytes infected with AA and AA/E-350G late passage cells, respectively, and higher expression of MAP2K1 in E-350G transduced keratinocytes. Our results indicate differences among HPV-16 variants that could explain, at least in part, differences in oncogenic potential attributed to these variants.

  1. Neuropathology in classical and variant ataxia-telangiectasia

    NARCIS (Netherlands)

    Verhagen, Mijke M. M.; Martin, Jean-Jacques; van Deuren, Marcel; Groote, Chantal Ceuterick-de; Weemaes, Corry M. R.; Kremer, Berry H. P. H.; Taylor, Malcolm A. R.; Willemsen, Michel A. A. P.; Lammens, Martin

    2012-01-01

    Ataxia-telangiectasia (A-T) is classically characterized by progressive neurodegeneration, oculocutaneous telangiectasia, immunodeficiency and elevated a-fetoprotein levels. Some patients, classified as variant A-T, exhibit a milder clinical course. In the latter patients extrapyramidal symptoms, in

  2. STUDY ON AN SIS EPIDEMIC MODEL WITH TIME VARIANT DELAY

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In this paper,we study an SIS epidemic model with a time variant delay.By means of Liapunov functional,some sufficient conditions of global stability to endemic equilibrium and disease free equilibrium have been obtained.The influence of time delay on the stability of equilibria is displayed.

  3. STUDY ON AN SIS EPIDEMIC MODEL WITH TIME VARIANT DELAY

    Institute of Scientific and Technical Information of China (English)

    YUAN Sanling; MA Zhien

    2002-01-01

    In this paper, we study an SIS epidemic model with a time variant delay.By means of Liapunov functional, some sufficient conditions of global stability to endemic equilibrium and disease free equilibrium have been obtained. The influence of time delay on the stability of equilibria is displayed.

  4. Variant origin of thyrolingual trunk from left common carotid artery

    Directory of Open Access Journals (Sweden)

    Budhiraja V

    2010-03-01

    Full Text Available A case is reported in which there was a variant origin of thyrolingual trunk from left common carotid artery 2 cm below its bifurcation in the neck. The trunk was running forward and medially and later it was dividing into upper lingual and lower superior thyroid branches. No such artery was seen on right side.

  5. Variant rabbit hemorrhagic disease virus in young rabbits, Spain.

    Science.gov (United States)

    Dalton, Kevin P; Nicieza, Inés; Balseiro, Ana; Muguerza, María A; Rosell, Joan M; Casais, Rosa; Álvarez, Ángel L; Parra, Francisco

    2012-12-01

    Outbreaks of rabbit hemorrhagic disease have occurred recently in young rabbits on farms on the Iberian Peninsula where rabbits were previously vaccinated. Investigation identified a rabbit hemorrhagic disease virus variant genetically related to apathogenic rabbit caliciviruses. Improved antivirus strategies are needed to slow the spread of this pathogen.

  6. Antigen Loss Variants: Catching Hold of Escaping Foes

    Science.gov (United States)

    Vyas, Maulik; Müller, Rolf; Pogge von Strandmann, Elke

    2017-01-01

    Since mid-1990s, the field of cancer immunotherapy has seen steady growth and selected immunotherapies are now a routine and preferred therapeutic option of certain malignancies. Both active and passive cancer immunotherapies exploit the fact that tumor cells express specific antigens on the cell surface, thereby mounting an immune response specifically against malignant cells. It is well established that cancer cells typically lose surface antigens following natural or therapy-induced selective pressure and these antigen-loss variants are often the population that causes therapy-resistant relapse. CD19 and CD20 antigen loss in acute lymphocytic leukemia and chronic lymphocytic leukemia, respectively, and lineage switching in leukemia associated with mixed lineage leukemia (MLL) gene rearrangements are well-documented evidences in this regard. Although increasing number of novel immunotherapies are being developed, majority of these do not address the control of antigen loss variants. Here, we review the occurrence of antigen loss variants in leukemia and discuss the therapeutic strategies to tackle the same. We also present an approach of dual-targeting immunoligand effectively retargeting NK cells against antigen loss variants in MLL-associated leukemia. Novel immunotherapies simultaneously targeting more than one tumor antigen certainly hold promise to completely eradicate tumor and prevent therapy-resistant relapses. PMID:28286501

  7. The Main Social Variants in the English Language

    Institute of Scientific and Technical Information of China (English)

    权红梅

    2002-01-01

    To use a language properly, we of course have to know the grammatical structures of the language and their meanings ,but we also have to know what forms of language are appropriate for given situations,and for this purpose,this thesis briefly explains the social variants of English,such as (informal English), (written English)and (American English).

  8. The Main Social Variants in the English Language

    Institute of Scientific and Technical Information of China (English)

    QUANHong-mei

    2002-01-01

    To use a language properly, we of course have to know the grammatical structures of the language and their meanings,but we also have to know what forms of language are appropriate for given situations,and for this purpose,this thesis briefly explains the social variants of English,such asl (informal English), (written English)and (American English).

  9. Interaction between 5 genetic variants and allergy in glioma risk

    DEFF Research Database (Denmark)

    Schoemaker, Minouk J; Robertson, Lindsay; Wigertz, Annette

    2010-01-01

    The etiology of glioma is barely known. Epidemiologic studies have provided evidence for an inverse relation between glioma risk and allergic disease. Genome-wide association data have identified common genetic variants at 5p15.33 (rs2736100, TERT), 8q24.21 (rs4295627, CCDC26), 9p21.3 (rs4977756...

  10. Common nonsynonymous variants in PCSK1 confer risk of obesity

    DEFF Research Database (Denmark)

    Benzinou, Michael; Creemers, John W M; Choquet, Helene

    2008-01-01

    Mutations in PCSK1 cause monogenic obesity. To assess the contribution of PCSK1 to polygenic obesity risk, we genotyped tag SNPs in a total of 13,659 individuals of European ancestry from eight independent case-control or family-based cohorts. The nonsynonymous variants rs6232, encoding N221D...

  11. Effects of Variant Rates and Noise on Epidemic Spreading

    Institute of Scientific and Technical Information of China (English)

    LI Wei; GAO Zong-Mao; GU Jiao

    2011-01-01

    We introduce variant rates, for both infection and recovery and noise into the susceptible-infected-removed (SIR)model for epidemic spreading. The changing rates are taken mainly due to the changing profiles of an epidemic during its evolution. However, the noise parameter which is taken from a given distribution, i.e. Gaussian can describe the fluctuations of the infection and recovery rates. The numerical simulations show that the SIR model with variant rates and noise and can improve the fitting with real SARS data in the near-stationary stage.%@@ We introduce variant rates,for both infection and recovery and noise into the susceptible-infected-removed(SIR)modelfor epidemic spreading.The changing rates are taken mainly due to the changing profiles of an epidemic during its evolution.However,the noise parameter which is taken from a given distribution,i.e.Gaussian can describe the fluctuations of the infection and recovery rates.The numerical simulations show that the SIR model with variant rates and noise and can improve the fitting with real SARS data in the near-stationary stage.

  12. Andes hantavirus variant in rodents, southern Amazon Basin, Peru.

    Science.gov (United States)

    Razuri, Hugo; Tokarz, Rafal; Ghersi, Bruno M; Salmon-Mulanovich, Gabriela; Guezala, M Claudia; Albujar, Christian; Mendoza, A Patricia; Tinoco, Yeny O; Cruz, Christopher; Silva, Maria; Vasquez, Alicia; Pacheco, Víctor; Ströher, Ute; Guerrero, Lisa Wiggleton; Cannon, Deborah; Nichol, Stuart T; Hirschberg, David L; Lipkin, W Ian; Bausch, Daniel G; Montgomery, Joel M

    2014-02-01

    We investigated hantaviruses in rodents in the southern Amazon Basin of Peru and identified an Andes virus variant from Neacomys spinosus mice. This finding extends the known range of this virus in South America and the range of recognized hantaviruses in Peru. Further studies of the epizoology of hantaviruses in this region are warranted.

  13. Database for Parkinson Disease Mutations and Rare Variants

    Science.gov (United States)

    2015-07-01

    G.W., Van Broeckhoven C, Vance, J.M.: “Parkinson Disease Variant Database ”. MDS 19th International Congress of Parkinson’s Disease and Movement...abstracts submitted to ( international ) meetings and announcements of seminars including presentation of the database . Page 9 ABSTRACT NUYTEMANS UDALL...

  14. De Novo Coding Variants Are Strongly Associated with Tourette Disorder

    NARCIS (Netherlands)

    Willsey, A. Jeremy; Fernandez, Thomas V.; Yu, Dongmei; King, Robert A.; Dietrich, Andrea; Xing, Jinchuan; Sanders, Stephan J.; Mandell, Jeffrey D.; Huang, Alden Y.; Richer, Petra; Smith, Louw; Dong, Shan; Samocha, Kaitlin E.; Neale, Benjamin M.; Coppola, Giovanni; Mathews, Carol A.; Tischfield, Jay A.; Scharf, Jeremiah M.; State, Matthew W.; Heiman, Gary A.

    2017-01-01

    Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186

  15. Multiple common variants for celiac disease influencing immune gene expression

    NARCIS (Netherlands)

    Dubois, Patrick C. A.; Trynka, Gosia; Franke, Lude; Hunt, Karen A.; Romanos, Jihane; Curtotti, Alessandra; Zhernakova, Alexandra; Heap, Graham A. R.; Adany, Roza; Aromaa, Arpo; Bardella, Maria Teresa; van den Berg, Leonard H.; Bockett, Nicholas A.; de la Concha, Emilio G.; Dema, Barbara; Fehrmann, Rudolf S. N.; Fernandez-Arquero, Miguel; Fiatal, Szilvia; Grandone, Elvira; Green, Peter M.; Groen, Harry J. M.; Gwilliam, Rhian; Houwen, Roderick H. J.; Hunt, Sarah E.; Kaukinen, Katri; Kelleher, Dermot; Korponay-Szabo, Ilma; Kurppa, Kalle; MacMathuna, Padraic; Maki, Markku; Mazzilli, Maria Cristina; McCann, Owen T.; Mearin, M. Luisa; Mein, Charles A.; Mirza, Muddassar M.; Mistry, Vanisha; Mora, Barbara; Morley, Katherine I.; Mulder, Chris J.; Murray, Joseph A.; Nunez, Concepcion; Oosterom, Elvira; Ophoff, Roel A.; Polanco, Isabel; Peltonen, Leena; Platteel, Mathieu; Rybak, Anna; Salomaa, Veikko; Schweizer, Joachim J.; Sperandeo, Maria Pia; Tack, Greetje J.; Turner, Graham; Veldink, Jan H.; Verbeek, Wieke H. M.; Weersma, Rinse K.; Wolters, Victorien M.; Urcelay, Elena; Cukrowska, Bozena; Greco, Luigi; Neuhausen, Susan L.; McManus, Ross; Barisani, Donatella; Deloukas, Panos; Barrett, Jeffrey C.; Saavalainen, Paivi; Wijmenga, Cisca; van Heel, David A.

    2010-01-01

    We performed a second-generation genome-wide association study of 4,533 individuals with celiac disease (cases) and 10,750 control subjects. We genotyped 113 selected SNPs with P(GWAS) <10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. Variants from 13 new regions re

  16. Genetic variants in CETP increase risk of intracerebral hemorrhage

    NARCIS (Netherlands)

    Anderson, Christopher D.; Falcone, Guido J.; Phuah, Chia Ling; Radmanesh, Farid; Brouwers, H. Bart; Battey, Thomas W K; Biffi, Alessandro; Peloso, Gina M.; Liu, Dajiang J.; Ayres, Alison M.; Goldstein, Joshua N.; Viswanathan, Anand; Greenberg, Steven M.; Selim, Magdy; Meschia, James F.; Brown, Devin L.; Worrall, Bradford B.; Silliman, Scott L.; Tirschwell, David L.; Flaherty, Matthew L.; Kraft, Peter; Jagiella, Jeremiasz M.; Schmidt, Helena; Hansen, Björn M.; Jimenez-Conde, Jordi; Giralt-Steinhauer, Eva; Elosua, Roberto; Cuadrado-Godia, Elisa; Soriano, Carolina; van Nieuwenhuizen, Koen M.; Klijn, Catharina J M; Rannikmae, Kristiina; Samarasekera, Neshika; Salman, Rustam Al Shahi; Sudlow, Catherine L.; Deary, Ian J.; Morotti, Andrea; Pezzini, Alessandro; Pera, Joanna; Urbanik, Andrzej; Pichler, Alexander; Enzinger, Christian; Norrving, Bo; Montaner, Joan; Fernandez-Cadenas, Israel; Delgado, Pilar; Roquer, Jaume; Lindgren, Arne; Slowik, Agnieszka; Schmidt, Reinhold; Kidwell, Chelsea S.; Kittner, Steven J.; Waddy, Salina P.; Langefeld, Carl D.; Abecasis, Goncalo; Willer, Cristen J.; Kathiresan, Sekar; Woo, Daniel; Rosand, Jonathan

    2016-01-01

    Objective: In observational epidemiologic studies, higher plasma high-density lipoprotein cholesterol (HDL-C) has been associated with increased risk of intracerebral hemorrhage (ICH). DNA sequence variants that decrease cholesteryl ester transfer protein (CETP) gene activity increase plasma HDL-C;

  17. Analysis of Trivium by a Simulated Annealing variant

    DEFF Research Database (Denmark)

    Borghoff, Julia; Knudsen, Lars Ramkilde; Matusiewicz, Krystian

    2010-01-01

    . A characteristic of equation systems that may be efficiently solvable by the means of such algorithms is provided. As an example, we investigate equation systems induced by the problem of recovering the internal state of the stream cipher Trivium. We propose an improved variant of the simulated annealing method...

  18. Retracing Atypical Development: A Preserved Speech Variant of Rett Syndrome

    Science.gov (United States)

    Marschik, Peter B.; Einspieler, Christa; Oberle, Andreas; Laccone, Franco; Prechtl, Heinz F. R.

    2009-01-01

    The subject of the present study is the development of a girl with the preserved speech variant of Rett disorder. Our data are based on detailed retrospective and prospective video analyses. Despite achieving developmental milestones, movement quality was already abnormal during the girl's first half year of life. In addition, early hand…

  19. Dysautonomic polyneuropathy as a variant of chronic inflammatory "demyelinating" polyneuropathy?

    Science.gov (United States)

    Wolf, Hans-Heinrich; Kornhuber, Malte Erich; Weis, Joachim; Posa, Andreas

    2016-08-01

    This report describes the clinical course over almost one decade of a male patient presenting with immune-mediated pure autonomic neuropathy resembling a distinct variant of chronic dysimmune polyneuropathies. We suppose autoantibodies directed against epitopes on autonomic axons or neurons causative for the symptoms.

  20. Prevalence of URAT1 allelic variants in the Roma population.

    Science.gov (United States)

    Stiburkova, Blanka; Gabrikova, Dana; Čepek, Pavel; Šimek, Pavel; Kristian, Pavol; Cordoba-Lanus, Elizabeth; Claverie-Martin, Felix

    2016-12-01

    The Roma represents a transnational ethnic group, with a current European population of 8-10 million. The evolutionary process that had the greatest impact on the gene pool of the Roma population is called the founder effect. Renal hypouricemia (RHUC) is a rare heterogenous inherited disorder characterized by impaired renal urate reabsorption. The affected individuals are predisposed to recurrent episodes of exercise-induced nonmyoglobinuric acute kidney injury and nephrolithiasis. To date, more than 150 patients with a loss-of-function mutation for the SLC22A12 (URAT1) gene have been found, most of whom are Asians. However, RHUC 1 patients have been described in a variety of ethnic groups (e.g., Arab Israelis, Iraqi Jews, Caucasians, and Roma) and in geographically noncontiguous countries. This study confirms our previous findings regarding the high frequency of SLC22A12 variants observed. Frequencies of the c.1245_1253del and c.1400C>T variants were found to be 1.92% and 5.56%, respectively, in a subgroup of the Roma population from five regions in three countries: Slovakia, Czech Republic, and Spain. Our findings suggested that the common dysfunction allelic variants of URAT1 exist in the general Roma population and thus renal hypouricemia should be kept in differential diagnostic algorithm on Roma patients with defect in renal tubular urate transport. This leads to confirm that the genetic drift in the Roma have increased the prevalence of hereditary disorders caused by very rare variants in major population.

  1. De Novo Coding Variants Are Strongly Associated with Tourette Disorder

    NARCIS (Netherlands)

    Willsey, A. Jeremy; Fernandez, Thomas V.; Yu, Dongmei; King, Robert A.; Dietrich, Andrea; Xing, Jinchuan; Sanders, Stephan J.; Mandell, Jeffrey D.; Huang, Alden Y.; Richer, Petra; Smith, Louw; Dong, Shan; Samocha, Kaitlin E.; Neale, Benjamin M.; Coppola, Giovanni; Mathews, Carol A.; Tischfield, Jay A.; Scharf, Jeremiah M.; State, Matthew W.; Heiman, Gary A.

    2017-01-01

    Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186 tri

  2. Host Genetic Variants in the Pathogenesis of Hepatitis C

    Directory of Open Access Journals (Sweden)

    Monika Rau

    2012-11-01

    Full Text Available Direct-acting antiviral drugs (DAAs are currently replacing antiviral therapy for Hepatitis C infection. Treatment related side effects are even worse and the emergence of resistant viruses must be avoided because of the direct-antiviral action. Altogether it remains a challenge to take treatment decisions in a clinical setting with cost restrictions. Genetic host factors are hereby essential to implement an individualized treatment concept. In recent years results on different genetic variants have been published with a strong association with therapy response, fibrosis and treatment-related side effects. Polymorphisms of the IL28B gene were identified as accurate predictors for therapy response and spontaneous clearance of HCV infection and are already used for diagnostic decisions. For RBV-induced side effects, such as hemolytic anemia, associations to genetic variants of inosine triphosphatase (ITPA were described and different SLC28 transporters for RBV-uptake have been successfully analyzed. Fibrosis progression has been associated with variants of Vitamin D receptor (VDR and ABCB11 (bile salt export pump. Cirrhotic patients especially have a high treatment risk and low therapy response, so that personalized antiviral treatment is mandatory. This review focuses on different host genetic variants in the pathogenesis of Hepatitis C at the beginning of a new area of treatment.

  3. Selection of antigenically advanced variants of seasonal influenza viruses

    Science.gov (United States)

    Ozawa, Makoto; Taft, Andrew S.; Das, Subash C.; Hanson, Anthony P.; Song, Jiasheng; Imai, Masaki; Wilker, Peter R.; Watanabe, Tokiko; Watanabe, Shinji; Ito, Mutsumi; Iwatsuki-Horimoto, Kiyoko; Russell, Colin A.; James, Sarah L.; Skepner, Eugene; Maher, Eileen A.; Neumann, Gabriele; Kelso, Anne; McCauley, John; Wang, Dayan; Shu, Yuelong; Odagiri, Takato; Tashiro, Masato; Xu, Xiyan; Wentworth, David E.; Katz, Jacqueline M.; Cox, Nancy J.; Smith, Derek J.; Kawaoka, Yoshihiro

    2016-01-01

    Influenza viruses mutate frequently, necessitating constant updates of vaccine viruses. To establish experimental approaches that may complement the current vaccine strain selection process, we selected antigenic variants from human H1N1 and H3N2 influenza virus libraries possessing random mutations in the globular head of the haemagglutinin protein (which includes the antigenic sites) by incubating them with human and/or ferret convalescent sera to human H1N1 and H3N2 viruses. Further, we selected antigenic escape variants from human viruses treated with convalescent sera and from mice that had been previously immunized against human influenza viruses. Our pilot studies with past influenza viruses identified escape mutants that were antigenically similar to variants that emerged in nature, establishing the feasibility of our approach. Our studies with contemporary human influenza viruses identified escape mutants before they caused an epidemic in 2014–2015. This approach may aid in the prediction of potential antigenic escape variants and the selection of future vaccine candidates before they become widespread in nature. PMID:27572841

  4. Autoimmune Cholangitis: A Variant Syndrome of Autoimmune Hepatitis

    OpenAIRE

    Brij Sharma; Sujeet Raina; Rajesh Sharma

    2014-01-01

    Autoimmune cholangitis (AIC) or autoimmune cholangiopathy is a chronic inflammation of liver and a variant syndrome of autoimmune hepatitis (AIH). We present a case of an adult female who had biochemical features of cholestasis and transaminasemia but aminotransferases were not in the hepatitis range and had histological evidence of bile duct injury which was subsequently diagnosed as autoimmune cholangitis.

  5. The Biological and Clinical Significance of Androgen Receptor Variants

    Science.gov (United States)

    2014-04-01

    3. Guo Z, Yang X, Sun F et al: A novel androgen receptor splice variant is up-regulated during prostate cancer progression and promotes andro ...prognostic of bio- chemical recurrence in multiple cohorts. Br J Cancer 201 0; 102: 570, 23. Haffner MC, Aryee MJ, Toubaji A et al : Andro - gen

  6. Multiple common variants for celiac disease influencing immune gene expression

    NARCIS (Netherlands)

    Dubois, Patrick C. A.; Trynka, Gosia; Franke, Lude; Hunt, Karen A.; Romanos, Jihane; Curtotti, Alessandra; Zhernakova, Alexandra; Heap, Graham A. R.; Adany, Roza; Aromaa, Arpo; Bardella, Maria Teresa; van den Berg, Leonard H.; Bockett, Nicholas A.; de la Concha, Emilio G.; Dema, Barbara; Fehrmann, Rudolf S. N.; Fernandez-Arquero, Miguel; Fiatal, Szilvia; Grandone, Elvira; Green, Peter M.; Groen, Harry J. M.; Gwilliam, Rhian; Houwen, Roderick H. J.; Hunt, Sarah E.; Kaukinen, Katri; Kelleher, Dermot; Korponay-Szabo, Ilma; Kurppa, Kalle; MacMathuna, Padraic; Maki, Markku; Mazzilli, Maria Cristina; McCann, Owen T.; Mearin, M. Luisa; Mein, Charles A.; Mirza, Muddassar M.; Mistry, Vanisha; Mora, Barbara; Morley, Katherine I.; Mulder, Chris J.; Murray, Joseph A.; Nunez, Concepcion; Oosterom, Elvira; Ophoff, Roel A.; Polanco, Isabel; Peltonen, Leena; Platteel, Mathieu; Rybak, Anna; Salomaa, Veikko; Schweizer, Joachim J.; Sperandeo, Maria Pia; Tack, Greetje J.; Turner, Graham; Veldink, Jan H.; Verbeek, Wieke H. M.; Weersma, Rinse K.; Wolters, Victorien M.; Urcelay, Elena; Cukrowska, Bozena; Greco, Luigi; Neuhausen, Susan L.; McManus, Ross; Barisani, Donatella; Deloukas, Panos; Barrett, Jeffrey C.; Saavalainen, Paivi; Wijmenga, Cisca; van Heel, David A.

    We performed a second-generation genome-wide association study of 4,533 individuals with celiac disease (cases) and 10,750 control subjects. We genotyped 113 selected SNPs with P(GWAS) <10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. Variants from 13 new regions

  7. Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease

    Directory of Open Access Journals (Sweden)

    Pfeiffer Ronald F

    2010-04-01

    Full Text Available Abstract Background Mitochondrial function is impaired in Parkinson's disease (PD and may contribute to the pathogenesis of PD, but the causes of mitochondrial impairment in PD are unknown. Mitochondrial dysfunction is recapitulated in cell lines expressing mitochondrial DNA (mtDNA from PD patients, implicating mtDNA variants or mutations, though the role of mtDNA variants or mutations in PD risk remains unclear. We investigated the potential contribution of mtDNA variants or mutations to the risk of PD. Methods We examined the possibility of a maternal inheritance bias as well as the association between mitochondrial haplogroups and maternal inheritance and disease risk in a case-control study of 168 multiplex PD families in which the proband and one parent were diagnosed with PD. 2-tailed Fisher Exact Tests and McNemar's tests were used to compare allele frequencies, and a t-test to compare ages of onset. Results The frequency of affected mothers of the proband with PD (83/167, 49.4% was not significantly different from the frequency of affected females of the proband generation (115/259, 44.4% (Odds Ratio 1.22; 95%CI 0.83 - 1.81. After correcting for multiple tests, there were no significant differences in the frequencies of mitochondrial haplogroups or of the 10398G complex I gene polymorphism in PD patients compared to controls, and no significant associations with age of onset of PD. Mitochondrial haplogroup and 10398G polymorphism frequencies were similar in probands having an affected father as compared to probands having an affected mother. Conclusions These data fail to demonstrate a bias towards maternal inheritance in familial PD. Consistent with this, we find no association of common haplogroup-defining mtDNA variants or for the 10398G variant with the risk of PD. However, these data do not exclude a role for mtDNA variants in other populations, and it remains possible that other inherited mitochondrial DNA variants, or somatic m

  8. Diagnostic shoulder arthroscopy: incidence of physiologic variants of joint structures

    Directory of Open Access Journals (Sweden)

    Martin Mikek

    2005-04-01

    Full Text Available Background: Shoulder arthroscopy first described by Burman already in 1930, has evolved only in last 15 years to become a common accepted diagnostic and therapeutic procedure in treatment of different shoulder conditions. Parallely to the advances in arthroscopic operative techniques also our knowledge about arthroscopic shoulder anatomy expanded and many physiologic variants in anatomical structures have been identified in glenohumeral joint. It is very important to be familiar with those when performing shoulder arthroscopy, since in some cases they can easily be mistaken for pathologic lesions which can lead to unnecessary and potentially harmful operative procedures.Methods: We prospectively evaluated arthroscopic shoulder anatomy in 54 consecutive shoulder arthroscopies performed for different shoulder conditions in our practice. In all patients diagnostic arthroscopy was performed following the SCOI protocol described by Snyder. With regard to the anatomy variants described in literature and its importance in shoulder arthroscopy, special attention was focused on three regions of glenohumeral joint: long head of biceps tendon with its anchor and adjacent superior labrum, anterior joint capsule with glenohumeral ligaments and subscapularis tendon and on anterior labrum. The incidence of the observed anatomical variants was calculated. The most common combinations of anatomy variants were described and schematically presented.Results: The most significant anatomical variant observed in the region of long head of biceps tendon, biceps anchor and superior labrum was sublabral sulcus that was observed in 17% of shoulders. The region of anterior capsule with glenohumeral ligaments and subscapularis tendon showed greatest anatomical variability, especially the MGHL and the IGHL were very variably expressed and in some cases also absent. In the region of anterior labrum two significant anatomical variants were observed, one of them sublabral hole

  9. Genetic variants in CETP increase risk of intracerebral hemorrhage

    Science.gov (United States)

    Falcone, Guido J.; Phuah, Chia‐Ling; Radmanesh, Farid; Brouwers, H. Bart; Battey, Thomas W. K.; Biffi, Alessandro; Peloso, Gina M.; Liu, Dajiang J.; Ayres, Alison M.; Goldstein, Joshua N.; Viswanathan, Anand; Greenberg, Steven M.; Selim, Magdy; Meschia, James F.; Brown, Devin L.; Worrall, Bradford B.; Silliman, Scott L.; Tirschwell, David L.; Flaherty, Matthew L.; Kraft, Peter; Jagiella, Jeremiasz M.; Schmidt, Helena; Hansen, Björn M.; Jimenez‐Conde, Jordi; Giralt‐Steinhauer, Eva; Elosua, Roberto; Cuadrado‐Godia, Elisa; Soriano, Carolina; van Nieuwenhuizen, Koen M.; Klijn, Catharina J. M.; Rannikmae, Kristiina; Samarasekera, Neshika; Salman, Rustam Al‐Shahi; Sudlow, Catherine L.; Deary, Ian J.; Morotti, Andrea; Pezzini, Alessandro; Pera, Joanna; Urbanik, Andrzej; Pichler, Alexander; Enzinger, Christian; Norrving, Bo; Montaner, Joan; Fernandez‐Cadenas, Israel; Delgado, Pilar; Roquer, Jaume; Lindgren, Arne; Slowik, Agnieszka; Schmidt, Reinhold; Kidwell, Chelsea S.; Kittner, Steven J.; Waddy, Salina P.; Langefeld, Carl D.; Abecasis, Goncalo; Willer, Cristen J.; Kathiresan, Sekar; Woo, Daniel; Rosand, Jonathan

    2016-01-01

    Objective In observational epidemiologic studies, higher plasma high‐density lipoprotein cholesterol (HDL‐C) has been associated with increased risk of intracerebral hemorrhage (ICH). DNA sequence variants that decrease cholesteryl ester transfer protein (CETP) gene activity increase plasma HDL‐C; as such, medicines that inhibit CETP and raise HDL‐C are in clinical development. Here, we test the hypothesis that CETP DNA sequence variants associated with higher HDL‐C also increase risk for ICH. Methods We performed 2 candidate‐gene analyses of CETP. First, we tested individual CETP variants in a discovery cohort of 1,149 ICH cases and 1,238 controls from 3 studies, followed by replication in 1,625 cases and 1,845 controls from 5 studies. Second, we constructed a genetic risk score comprised of 7 independent variants at the CETP locus and tested this score for association with HDL‐C as well as ICH risk. Results Twelve variants within CETP demonstrated nominal association with ICH, with the strongest association at the rs173539 locus (odds ratio [OR] = 1.25, standard error [SE] = 0.06, p = 6.0 × 10−4) with no heterogeneity across studies (I 2 = 0%). This association was replicated in patients of European ancestry (p = 0.03). A genetic score of CETP variants found to increase HDL‐C by ∼2.85mg/dl in the Global Lipids Genetics Consortium was strongly associated with ICH risk (OR = 1.86, SE = 0.13, p = 1.39 × 10−6). Interpretation Genetic variants in CETP associated with increased HDL‐C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL‐raising strategies, further exploration of potential adverse cerebrovascular outcomes may be warranted. Ann Neurol 2016;80:730–740 PMID:27717122

  10. Estrogen withdrawal, increased breast cancer risk and the KRAS-variant

    Science.gov (United States)

    McVeigh, Terri P; Jung, Song-Yi; Kerin, Michael J; Salzman, David W; Nallur, Sunitha; Nemec, Antonio A; Dookwah, Michelle; Sadofsky, Jackie; Paranjape, Trupti; Kelly, Olivia; Chan, Elcie; Miller, Nicola; Sweeney, Karl J; Zelterman, Daniel; Sweasy, Joann; Pilarski, Robert; Telesca, Donatello; Slack, Frank J; Weidhaas, Joanne B

    2015-01-01

    The KRAS-variant is a biologically functional, microRNA binding site variant, which predicts increased cancer risk especially for women. Because external exposures, such as chemotherapy, differentially impact the effect of this mutation, we evaluated the association of estrogen exposures, breast cancer (BC) risk and tumor biology in women with the KRAS-variant. Women with BC (n = 1712), the subset with the KRAS-variant (n = 286) and KRAS-variant unaffected controls (n = 80) were evaluated, and hormonal exposures, KRAS-variant status, and pathology were compared. The impact of estrogen withdrawal on transformation of isogenic normal breast cell lines with or without the KRAS-variant was studied. Finally, the association and presentation characteristics of the KRAS-variant and multiple primary breast cancer (MPBC) were evaluated. KRAS-variant BC patients were more likely to have ovarian removal pre-BC diagnosis than non-variant BC patients (p = 0.033). In addition, KRAS-variant BC patients also appeared to have a lower estrogen state than KRAS-variant unaffected controls, with a lower BMI (P < 0.001). Finally, hormone replacement therapy (HRT) discontinuation in KRAS-variant patients was associated with a diagnosis of triple negative BC (P < 0.001). Biologically confirming our clinical findings, acute estrogen withdrawal led to oncogenic transformation in KRAS-variant positive isogenic cell lines. Finally, KRAS-variant BC patients had greater than an 11-fold increased risk of presenting with MPBC compared to non-variant patients (45.39% vs 6.78%, OR 11.44 [3.42–37.87], P < 0.001). Thus, estrogen withdrawal and a low estrogen state appear to increase BC risk and to predict aggressive tumor biology in women with the KRAS-variant, who are also significantly more likely to present with multiple primary breast cancer. PMID:25961464

  11. Benchmarking distributed data warehouse solutions for storing genomic variant information

    Science.gov (United States)

    Wiewiórka, Marek S.; Wysakowicz, Dawid P.; Okoniewski, Michał J.

    2017-01-01

    Abstract Genomic-based personalized medicine encompasses storing, analysing and interpreting genomic variants as its central issues. At a time when thousands of patientss sequenced exomes and genomes are becoming available, there is a growing need for efficient database storage and querying. The answer could be the application of modern distributed storage systems and query engines. However, the application of large genomic variant databases to this problem has not been sufficiently far explored so far in the literature. To investigate the effectiveness of modern columnar storage [column-oriented Database Management System (DBMS)] and query engines, we have developed a prototypic genomic variant data warehouse, populated with large generated content of genomic variants and phenotypic data. Next, we have benchmarked performance of a number of combinations of distributed storages and query engines on a set of SQL queries that address biological questions essential for both research and medical applications. In addition, a non-distributed, analytical database (MonetDB) has been used as a baseline. Comparison of query execution times confirms that distributed data warehousing solutions outperform classic relational DBMSs. Moreover, pre-aggregation and further denormalization of data, which reduce the number of distributed join operations, significantly improve query performance by several orders of magnitude. Most of distributed back-ends offer a good performance for complex analytical queries, while the Optimized Row Columnar (ORC) format paired with Presto and Parquet with Spark 2 query engines provide, on average, the lowest execution times. Apache Kudu on the other hand, is the only solution that guarantees a sub-second performance for simple genome range queries returning a small subset of data, where low-latency response is expected, while still offering decent performance for running analytical queries. In summary, research and clinical applications that require

  12. [Clinico-morphological variants of gastric mucosa atrophic lesions].

    Science.gov (United States)

    Naumova, L A; Pal'tsev, A I; Beliaeva, Ia Iu

    2009-01-01

    To characterize clinicomorphological manifestations of atrophic process (AP) in gastric mucosa (GM) in chronic atrophic gastritis (CAG) associated and not associated with Helicobacter pylori infection. Clinicoendoscopic and pathomorphological (light microscopy of gastric biopsies, 6 point scale assessment of dysregeneratory alterations) investigations were made in 98 patients aged 16 to 68 years. H. pylori-negative CAG was diagnosed in 52 of them, H. pylori-positive one in 46 patients (groups 1 and 2, respectively). A comparative clinicomorphological analysis has identified 2 variants of AP morphogenesis in GM. Variant 1 is not associated with H. pylori but associated with a combined action of several endogenic risk factors of chronic gastritis or failure of regeneration, with diffuse or diffuse-focal changes with initial prevalence of dysregeneratory changes in a fundal stomach manifesting as a trend to atrophy of the glands. Clinically, this variant is characterized by longer disease, frequent systemic atrophic lesions of gastrointestinal mucosa, prevalent complaints of dyspeptic pain. Variant 2 is associated with a combined action of endo- and exogenic factors, H. pylori infection in particular, pathogenetic components of "chemical" gastritis (duodenogastric reflux, malnutrition), prevalence of dysregeneratory and sclerotic alterations in the antral stomach. GM atrophy is characterized by a significant frequency of concomitant endocrinopathies, undifferentiated connective tissue dysplasia, systemic lesions, structurally--by multidirectional disorders of proliferation and differentiation. First of all, it is the result of impaired regulation of regenerative processes. AP polyetiology and different morphogenetic variants in GM suggest necessity of both individual diagnostic algorithm and pathogenetically sound therapy in each individual case.

  13. Rare variants in ischemic stroke: an exome pilot study.

    Directory of Open Access Journals (Sweden)

    John W Cole

    Full Text Available The genetic architecture of ischemic stroke is complex and is likely to include rare or low frequency variants with high penetrance and large effect sizes. Such variants are likely to provide important insights into disease pathogenesis compared to common variants with small effect sizes. Because a significant portion of human functional variation may derive from the protein-coding portion of genes we undertook a pilot study to identify variation across the human exome (i.e., the coding exons across the entire human genome in 10 ischemic stroke cases. Our efforts focused on evaluating the feasibility and identifying the difficulties in this type of research as it applies to ischemic stroke. The cases included 8 African-Americans and 2 Caucasians selected on the basis of similar stroke subtypes and by implementing a case selection algorithm that emphasized the genetic contribution of stroke risk. Following construction of paired-end sequencing libraries, all predicted human exons in each sample were captured and sequenced. Sequencing generated an average of 25.5 million read pairs (75 bp×2 and 3.8 Gbp per sample. After passing quality filters, screening the exomes against dbSNP demonstrated an average of 2839 novel SNPs among African-Americans and 1105 among Caucasians. In an aggregate analysis, 48 genes were identified to have at least one rare variant across all stroke cases. One gene, CSN3, identified by screening our prior GWAS results in conjunction with our exome results, was found to contain an interesting coding polymorphism as well as containing excess rare variation as compared with the other genes evaluated. In conclusion, while rare coding variants may predispose to the risk of ischemic stroke, this fact has yet to be definitively proven. Our study demonstrates the complexities of such research and highlights that while exome data can be obtained, the optimal analytical methods have yet to be determined.

  14. Multiple infections of Anaplasma platys variants in Philippine dogs

    Directory of Open Access Journals (Sweden)

    Adrian Patalinghug Ybañez

    2016-12-01

    Full Text Available Aim: Anaplasma platys, the causative agent of infectious canine cyclic thrombocytopenia, is a tick-borne pathogen that also has been implicated as potentially zoonotic. To provide molecular evidence on the multiple infections of A. platys variants in Philippine dogs. Materials and Methods: DNA fragments of A. platys from infected dogs in the Philippines were molecularly characterized. For screening, 25 dogs suspected to have canine anaplasmosis were tested using a 16S rRNA-based nested polymerase chain reaction (PCR. Infection was confirmed by sequencing of positive amplicons. Second round PCR targeting a longer 16S rRNA fragment was subsequently performed on the first round PCR amplicons of the positive samples. Further characterization using the heat-shock operon (groEL gene was also performed on the A. platys-positive samples. Results: 10 16S rRNA sequences were obtained and found 99.6-100% identical to each other and 99.6-99.7% identical to the closest registered A. platys sequences. On the other hand, 36 groEL clone sequences were obtained and found to be 85.1-99.8% identical with each other and 85.0-88.9% identical to the closest previously registered A. platys sequences. Four dogs were found coinfected with 2-3 groEL variant sequences. Phylogenetic analyses suggest that the detected A. platys in the Philippines may represent unique variants. Conclusion: A. platys variants were detected in Philippine dogs. Coinfection of different A. platys variants in dogs was also demonstrated. The present study may indicate the potential genetic diversity of A. platys in the country.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Multiple Gene Variants in Hypertrophic Cardiomyopathy in the Era of Next-Generation Sequencing.

    Science.gov (United States)

    Burns, Charlotte; Bagnall, Richard D; Lam, Lien; Semsarian, Christopher; Ingles, Jodie

    2017-08-01

    Multiple likely pathogenic/pathogenic (LP/P; ≥2) variants in patients with hypertrophic cardiomyopathy were described 10 years ago with a prevalence of 5%. We sought to re-examine the significance of multiple rare variants in patients with hypertrophic cardiomyopathy in the setting of comprehensive and targeted panels. Of 758 hypertrophic cardiomyopathy probands, we included 382 with ≥45 cardiomyopathy genes screened. There were 224 (59%) with ≥1 rare variant (allele frequency ≤0.02%). Variants were analyzed using varying sized gene panels to represent comprehensive or targeted testing. Based on a 45-gene panel, 127 (33%) had a LP/P variant, 139 (36%) had variants of uncertain significance, and 66 (17%) had multiple rare variants. A targeted 8-gene panel yielded 125 (32%) LP/P variants, 52 (14%) variants of uncertain significance, and 14 (4%) had multiple rare variants. No proband had 2 LP/P variants. Including affected family members (total n=412), cluster-adjusted analyses identified a phenotype effect, with younger age (odds ratio, 0.95; 95% confidence interval, 0.92-0.98; P=0.004) and family history of sudden cardiac death (odds ratio, 3.5; 95% confidence interval, 1.3-9.9; P=0.02) significantly more likely in multiple versus single variant patients when considering an 8-gene panel but not larger panels. Those with multiple variants had worse event-free survival from all-cause death, cardiac transplantation, and cardiac arrest (log-rank P=0.008). No proband had multiple LP/P variants in contrast to previous reports. However, multiple rare variants regardless of classification were seen in 4% and contributed to earlier disease onset and cardiac events. Our findings support a cumulative variant hypothesis in hypertrophic cardiomyopathy. © 2017 American Heart Association, Inc.

  17. Warthin-like variant of papillary thyroid carcinoma: A diagnosis not to be missed

    Directory of Open Access Journals (Sweden)

    Gopal Reddy Shilpa

    2015-01-01

    Full Text Available The Warthin-like variant of papillary thyroid carcinoma (PTC is a recently described, uncommon variant of PTC. Proper identification of this variant is warranted as it shows good clinical behavior when compared with other oncocytic rich neoplasms of the thyroid. We present a case of Warthin-like variant of PTC in a 40-year-old female patient and describe the clinicopathological features, along with the differential diagnosis of this rare tumor.

  18. TDP-43 protein variants as biomarkers in amyotrophic lateral sclerosis.

    Science.gov (United States)

    Williams, Stephanie M; Khan, Galam; Harris, Brent T; Ravits, John; Sierks, Michael R

    2017-01-25

    TDP-43 aggregates accumulate in individuals affected by amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases, representing potential diagnostic and therapeutic targets. Using an atomic force microscopy based biopanning protocol developed in our lab, we previously isolated 23 TDP-43 reactive antibody fragments with preference for human ALS brain tissue relative to frontotemporal dementia, a related neurodegeneration, and healthy samples from phage-displayed single chain antibody fragment (scFv) libraries. Here we further characterize the binding specificity of these different scFvs and identify which ones have promise for detecting ALS biomarkers in human brain tissue and plasma samples. We developed a sensitive capture ELISA for detection of different disease related TDP-43 variants using the scFvs identified from the ALS biopanning. We show that a wide variety of disease selective TDP-43 variants are present in ALS as the scFvs show different reactivity profiles amongst the ALS cases. When assaying individual human brain tissue cases, three scFvs (ALS-TDP6, ALS-TDP10 and ALS-TDP14) reacted with all the ALS cases and 12 others reacted with the majority of the ALS cases, and none of the scFvs reacted with any control samples. When assaying individual human plasma samples, 9 different scFvs reacted with all the sporadic ALS samples and again none of them reacted with any control samples. These 9 different scFvs had different patterns of reactivity with plasma samples obtained from chromosome 9 open reading frame 72 (c9orf72) cases indicating that these familial ALS genetic variants may display different TDP-43 pathology than sporadic ALS cases. These results indicated that a range of disease specific TDP-43 variants are generated in ALS patients with different variants being generated in sporadic and familial cases. We show that a small panel of scFvs recognizing different TDP-43 variants can generate a neuropathological and plasma biomarker

  19. Anatomical Knee Variants in Discoid Lateral Meniscal Tears

    Science.gov (United States)

    Chen, Xu-Xu; Li, Jian; Wang, Tao; Zhao, Yang; Kang, Hui

    2017-01-01

    Background: Discoid lateral meniscus was a common meniscal dysplasia and was predisposed to tear. There were some anatomical knee variants in patients with discoid lateral meniscus. The aim of this study was to analyze the relationship between anatomical knee variants and discoid lateral meniscal tears. Methods: There were totally 125 cases of discoid lateral meniscus enrolled in this study from February 2008 to December 2013. Eighty-seven patients who underwent arthroscopic surgery for right torn discoid lateral meniscus were enrolled in the torn group. An additional 38 patients who were incidentally identified as having intact discoid lateral menisci on magnetic resonance imaging (MRI) findings were included in the control group. All patients were evaluated for anatomical knee variants on plain radiographs, including lateral joint space distance, height of the lateral tibial spine, height of the fibular head, obliquity of the lateral tibial plateau, squaring of the lateral femoral condyle, cupping of the lateral tibial plateau, lateral femoral condylar notch, and condylar cutoff sign. The relationship between anatomical variants and meniscal tear was evaluated. These anatomical variants in cases with complete discoid meniscus were also compared with those in cases with incomplete discoid meniscus. Results: There were no significant differences between the two groups in lateral joint space distance (P = 0.528), height of the lateral tibial spine (P = 0.927), height of the fibular head (P = 0.684), obliquity of the lateral tibial plateau (P = 0.672), and the positive rates of squaring of the lateral femoral condyle (P = 0.665), cupping of the lateral tibial plateau (P = 0.239), and lateral femoral condylar notch (P = 0.624). The condylar cutoff sign was significantly different between the two groups, with the prominence ratio in the torn group being smaller than that in the control group (0.74 ± 0.11 vs. 0.81 ± 0.04, P = 0.049). With the decision value of the

  20. Methods for engineering polypeptide variants via somatic hypermutation and polypeptide made thereby

    Science.gov (United States)

    Tsien, Roger Y; Wang, Lei

    2015-01-13

    Methods using somatic hypermutation (SHM) for producing polypeptide and nucleic acid variants, and nucleic acids encoding such polypeptide variants are disclosed. Such variants may have desired properties. Also disclosed are novel polypeptides, such as improved fluorescent proteins, produced by the novel methods, and nucleic acids, vectors, and host cells comprising such vectors.

  1. Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model

    Science.gov (United States)

    Within cells and tissues, the maternally inherited mitochondrial genome (mtDNA) is present in multimeric form and can harbour naturally occurring variants. Whilst high variant load can cause mitochondrial disease, naturally occurring mtDNA variants likely persist at low levels across generations of ...

  2. Rare novel variants in the ZIC3 gene cause X-linked heterotaxy

    DEFF Research Database (Denmark)

    Paulussen, Aimee D C; Steyls, Anja; Vanoevelen, Jo

    2016-01-01

    male deaths due to heterotaxy in the family (n=1). All variants were located within the zinc-finger domains or leading to a truncation before these domains. Truncating variants showed abnormal trafficking of mutated ZIC3 proteins, whereas the missense variant showed normal trafficking. Overexpression...

  3. Genetic Variants in KLOTHO Associate With Cognitive Function in the Oldest Old Group

    DEFF Research Database (Denmark)

    Mengel-From, Jonas; Sørensen, Mette; Nygaard, Marianne

    2016-01-01

    cognitive measures in two cohort strata. The haplotype effect was stronger than that of KL-VS. Two variants, rs2283368 and rs9526984, were the only variants significantly associated with cognitive decline over 7 years. We discuss an age-dependent effect of KL and the possibility that multiple gene variants...

  4. Graphic visualization of non-variant phase transformations in binary systems in course of cooling

    Directory of Open Access Journals (Sweden)

    Martin Nekuda

    2006-01-01

    Full Text Available Non-variant phase transformations in the binary diagrams have both, some common features and some differences. The authors arranged an interactive animation by the help of the computer to catch the time course of non-variant transformations in many contexts. The program helps to illustrate and describe the matter all of non-variant transformations.

  5. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis

    NARCIS (Netherlands)

    Rivas, Manuel A.; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A. Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Soeren; Kurki, Mitja I.; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K.; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L. E.; Ananthakrishnan, Ashwin N.; Luo, Yang; Heap, Graham A.; Visschedijk, Marijn C.; MacArthur, Daniel G.; Neale, Benjamin M.; Ahmad, Tariq; Anderson, Carl A.; Brant, Steven R.; Duerr, Richard H.; Silverberg, Mark S.; Cho, Judy H.; Palotie, Aarno; Saavalainen, Paivi; Kontula, Kimmo; Farkkila, Martti; McGovern, Dermot P. B.; Franke, Andre; Stefansson, Kari; Rioux, John D.; Xavier, Ramnik J.; Daly, Mark J.

    2016-01-01

    Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associ

  6. Functional characterization of BRCA1 gene variants by mini-gene splicing assay

    DEFF Research Database (Denmark)

    Steffensen, Ane Y; Dandanell, Mette; Jønson, Lars

    2014-01-01

    Mutational screening of the breast cancer susceptibility gene BRCA1 leads to the identification of numerous pathogenic variants such as frameshift and nonsense variants, as well as large genomic rearrangements. The screening moreover identifies a large number of variants, for example, missense...

  7. Multidetector CT angiography of renal vasculature: normal anatomy and variants

    Energy Technology Data Exchange (ETDEWEB)

    Tuerkvatan, Aysel; Oezdemir, Mustafa; Cumhur, Turhan; Oelcer, Tuelay [Tuerkiye Yueksek ihtisas Hospital, Department of Radiology, Sihhiye, Ankara (Turkey)

    2009-01-15

    Knowledge of the variations in renal vascular anatomy is important before laparoscopic donor or partial nephrectomy and vascular reconstruction for renal artery stenosis or abdominal aortic aneurysm. Recently, multidetector computed tomographic (MDCT) angiography has become a principal imaging investigation for assessment of the renal vasculature and has challenged the role of conventional angiography. It is an excellent imaging technique because it is a fast and non-invasive tool that provides highly accurate and detailed evaluation of normal renal vascular anatomy and variants. The number, size and course of the renal arteries and veins are easily identified by MDCT angiography. The purpose of this pictorial essay is to illustrate MDCT angiographic appearance of normal anatomy and common variants of the renal vasculature. (orig.)

  8. Rhabdomyolysis and Autoimmune Variant Stiff-Person Syndrome.

    Science.gov (United States)

    Gangadhara, Shreyas; Gangadhara, Suhas; Gandhy, Chetan; Robertson, Derrick

    2016-10-24

    Stiff-person syndrome (SPS) is a rare neurologic disorder characterized by waxing and waning muscular rigidity, stiffness and spasms. Three subtypes have been described: paraneoplastic, autoimmune and idiopathic. Rhabdomyolysis has been described in the paraneoplastic variant, but to our knowledge no case has been reported involving the autoimmune variant. We report a case report of a 50-year-old man with history of SPS who presented with recurrent episodes of severe limb and back spasms. He was hospitalized on two separate occasions for uncontrollable spasms associated with renal failure and creatinine phosphokinase elevations of 55,000 and 22,000 U/L respectively. Laboratory tests were otherwise unremarkable. The acute renal failure resolved during both admissions with supportive management. Rhabdomyolysis has the potential to be fatal and early diagnosis is essential. It should be considered in patients who have SPS and are experiencing an exacerbation of their neurologic condition.

  9. Rhabdomyolysis and Autoimmune Variant Stiff-Person Syndrome

    Science.gov (United States)

    Gangadhara, Shreyas; Gangadhara, Suhas; Gandhy, Chetan; Robertson, Derrick

    2016-01-01

    Stiff-person syndrome (SPS) is a rare neurologic disorder characterized by waxing and waning muscular rigidity, stiffness and spasms. Three subtypes have been described: paraneoplastic, autoimmune and idiopathic. Rhabdomyolysis has been described in the paraneoplastic variant, but to our knowledge no case has been reported involving the autoimmune variant. We report a case report of a 50-year-old man with history of SPS who presented with recurrent episodes of severe limb and back spasms. He was hospitalized on two separate occasions for uncontrollable spasms associated with renal failure and creatinine phosphokinase elevations of 55,000 and 22,000 U/L respectively. Laboratory tests were otherwise unremarkable. The acute renal failure resolved during both admissions with supportive management. Rhabdomyolysis has the potential to be fatal and early diagnosis is essential. It should be considered in patients who have SPS and are experiencing an exacerbation of their neurologic condition. PMID:28028432

  10. On Bijective Variants of the Burrows-Wheeler Transform

    CERN Document Server

    Kufleitner, Manfred

    2009-01-01

    The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation conjugates of the input word, whereas the ST of order k only uses the first k letters for sorting all such conjugates. If two conjugates start with the same prefix of length k, then the indices of the rotations are used for tie-breaking. Both transforms output the sequence of the last letters of the sorted list and the index of the input within the sorted list. In this paper, we discuss a bijective variant of the BWT (due to Scott), proving its correctness and relations to other results due to Gessel and Reutenauer (1993) and Crochemore, Desarmenien, and Perrin (2005). Further, we present a novel bijective variant of the ST.

  11. A new hypercube variant: Fractal Cubic Network Graph

    Directory of Open Access Journals (Sweden)

    Ali Karci

    2015-03-01

    Full Text Available Hypercube is a popular and more attractive interconnection networks. The attractive properties of hypercube caused the derivation of more variants of hypercube. In this paper, we have proposed two variants of hypercube which was called as “Fractal Cubic Network Graphs”, and we have investigated the Hamiltonian-like properties of Fractal Cubic Network Graphs FCNGr(n. Firstly, Fractal Cubic Network Graphs FCNGr(n are defined by a fractal structure. Further, we show the construction and characteristics analyses of FCNGr(n where r=1 or r=2. Therefore, FCNGr(n is a Hamiltonian graph which is obtained by using Gray Code for r=2 and FCNG1(n is not a Hamiltonian Graph. Furthermore, we have obtained a recursive algorithm which is used to label the nodes of FCNG2(n. Finally, we get routing algorithms on FCNG2(n by utilizing routing algorithms on the hypercubes.

  12. Analysis of histones and histone variants in plants.

    Science.gov (United States)

    Trivedi, Ila; Rai, Krishan Mohan; Singh, Sunil Kumar; Kumar, Verandra; Singh, Mala; Ranjan, Amol; Lodhi, Niraj; Sawant, Samir V

    2012-01-01

    Histone proteins are the major protein components of chromatin - the physiologically relevant form of the genome (or epigenome) in all eukaryotic cells. For many years, histones were considered passive structural components of eukaryotic chromatin. In recent years, it has been demonstrated that dynamic association of histones and their variants to the genome plays a very important role in gene regulation. Histones are extensively modified during posttranslation viz. acetylation, methylation, phosphorylation, ubiquitylation, etc., and the identification of these covalent marks on canonical and variant histones is crucial for the understanding of their biological significance. Different biochemical techniques have been developed to purify and separate histone proteins; here, we describe techniques for analysis of histones from plant tissues.

  13. Intergenic spacer length variants in Old Portuguese bread wheat cultivars

    Indian Academy of Sciences (India)

    Ana Carvalho; Henrique Guedes-Pinto; José Lima-Brito

    2011-08-01

    The intergenic spacer of the ribosomal DNA is highly variable, but is location specific in the nucleolar organizer region of the chromosomes. This study provides an event of high level of polymorphism / size variation and occurrence of 14 unique phenotypes in 48 landraces of Portuguese bread wheat cultivars for IGS-amplified products obtained by PCR-RFLP technique performed with TaqI. The attendant IGS polymorphism has been used to deduce affinities between landraces. Some of the high molecular weight IGS allelic variants were also probed for their chromosomal localization by sequential silver nitrate staining and fluorescence in situ hybridization. However, only the intergenic spacer allelic variant of 3.1 kb could be successfully hybridized, and was observed to be physically located on the chromosome pair 1B in the NOR loci of the cultivar ‘Magueija’.

  14. Canine parvovirus (CPV-2) variants circulating in Nigerian dogs

    Science.gov (United States)

    Apaa, T. T.; Daly, J. M.; Tarlinton, R. E.

    2016-01-01

    Canine parvovirus type 2 (CPV-2) is a highly contagious viral disease with three variants (CPV-2a, CPV-2b and CPV-2c) currently circulating in dogs worldwide. The main aim of this study was to determine the prevalent CPV-2 variant in faecal samples from 53 dogs presenting with acute gastroenteritis suspected to be and consistent with CPV-2 to Nigerian Veterinary Clinics in 2013–2014. Seventy-five per cent of these dogs tested positive for CPV-2 in a commercial antigen test and/or by PCR. Partial sequencing of the VP2 gene of six of these demonstrated them to be CPV-2a. Most of the dogs (60 per cent) were vaccinated, with 74 per cent of them puppies less than six months old. PMID:27933190

  15. Discovery of the improved antagonistic prolactin variants by library screening.

    Science.gov (United States)

    Liu, Yun; Gong, Wei; Breinholt, Jens; Nørskov-Lauritsen, Leif; Zhang, Jinchao; Ma, Qinhong; Chen, Jianhe; Panina, Svetlana; Guo, Wei; Li, Tengkun; Zhang, Jingyuan; Kong, Meng; Liu, Zibing; Mao, Jingjing; Christensen, Leif; Hu, Sean; Wang, Lingyun

    2011-11-01

    Prolactin (PRL), a potent growth stimulator of the mammary epithelium, has been suggested to be a factor contributing to the development and progression of breast and prostate cancer. Several PRL receptor (PRLR) antagonists have been identified in the past decades, but their in vivo growth inhibitory potency was restricted by low receptor affinity, rendering them pharmacologically unattractive for clinical treatment. Thus, higher receptor affinity is essential for the development of improved PRLR antagonistic variants with improved in vivo potency. In this study, we generated Site 1 focused protein libraries of human G129R-PRL mutants and screened for those with increased affinity to the human PRLR. By combining the mutations with enhanced affinities for PRLR, we identified a novel G129R-PRL variant with mutations at Site 1 that render nearly 50-fold increase in the antagonistic potency in vitro.

  16. Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques

    Science.gov (United States)

    Menendez, M. C.; Palenque, E.; Navarro, M. C.; Nuñez, M. C.; Rebollo, M. J.; Garcia, M. J.

    2001-01-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members. PMID:11724827

  17. Renal Clear Cell Sarcoma - Anaplastic Variant: A Rare Entity.

    Science.gov (United States)

    Walke, Vaishali Atmaram; Shende, Nitin Y; Kumbhalkar, D T

    2017-01-01

    Clear Cell Sarcoma of Kidney (CCSK) is known for its morphologic diversity, aggressive behaviour, tendency to recur and metastasis to bone. Amongst the various morphologic subtypes, anaplastic CCSK is associated with worse prognosis. Here, we report a case of this rare variant of CCSK. A five-year-old boy presented with history of lump and pain in abdomen since one week. The Computed Tomography (CT) scan revealed a large mass occupying the middle and inferior pole of right kidney. The clinical impression was Wilms tumour. Nephrectomy specimen was received and the diagnosis of CCSK anaplastic variant was offered only after excluding the differentials and after performing ancillary tests such as Immunohistochemistry (IHC). Thus, this case emphasizes the diagnostic challenges on morphology and the essential role of IHC in arriving at a definitive diagnosis, because failure to do so may deprive the child from optimal treatment.

  18. Dentinogenic Ghost Cell Tumor of the Peripheral Variant Mimicking Epulis

    Directory of Open Access Journals (Sweden)

    Uddipan Kumar

    2010-01-01

    Full Text Available Dentinogenic ghost cell tumor (DGCT is an uncommon locally invasive odontogenic tumor regarded by many as a variant of calcifying odontogenic cyst. The peripheral variant of this clinical rarity appears as a well-circumscribed mass mimicking a nonspecific gingival enlargement. Microscopic appearance of odontogenic epithelium admixed with focal areas of dentinoid formation and sheets of ghost cells giving the definitive diagnosis of dentinogenic ghost cell tumor imply that microscopic examination is compulsory for any gingival mass. Van Gieson histochemical stain further confirmed the nature of dentinoid-like material. A complete workup of a case of peripheral dentinogenic ghost cell tumor is presented in this paper and the current concept as well as the appraisal of literature is presented.

  19. Reticular type parotid myoepithelial carcinoma: an intriguing variant and mimicker.

    Science.gov (United States)

    Azizun-Nisa; Kazi, Javed Iqbal; Jamal, Saba

    2013-05-01

    Myoepithelial carcinoma, the malignant counterpart of benign myoepithelioma, is one of the rarest salivary gland neoplasms. It is composed almost exclusively of tumour cells with myoepithelial differentiation, characterized by infiltrative growth and potential for metastasis. We herein, report a case of myoepithelial carcinoma in a 50 years old male with reticular morphology. Reticular variant of myoepithelial carcinoma may be mistaken for a variety of benign and malignant epithelial and mesenchymal tumours including mixed tumour (pleomorphic adenoma), adenoid cystic carcinoma, basal cell adenoma and epithelial myoepithelial carcinoma. Complete surgical excision is the mainstay of therapy. The role of radiation therapy and chemotherapy is not yet established. Awareness of this variant is emphasized to prevent misdiagnosis.

  20. Genetic variants of the human dipeptide transporter PEPT1

    DEFF Research Database (Denmark)

    Anderle, Pascale; Nielsen, Carsten Uhd; Pinsonneault, Julia

    2006-01-01

    We tested whether genetic polymorphisms affect activity of the dipeptide transporter PEPT1, which mediates bioavailability of peptidomimetic drugs. All 23 exons and adjoining intronic sections of PEPT1 (SLC15A1) were sequenced in 247 individuals of various ethnic origins (Coriell collection). Of 38...... single nucleotide polymorphisms (SNPs), 21 occurred in intronic and non-coding regions and 17 in exonic coding region, of which nine were nonsynonymous. Eight nonsynonymous variants were cloned into expression vectors and functionally characterized after transient transfection into Cos7 and Chinese...... formation of a splice variant (PEPT1-RF). PEPT1-RF mRNA levels ranged from 2 to 44% of total PEPT1-related mRNA, with potential consequences for drug absorption. Together with previous results, this study reveals a relatively low level of genetic variability in polymorphisms affecting both protein function...

  1. Metaplastic breast carcinoma; melanocytic variant, a very rare tumour

    Science.gov (United States)

    Nzegwu, Martin A.; Sule, Emmanuel; Uzoigwe, Joseph; Achi, Franklyn

    2015-01-01

    Metaplastic breast carcinoma (MBC) is a rare heterogeneous malignancy, accounting for <1% of all invasive breast carcinomas, in which adenocarcinoma is found to coexist with an admixture of spindle, squamous, chondroid or bone-forming neoplastic cells. Melanocytic variant was first described by Ruffolo et al. in 1997. We report a case of MBC, melanocytic variant, in a 57-year-old Nigerian female who presented with a left breast mass 8 cm in diameter in the upper outer quadrant, hard and gradually increase in size to become painful. Breast examination showed gross asymmetry. Left breast was oedematous and shiny with extensive peau d'orange. No palpable axillary nodes were seen. Chest X-ray and abdominal ultrasound scan showed no involvement. Breast biopsy revealed an invasive metaplastic ductal carcinoma with melanocytic differentiation. PMID:25666364

  2. Matrix metalloproteinase-2 gene variants and abdominal aortic aneurysm.

    Science.gov (United States)

    Smallwood, L; Warrington, N; Allcock, R; van Bockxmeer, F; Palmer, L J; Iacopetta, B; Golledge, J; Norman, P E

    2009-08-01

    To investigate associations between two polymorphisms of the matrix metalloproteinase-2 gene (MMP2) and the incidence and progression of abdominal aortic aneurysm (AAA). Cases and controls were recruited from a trial of screening for AAAs. The association between two variants of MMP2 (-1360C>T, and +649C>T) in men with AAA (n=678) and in controls (n=659) was examined using multivariate analyses. The association with AAA expansion (n=638) was also assessed. In multivariate analyses with adjustments for multiple testing, no association between either SNP and AAA presence or expansion was detected. MMP2 -1360C>T and +649C>T variants are not risk factors for AAA.

  3. Solution behaviour of Human Serum Albumin and GLP-1variants

    DEFF Research Database (Denmark)

    Sønderby, Pernille

    interaction is critical for the long term stability of a pharmaceutical. Protein complex formation is important for extended half-life in vivo and is essential to cellular communication such as the induction of the insulin response. This thesis focuses on human serum albumin (HSA) as a central player...... approach to half-life extension is conjugation of molecules to HSA. In this part of the thesis, novel GLP-1-albumin conjugates developed by Albumedix A/S where examined by a combined approach of pharmacokinetic studies and solution structure determination with SAXS. GLP-1 was conjugated to Cys34...... of recombinant HSA (rHSA) and two rHSA variants with lower (NB) and higher binding (HB) affinity to the neonatal Fc receptor (FcRn). Binding kinetics showed that the conjugation had limited effect on the binding properties of the conjugates to FcRn compared to the respective rHSA variants. Increased in-vivo half...

  4. A Survey: variants of TCP in Ad-hoc networks

    Directory of Open Access Journals (Sweden)

    Komal Zaman

    2013-11-01

    Full Text Available MANET (Mobile Ad-hoc network forms a temporary network of wireless mobile nodes without any infrastructure where all nodes are allowed to move freely, configure themselves and interconnect with its neighbors to perform peer to peer communication and transmission. TCP (Transmission Control Protocol offers reliable, oriented connection and mechanism of end to end delivery. This article provides the review and comparison of existing variants of TCP for instance: The TCP Tahoe, The TCP Reno, The TCP New Reno, The Lite, The Sack, The TCP Vegas, Westwood and The TCP Fack. TCP’s performance depends on the type of its variants due to missing of congestion control or improper activation procedures such as Slow Start, Fast Retransmission, and Congestion Avoidance, Retransmission, Fast Recovery, Selective Acknowledgement mechanism and Congestion Control. This analysis is essential to be aware about a better TCP implementation for a specific scenario and then nominated a suitable one.

  5. Characterization of a Mycobacterium intracellulare variant strain by molecular techniques.

    Science.gov (United States)

    Menendez, M C; Palenque, E; Navarro, M C; Nuñez, M C; Rebollo, M J; Garcia, M J

    2001-12-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members.

  6. Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

    Directory of Open Access Journals (Sweden)

    Tonia C. Carter

    2016-01-01

    Full Text Available Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.

  7. Dandy-Walker variant associated with bipolar affective disorder

    Directory of Open Access Journals (Sweden)

    Anand Lingeswaran

    2009-01-01

    Full Text Available The Dandy-Walker malformation is a congenital brain malformation, typically involving the fourth ventricle and the cerebellum. To date, the Dandy-Walker syndrome has not been described in association with bipolar disorder type I mania, and therefore we briefly report the case of a Dandy-Walker variant associated with acute mania. A 10-year-old boy was brought by his mother to the outpatient clinic of the Department of Psychiatry of a tertiary care hospital, with symptoms of mania. The MRI brain of the patient showed a posterior fossa cystic lesion, a giant cisterna magna communicating with the fourth ventricle and mild hypoplasia of the cerebellar vermis, with the rest of the structures being normal and no signs of hydrocephalus. These findings showed that the patient had a Dandy-Walker variant. He responded partially to valproate and olanzepine, which controlled the acute manic symptoms in the ward.

  8. Determining the pathogenicity of genetic variants associated with cardiac channelopathies.

    Science.gov (United States)

    Campuzano, Oscar; Allegue, Catarina; Fernandez, Anna; Iglesias, Anna; Brugada, Ramon

    2015-01-22

    Advancements in genetic screening have generated massive amounts of data on genetic variation; however, a lack of clear pathogenic stratification has left most variants classified as being of unknown significance. This is a critical limitation for translating genetic data into clinical practice. Genetic screening is currently recommended in the guidelines for diagnosis and treatment of cardiac channelopathies, which are major contributors to sudden cardiac death in young people. We propose to characterize the pathogenicity of genetic variants associated with cardiac channelopathies using a stratified scoring system. The development of this system was considered by using all of the tools currently available to define pathogenicity. The use of this scoring system could help clinicians to understand the limitations of genetic associations with a disease, and help them better define the role that genetics can have in their clinical routine.

  9. Spatially variant convolution with scaled B-splines.

    Science.gov (United States)

    Muñoz-Barrutia, Arrate; Artaechevarria, Xabier; Ortiz-de-Solorzano, Carlos

    2010-01-01

    We present an efficient algorithm to compute multidimensional spatially variant convolutions--or inner products--between N-dimensional signals and B-splines--or their derivatives--of any order and arbitrary sizes. The multidimensional B-splines are computed as tensor products of 1-D B-splines, and the input signal is expressed in a B-spline basis. The convolution is then computed by using an adequate combination of integration and scaled finite differences as to have, for moderate and large scale values, a computational complexity that does not depend on the scaling factor. To show in practice the benefit of using our spatially variant convolution approach, we present an adaptive noise filter that adjusts the kernel size to the local image characteristics and a high sensitivity local ridge detector.

  10. Ethical considerations in presymptomatic testing for variant CJD

    OpenAIRE

    Duncan, R.; Delatycki, M; S. Collins(NUI, Galway); Boyd, A; Masters, C.; Savulescu, J

    2005-01-01

    Variant Creutzfeldt–Jakob disease (vCJD) is a fatal, transmissible, neurodegenerative disorder for which there is currently no effective treatment. vCJD arose from the zoonotic spread of bovine spongiform encephalopathy. There is now compelling evidence for human to human transmission through blood transfusions from presymptomatic carriers and experts are warning that the real epidemic may be yet to come. Imperatives exist for the development of reliable, non-invasive presymptomatic diagnosti...

  11. Neurophysiologic effect of GWAS derived schizophrenia and bipolar risk variants.

    Science.gov (United States)

    Hall, Mei-Hua; Levy, Deborah L; Salisbury, Dean F; Haddad, Steve; Gallagher, Patience; Lohan, Mary; Cohen, Bruce; Ongür, Dost; Smoller, Jordan W

    2014-01-01

    Genome-wide association studies (GWAS) have identified multiple single nucleotide polymorphisms (SNPs) as disease associated variants for schizophrenia (SCZ), bipolar disorder (BPD), or both. Although these results are statistically robust, the functional effects of these variants and their role in the pathophysiology of SCZ or BPD remain unclear. Dissecting the effects of risk genes on distinct domains of brain function can provide important biological insights into the mechanisms by which these genes may confer illness risk. This study used quantitative event related potentials to characterize the neurophysiological effects of well-documented GWAS-derived SCZ/BPD susceptibility variants in order to map gene effects onto important domains of brain function. We genotyped 199 patients with DSM-IV diagnoses of SCZ or BPD and 74 healthy control subjects for 19 risk SNPs derived from previous GWAS findings and tested their association with five neurophysiologic traits (P3 amplitude, P3 latency, N1 amplitude, P2 amplitude, and P50 sensory gating responses) known to be abnormal in psychosis. The TCF4 SNP rs17512836 risk allele showed a significant association with reduced auditory P3 amplitude (P = 0.00016) after correction for multiple testing. The same allele was also associated with delayed P3 latency (P = 0.005). Our results suggest that a SCZ risk variant in TCF4 is associated with neurophysiologic traits thought to index attention and working memory abnormalities in psychotic disorders. These findings suggest a mechanism by which TCF4 may contribute to the neurobiological basis of psychotic illness.

  12. Consideration of Cosegregation in the Pathogenicity Classification of Genomic Variants

    OpenAIRE

    Jarvik, Gail P.; Browning, Brian L.

    2016-01-01

    The American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) recently published important new guidelines aiming to improve and standardize the pathogenicity classification of genomic variants. The Clinical Sequencing Exploratory Research (CSER) consortium evaluated the use of these guidelines across nine laboratories. One identified obstacle to consistent usage of the ACMG-AMP guidelines is the lack of a definition of cosegregation as criteria for ...

  13. Enterococcus faecium small colony variant endocarditis in an immunocompetent patient

    Directory of Open Access Journals (Sweden)

    S. Hernández Egido

    2016-01-01

    Full Text Available Small colony variants (SCV are slow-growing subpopulations of bacteria usually associated with auxotrophism, causing persistent or recurrent infections. Enterococcus faecalis SCV have been seldom described, and only one case of Enterococcus faecium SCV has been reported, associated with sepsis in a leukaemia patient. Here we report the first case described of bacteraemia and endocarditis by SCV E. faecium in an immunocompetent patient.

  14. Spatially variant tomographic imaging: Estimation, identification, and optimization

    Energy Technology Data Exchange (ETDEWEB)

    Baker, John Robert [Univ. of California, Berkeley, CA (United States)

    1991-11-01

    This thesis is an investigation of methods for processing multidimensional signals acquired using modern tomography systems that have an anisotropic or spatially variant response function. The main result of this research is the discovery of a new method to obtain better estimators of an unknown spatial intensity distribution by incorporating detailed knowledge about the tomograph system response function and statistical properties of the acquired signal into a mathematical model.

  15. Variantes anatómicas del septum pellucidum

    Directory of Open Access Journals (Sweden)

    P. Sartori

    2015-04-01

    Durante la vida embrionaria existen variantes anatómicas del septum pellucidum que se disponen en sentido rostro-dorsal. Estas son el cavum del septum pellucidum, el cavum vergae y el cavum velum interpositum. Su presencia o ausencia puede estar relacionada con alteraciones del desarrollo del sistema nervioso y trastornos cognitivo-psiquiátricos, por lo que deben conocerse bien para evitar diagnósticos erróneos.

  16. Transstyloid, transscaphoid, transcapitate fracture: a variant of scaphocapitate fractures.

    LENUS (Irish Health Repository)

    Burke, Neil G

    2014-01-01

    Transstyloid, transscaphoid, transcapitate fractures are uncommon. We report the case of a 28-year-old man who sustained this fracture following direct trauma. The patient was successfully treated by open reduction internal fixation of the scaphoid and proximal capitate fragment, with a good clinical outcome at 1-year follow-up. This pattern is a new variant of scaphocapitate fracture as involves a fracture of the radial styloid as well.

  17. THERAPEUTIC IMPLICATIONS OF GENETIC RISK VARIANTS FOR CORONARY ARTERY DISEASE

    Directory of Open Access Journals (Sweden)

    Rajiv Kumar Srivastava

    2017-02-01

    Full Text Available BACKGROUND This review covers therapeutic implication of genetic risk variant responsible for coronary artery disease by utilising the highdensity single-nucleotide microarrays to screen the entire human genome. The sequence of the human genome provides the blueprint for life. Approximately, 99.5% of the human genome Deoxyribonucleic Acid (DNA sequence is identical among humans with 0.5% of the genome sequence (15 million bps accounting for all individual differences. MATERIALS AND METHODS The new technology of the computerised chip array of millions of Single-Nucleotide Polymorphisms (SNPs as Deoxyribonucleic Acid (DNA markers makes it possible to study and detect genetic predisposition to common polygenic disorders such as Coronary Artery Disease (CAD. The sample sizes required for these studies are massive and large; worldwide consortiums such as Coronary Artery Disease Genome-wide Replication and Meta-Analysis (CARDIoGRAM study have been formed to accommodate this requirement. After the identification of 9p21 progress to detect genetic predisposition has been remarkable. RESULTS There are currently a total of 50 genetic risk variants predisposing to CAD of genome-wide significance with confirmation in independent populations. Rare variants (Minor Allele Frequency, MAF <5% will require direct sequencing to detect genetic predisposition. CONCLUSION We can develop new biomarkers for detecting early CAD as well as unique targets for novel therapy. The challenge for the future will be to identify the molecular mechanisms mediating the risk of those genetic risk variants that act through nonconventional risk factors. The ultimate objective for the future is the sequencing and functional analysis of the causative polymorphisms for its therapeutic implications.

  18. Molecular basis for Duarte and Los Angeles variant galactosemia

    Energy Technology Data Exchange (ETDEWEB)

    Langley, S.D.; Lai, K.; Dembure, P.P. [Emory Univ. School of Medicine, Atlanta, GA (United States)] [and others

    1997-02-01

    Human erythrocytes that are homozygous for the Duarte enzyme variant of galactosemia (D/D) have a characteristic isoform on isoelectric focusing and 50% reduction in galactose-1-phosphate uridyltransferase (GALT) enzyme activity. The Duarte biochemical phenotype has a molecular genotype of N314D/N314D. The characteristic Duarte isoform is also associated with a variant called the {open_quotes}Los Angeles (LA) phenotype,{close_quotes} which has increased GALT enzyme activity. We evaluated GALT enzyme activity and screened the GALT genes of 145 patients with one or more N314D-containing alleles. We found seven with the LA biochemical phenotype, and all had a 1721C{r_arrow}T transition in exon 7 in cis with the N314D missense mutation. The 1721C{r_arrow}T transition is a neutral polymorphism for leucine at amino acid 218 (L218L). In pedigree analyses, this 1721C{r_arrow}T transition segregated with the LA phenotype of increased GALT activity in three different biochemical phenotypes (LA/N, LA/G, and LA/D). To determine the mechanism for increased activity of the LA variant, we compared GALT mRNA, protein abundance, and enzyme thermal stability in lymphoblast cell lines of D and LA phenotypes with comparable genotypes. GALT protein abundance was increased in LA compared to D alleles, but mRNA was similar among all genotypes. We conclude that the codon change N314D in cis with the base-pair transition 1721C{r_arrow}T produces the LA variant of galactosemia and that this nucleotide change increases GALT activity by increasing GALT protein abundance without increasing transcription or decreasing thermal lability. A favorable codon bias for the mutated codon with consequently increased translation rates is postulated as the mechanism. 23 refs., 3 figs., 4 tabs.

  19. Search for Genetic Variants Underlying Musical Aptitude and Related Traits

    OpenAIRE

    Ukkola-Vuoti, Liisa

    2013-01-01

    Music perception and practice represents complex cognitive functions of the brain. There is an abundance of data about the neurophysiological effects of music on the human brain, but heritability and especially molecular studies have been lacking. The development of genome technologies and bioinformatics has enabled the identification of genetic variants underlying complex human traits. These methods can be applied to normal human traits like music perception and performance. Prior to th...

  20. Spatially variant tomographic imaging: Estimation, identification, and optimization

    Energy Technology Data Exchange (ETDEWEB)

    Baker, J.R.

    1991-11-01

    This thesis is an investigation of methods for processing multidimensional signals acquired using modern tomography systems that have an anisotropic or spatially variant response function. The main result of this research is the discovery of a new method to obtain better estimators of an unknown spatial intensity distribution by incorporating detailed knowledge about the tomograph system response function and statistical properties of the acquired signal into a mathematical model.

  1. Common genetic variants influence human subcortical brain structures

    OpenAIRE

    Hibar, Derrek P.; Stein, Jason L.; Renteria, Miguel E.; Arias-Vasquez, Alejandro,; Desrivieres, 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

    2015-01-01

    The highly complex structure of the human brain is strongly shaped by genetic influences(1). Subcortical brain regions form circuits with cortical areas to coordinate movement(2), learning, memory(3) and motivation(4), and altered circuits can lead to abnormal behaviour and disease(5). 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 de...

  2. Blood type, ABO genetic variants, and ovarian cancer survival.

    Science.gov (United States)

    Cozzi, Gabriella D; Levinson, Rebecca T; Toole, Hilary; Snyder, Malcolm-Robert; Deng, Angie; Crispens, Marta A; Khabele, Dineo; Beeghly-Fadiel, Alicia

    2017-01-01

    Blood type A and the A1 allele have been associated with increased ovarian cancer risk. With only two small studies published to date, evidence for an association between ABO blood type and ovarian cancer survival is limited. We conducted a retrospective cohort study of Tumor Registry confirmed ovarian cancer cases from the Vanderbilt University Medical Center with blood type from linked laboratory reports and ABO variants from linked Illumina Exome BeadChip data. Associations with overall survival (OS) were quantified by hazard ratios (HR) and confidence intervals (CI) from proportional hazards regression models; covariates included age, race, stage, grade, histologic subtype, and year of diagnosis. ABO phenotype (N = 694) and/or genotype (N = 154) data were available for 713 predominantly Caucasian (89.3%) cases. In multivariable models, blood type A had significantly better OS compared to either O (HR: 0.75, 95% CI: 0.60-0.93) or all non-A (HR: 0.77, 95% CI: 0.63-0.94) cases. Similarly, missense rs1053878 minor allele carriers (A2) had better OS (HR: 0.50, 95% CI: 0.25-0.99). Among Caucasians, this phenotype association was strengthened, but the genotype association was attenuated; instead, four variants sharing moderate linkage disequilibrium with the O variant were associated with better OS (HR: 0.62, 95% CI: 0.39-0.99) in unadjusted models. Blood type A was significantly associated with longer ovarian cancer survival in the largest such study to date. This finding was supported by genetic analysis, which implicated the A2 allele, although O related variants also had suggestive associations. Further research on ABO and ovarian cancer survival is warranted.

  3. Lesson Twenty-two The early repolarization variant

    Institute of Scientific and Technical Information of China (English)

    鲁端; 王劲

    2007-01-01

    @@ The ST-segment elevation seen in apparently healthy and asymptomatic persons,the so-called early repolarization variant (ERPV)1.Hiss et al reported that 91% of 6014 healthy men in the US Air Force who were between 16 and 58 years old had an ST-segment elevation of 0.1 to 0.3 mV in one or more precordial leads2.The elevation was most common and marked in lead V2.

  4. Emotional evaluation and memory in behavioral variant frontotemporal dementia

    OpenAIRE

    St. Jacques, Peggy L.; Grady, Cheryl; Davidson, Patrick S. R.; Chow, Tiffany W

    2015-01-01

    Behavioral variant frontotemporal dementia (bvFTD) affects emotional evaluation, but less is known regarding the patients' ability to remember emotional stimuli. Here, bvFTD patients and age-matched controls studied positive, negative, and neutral pictures followed by a recognition memory test. Compared to controls, bvFTD patients showed a reduction in emotional evaluation of negative scenes, but not of positive or neutral scenes. Additionally, the patients showed an overall reduction in reco...

  5. Quantifying the contribution of genetic variants for survival phenotypes.

    Science.gov (United States)

    Müller, Martina; Döring, Angela; Küchenhoff, Helmut; Lamina, Claudia; Malzahn, Dörthe; Bickeböller, Heike; Vollmert, Caren; Klopp, Norman; Meisinger, Christa; Heinrich, Joachim; Kronenberg, Florian; Wichmann, H Erich; Heid, Iris M

    2008-09-01

    Particularly in studies based on population representative samples, it is of major interest what impact a genetic variant has on the phenotype of interest, which cannot be answered by mere association estimates alone. One possible measure for quantifying the phenotype's variance explained by the genetic variant is R(2). However, for survival outcomes, no clear definition of R(2) is available in the presence of censored observations. We selected three criteria proposed for this purpose in the literature and compared their performance for single nucleotide polymorphism (SNP) data through simulation studies and for mortality data with candidate SNPs in the general population-based KORA cohort. The evaluated criteria were based on: (1) the difference of deviance residuals, (2) the variation of individual survival curves, and (3) the variation of Schoenfeld residuals. Our simulation studies included various censoring and genetic scenarios. The simulation studies revealed that the deviance residuals' criterion had a high dependence on the censoring percentage, was generally not limited to the range [0; 1] and therefore lacked interpretation as a percentage of explained variation. The second criterion (variation of survival curves) hardly reached values above 60%. Our requirements were best fulfilled by the criterion based on Schoenfeld residuals. Our mortality data analysis also supported the findings in simulation studies. With the criterion based on Schoenfeld residuals, we recommend a powerful and flexible tool for genetic epidemiological studies to refine genetic association studies by judging the contribution of genetic variants to survival phenotype.

  6. A Galeazzi-variant type fracture-dislocation in adults.

    Science.gov (United States)

    Vaishya, Raju; Shrestha, Sundar Kumar; Vaish, Abhishek

    2013-01-01

    Fracture of either radius or ulna with a dislocation either at the proximal or distal radioulnar joint (DRUJ) is not a common injury and is inherently unstable. Here we report a case series, with both-bone forearm fractures associated with dislocation of DRUJ, as a Galeazzi-variant type fracture-dislocation, and try to analyze this injury pattern. The study was based on 6 patients having Galeazzi-variant type fracture-dislocation of different age (20 to 45 years). All fractures were closed type. Two fractures involved the same level and three fractures were at different levels of radius and ulna shaft. After thorough examination and investigations they were treated with limited contact dynamic compression plate without additional fixation for DRUJ. All cases were followed up for 24 weeks. The maximum incidence occurred in age group between 31 and 40 years. All the fractures of both radius and ulna were united in average time of 12 weeks. Range of motion of wrist and elbow, supination and pronation at final follow-up were normal. There was no subsequent re-subluxation or dislocation of the DRUJ in any of the cases. Galeazzi variant in adult is a new undescribed pattern of forearm with wrist injury. Stable open reduction and internal fixation of both-bone forearm fractures is mandatory, followed by 3 to 4 weeks of immobilization in a cast for the healing of disrupted DRUJ.

  7. Melanocortin-1 receptor gene variants in four Chinese ethnic populations

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    There is strong relationship between melanocortin-1 receptor (MC1R) gene variants and human hair color and skin type.Based on a sequencing study of MC1R gene in 50 individuals from the Uygur,Tibetan,Wa and Dai ethnic populations,we discuss the occurrence of 7 mc1r variants consisting of 5 nonsynonymous sites (Val60Leu,Arg67Gln,Val92Met,Arg163Gln and Ala299Val) and 2 synonymous sites (C414T and A942G),among which C414T and Ala299Val were reported for the first time.Confirmation and analysis were also made of 122 individuals at three common point mutations (Val92Met,Arg163Gln,A942G) using PCR-SSCP.The frequency of Arg163Gln variant varies in the four ethnic populations,with percentage of 40%,85.0%,66.2% and 72.7%,respectively,while those of Val92Met and A942G are roughly similar in these four populations.The different environments,migration and admixture of various ethnic groups in China might have impact on the observed frequency of Arg163Gln.

  8. FGFR4 polymorphic variants modulate phenotypic features of Cushing disease.

    Science.gov (United States)

    Nakano-Tateno, Tae; Tateno, Toru; Hlaing, Maw Maw; Zheng, Lei; Yoshimoto, Katsuhiko; Yamada, Shozo; Asa, Sylvia L; Ezzat, Shereen

    2014-04-01

    Cushing disease is a potentially lethal condition resulting from hormone excess, usually due to a small pituitary tumor that fails to respond to negative feedback inhibition. A minority of patients develop larger, more aggressive tumors of the same lineage but with modest hormone excess. Here we show that a common polymorphism in the fibroblast growth factor receptor 4 (FGFR4) transmembrane domain yields receptor isoforms with distinct properties that mediate these biological differences. Forced expression of the major FGFR4-G388 variant allele supports pY-signal transducer and activator of transcription (STAT3) responses. In contrast, expression of the minor FGFR4-R388 allele enhances STAT3 serine phosphorylation, driving cellular growth. In addition, FGFR4-R388 enhances glucocorticoid receptor phosphorylation and nuclear translocation. Consistent with these findings, glucocorticoid administration resulted in enhanced hormone negative feedback in mice with knock-in of the FGFR4 variant allele. Moreover, clinical data from patients with pituitary tumors revealed that those homozygous for the R388 allele have a higher frequency of silent corticotroph macroadenomas than FGFR4-G388 carriers, who were more likely to have small but hormonally active microadenomas. These findings demonstrate that the FGFR4 transmembrane polymorphic variants can modulate cellular growth and sensitivity to glucocorticoid hormone negative feedback through distinct STAT3 modifications of relevance to the human forms of Cushing disease.

  9. Genetic variants in epigenetic genes and breast cancer risk.

    Science.gov (United States)

    Cebrian, Arancha; Pharoah, Paul D; Ahmed, Shahana; Ropero, Santiago; Fraga, Mario F; Smith, Paula L; Conroy, Don; Luben, Robert; Perkins, Barbara; Easton, Douglas F; Dunning, Alison M; Esteller, Manel; Ponder, Bruce A J

    2006-08-01

    Epigenetic events, resulting changes in gene expression capacity, are important in tumour progression, and variation in genes involved in epigenetic mechanisms might therefore be important in cancer susceptibility. To evaluate this hypothesis, we examined common variants in 12 genes coding for DNA methyltransferases (DNMT), histone acetyltransferases, histone deacetyltransferases, histone methyltrasferases and methyl-CpG binding domain proteins, for association with breast cancer in a large case-control study (N cases = 4474 and N controls = 4580). We identified 63 single nucleotide polymorphisms (SNPs) that efficiently tag all the known common variants in these genes, and are also expected to tag any unknown SNP in each gene. We found some evidence for association for six SNPs: DNMT3b-c31721t [P (2 df) = 0.007], PRDM2-c99243 t [P (2 df) = 0.03] and t105413c [P-recessive = 0.05], EHMT1-g-9441a [P (2df) = 0.05] and g41451t (P-trend = 0.04), and EHMT2-S237S [P (2df) = 0.04]. The most significant result was for DNMT3b-c31721t (P-trend = 0.124 after adjusting for multiple testing). However, there were three other results with P variants in histone methyltransferases, and warrant the design of larger epidemiological and biochemical studies to establish the true meaning of these findings.

  10. Carcinoma papilar tiroideo variante esclerosante difuso Diffuse Sclerosing Variant of Papillary Thyroid Carcinoma

    Directory of Open Access Journals (Sweden)

    JL D'Addino

    2012-06-01

    Full Text Available Objetivo: Presentar un carcinoma inusual de tiroides y de difícil diagnóstico, su manejo y evolución. Caso clínico: Paciente de raza blanca de 37 años, desde hace 6 meses presentaba formación laterocervical derecha asintomática y ecografía con nódulo tiroideo sobre tiroides heterogénea. Sin antecedentes personales ni familiares de importancia. La punción de una adenopatía regional resultó adenocarcinoma y la del nódulo tiroideo: quiste coloide. Se intervino quirúrgicamente efectuándose un vaciamiento radical derecho y la biopsia por congelación informó carcinoma tiroideo por lo que se completó con vaciamiento cervical izquierdo y tiroidectomía total. La biopsia diferida fue: "carcinoma papilar difuso esclerosante con metástasis ganglionares en 5 de 6 ganglios peritiroideos derechos y en 7 de 9 ganglios cervicales, correspondiendo a 4 derechos y 3 izquierdos. Estadio: I, T3-N1b-M0. Se trató posteriormente con 3 dosis de yodo 131 y radioterapia externa por compromiso ganglionar mediastinal. A 6 meses de seguimiento hasta el presente, continúa libre de enfermedad. Los individuos con insulinorresistencia y síndrome metabólico presentan aumento del tamaño de la glándula tiroides y mayor prevalencia de nódulos. Tanto la insulina como la TSH se constituyen en factores de crecimiento para las células tiroideas, y los niveles de TSH son mayores en individuos con síndrome metabólico, presente en este caso. Conclusión: El carcinoma papilar, variante difusa esclerosante es un tumor inusual, de evolución más agresiva y con rápido compromiso extratiroideo y metástasis a distancia. Los autores declaran no poseer conflictos de interés.Objective: To report a case of a diffuse sclerosing papillary carcinoma, a rare type of thyroid carcinoma, of difficult diagnosis, its management and further follow-up. Case: 37-year-old white male who presented with a 6-month history of sudden onset of an asymptomatic right-sided lateral

  11. Estimating the contribution of genetic variants to difference in incidence of disease between population groups.

    Science.gov (United States)

    Moonesinghe, Ramal; Ioannidis, John P A; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-08-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene-environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal.

  12. Phenotypic and Enzymatic Comparative Analysis of the KPC Variants, KPC-2 and Its Recently Discovered Variant KPC-15

    Science.gov (United States)

    Yang, Yijun

    2014-01-01

    Sixteen different variants (KPC-2 to KPC-17) in the KPC family have been reported, and most current studies are focusing on KPC-2 and KPC-3. The KPC-15 variant, which isolated from Klebsiella pneumoniae in a Chinese hospital, was a recently discovered KPC enzyme. To compare the characteristics of KPC-15 and KPC-2, the variants were determined by susceptibility testing, PCR amplification and sequencing, and study of kinetic parameters. The strain harboring the KPC-15 showed resistance to 18 conventional antimicrobial agents, especially to cabapenem antibiotics, and the strain involving the KPC-2 also indicated resistance to cabapenem antibiotics, but both strains were susceptible to polymyxin B and colistin. The conjugation experiments showed that the changes of MIC values to the antibiotics were due to the transferred plasmids. The differences of amino acids were characterised at sites of 119 leucine and 146 lysine with KPC-15 and KPC-2. The minimum evolution tree indicated the KPC alleles evolution, and showed that the KPC-15 appeared to be homogenous with KPC-4 closely. Steady-state kinetic parameters showed the catalytic efficiency of KPC-15 was higher than that of KPC-2 for all tested antibiotics in this study. The catalytic efficiency of KPC-15 caused resistance to β-lactam antibiotics was higher than that of KPC-2. Meanwhile, an evolutionary transformation changed KPC from an efficient carbapenemase to its variants (KPC-15) with better ceftazidimase catalytic efficiency, and the old antibiotics polymyxin B and colistin might play a role in the therapy for multi-resistant strains. PMID:25360633

  13. Phenotypic and enzymatic comparative analysis of the KPC variants, KPC-2 and its recently discovered variant KPC-15.

    Directory of Open Access Journals (Sweden)

    Dongguo Wang

    Full Text Available Sixteen different variants (KPC-2 to KPC-17 in the KPC family have been reported, and most current studies are focusing on KPC-2 and KPC-3. The KPC-15 variant, which isolated from Klebsiella pneumoniae in a Chinese hospital, was a recently discovered KPC enzyme. To compare the characteristics of KPC-15 and KPC-2, the variants were determined by susceptibility testing, PCR amplification and sequencing, and study of kinetic parameters. The strain harboring the KPC-15 showed resistance to 18 conventional antimicrobial agents, especially to cabapenem antibiotics, and the strain involving the KPC-2 also indicated resistance to cabapenem antibiotics, but both strains were susceptible to polymyxin B and colistin. The conjugation experiments showed that the changes of MIC values to the antibiotics were due to the transferred plasmids. The differences of amino acids were characterised at sites of 119 leucine and 146 lysine with KPC-15 and KPC-2. The minimum evolution tree indicated the KPC alleles evolution, and showed that the KPC-15 appeared to be homogenous with KPC-4 closely. Steady-state kinetic parameters showed the catalytic efficiency of KPC-15 was higher than that of KPC-2 for all tested antibiotics in this study. The catalytic efficiency of KPC-15 caused resistance to β-lactam antibiotics was higher than that of KPC-2. Meanwhile, an evolutionary transformation changed KPC from an efficient carbapenemase to its variants (KPC-15 with better ceftazidimase catalytic efficiency, and the old antibiotics polymyxin B and colistin might play a role in the therapy for multi-resistant strains.

  14. 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

    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...... the functional effects of these variants. The prediction results of those identified in the ESP and ExAC and those not identified in the ESP and ExAC were compared. In 12 genes, 60 LVNC-associated missense/nonsense variants were identified. MYH7 was the predominant gene, encompassing 24 of the 60 LVNC...

  15. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

    DEFF Research Database (Denmark)

    Hendricks, Audrey E; Bochukova, Elena G; Marenne, Gaëlle

    2017-01-01

    Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS......, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF∼0...... the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do...

  16. Common and rare variants in SCN10A modulate the risk of atrial fibrillation

    DEFF Research Database (Denmark)

    Jabbari, Javad; Olesen, Morten S; Yuan, Lei;

    2015-01-01

    is in high linkage disequilibrium with the nonsynonymous variant in SCN10A, rs6795970 (V1073A, r(2)=0.933). We therefore sought to determine whether common and rare SCN10A variants are associated with early onset AF. METHODS AND RESULTS: SCN10A was sequenced in 225 AF patients in whom there was no evidence...... of other cardiovascular disease or dysfunction (lone AF). In an association study of the rs6795970 single nucleotide polymorphism variant, we included 515 AF patients and 2 control cohorts of 730 individuals free of AF and 6161 randomly sampled individuals. Functional characterization of SCN10A variants...... was performed by whole-cell patch-clamping. In the lone AF cohort, 9 rare missense variants and 1 splice site donor variant were detected. Interestingly, AF patients were found to have higher G allele frequency of rs6795970, which encodes the alanine variant at position 1073 (described from here on as A1073...

  17. Efeito da idade e da testosterona sobre a expressão fisiologica de adrenoceptores alfa-1 em ductos deferentes de ratos

    OpenAIRE

    Jose Luiz Tatagiba Lamas

    1990-01-01

    Resumo: O objetivo deste trabalho é determinar o efeito do processo de desenvolvimento e envelhecimento e de uma dose de testosterona, administrada no 22° dia de vida sobre a resposta contrátil de ductos diferentes de ratos Wistar pré-púrberes (3semanas), jovens (3 meses) e senis (22 meses). Um grupo de ratos pré-púrberes foi tratado com testosterona (1mg/kg, SC) 24 horas antes do experimento. Foram obtida curvas concentração-efeito à noradrenalina em ductos diferentes submetidos a três condi...

  18. Respostas fisiologicas em căes suplementados com lecitina de soja e Lecipalm® : estudo sobre os parametros metabolicos, bioquimicos e hematologicos /

    OpenAIRE

    Marconcin, Solange Aparecida

    2008-01-01

    Orientadora: ProfŞ DrŞ Ana Vitoria Fischer da Silva Dissertaçăo (mestrado) - Universidade Federal do Paraná, Setor de Cięncias Agrárias, Programa de Pós-Graduaçăo em Ciencias Veterinárias. Defesa: Curitiba, 2008 Inclui bibliografia

  19. The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.

    Science.gov (United States)

    Saul, Robert; Lutz, Michael W; Burns, Daniel K; Roses, Allen D; Chiba-Falek, Ornit

    2016-09-01

    Short structural variants (SSVs) are short genomic variants (prototype bioinformatics tool, "SSV evaluation system," which is a searchable, annotated database of SSVs in the human genome, with associated customizable scoring software that is used to evaluate and prioritize SSVs that are most likely to have significant biological effects and impact on disease risk. This new bioinformatics tool is a component in a larger strategy that we have been using to discover potentially important SSVs within candidate genomic regions that have been identified in genome-wide association studies, with the goal to prioritize potential functional/causal SSVs and focus the follow-up experiments on a relatively small list of strong candidate SSVs. We describe our strategy and discuss how we have used the SSV evaluation system to discover candidate causal variants related to complex neurodegenerative diseases. We present the SSV evaluation system as a powerful tool to guide genetic investigations aiming to uncover SSVs that underlie human complex diseases including neurodegenerative diseases in aging.

  20. Comparison of Motor Inhibition in Variants of the Instructed-Delay Choice Reaction Time Task.

    Science.gov (United States)

    Quoilin, Caroline; Lambert, Julien; Jacob, Benvenuto; Klein, Pierre-Alexandre; Duque, Julie

    2016-01-01

    Using instructed-delay choice reaction time (RT) paradigms, many previous studies have shown that the motor system is transiently inhibited during response preparation: motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) over the primary motor cortex are typically suppressed during the delay period. This effect has been observed in both selected and non-selected effectors, although MEP changes in selected effectors have been more inconsistent across task versions. Here, we compared changes in MEP amplitudes in three different variants of an instructed-delay choice RT task. All variants required participants to choose between left and right index finger movements but the responses were either provided "in the air" (Variant 1), on a regular keyboard (Variant 2), or on a response device designed to control from premature responses (Variant 3). The task variants also differed according to the visual layout (more concrete in Variant 3) and depending on whether participants received a feedback of their performance (absent in Variant 1). Behavior was globally comparable between the three variants of the task although the propensity to respond prematurely was highest in Variant 2 and lowest in Variant 3. MEPs elicited in a non-selected hand were similarly suppressed in the three variants of the task. However, significant differences emerged when considering MEPs elicited in the selected hand: these MEPs were suppressed in Variants 1 and 3 whereas they were often facilitated in Variant 2, especially in the right dominant hand. In conclusion, MEPs elicited in selected muscles seem to be more sensitive to small variations to the task design than those recorded in non-selected effectors, probably because they reflect a complex combination of inhibitory and facilitatory influences on the motor output system. Finally, the use of a standard keyboard seems to be particularly inappropriate because it encourages participants to respond promptly with no

  1. Simple and complex dysembryoplastic neuroepithelial tumors (DNT) variants: clinical profile, MRI, and histopathology

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Alexandre R.; Clusmann, Hans; Lehe, Marec von; Schramm, Johannes [University of Bonn Medical Center, Department of Neurosurgery, Bonn (Germany); Niehusmann, Pitt; Becker, Albert J. [University of Bonn Medical Center, Department of Neuropathology, Bonn (Germany); Urbach, Horst [University of Bonn Medical Center, Department of Radiology, Bonn (Germany)

    2009-07-15

    Dysembryoplastic neuroepithelial tumors (DNTs) are long-term epilepsy associated tumors subdivided into simple and complex variants. The purpose of this study was to relate different DNT components identified on magnetic resonance imaging (MRI) to histopathological features and to test the hypothesis that glial nodules as a histopathological feature of complex variants induce an occasional glioma misdiagnosis. Clinical, MRI, and histopathologic features of DNTs operated between 1988 and 2008 were reviewed. From a total of 61 DNTs, 48 simple and 13 complex variants were identified. Multiple or single pseudocysts in a cortical/subcortical location with small cysts sometimes separated from the tumor represented the glioneuronal element and were found in all DNTs. FLAIR hyperintense tissue was found between pseudocysts but - in neocortical DNTs - also circumscript in deeper tumor parts. Calcification and hemorrhages in this location occurred in four of 13 complex variants, and one of these patients was also the only one with tumor growth. Patients with complex variants had earlier seizure onset, and complex variants were more often located outside the temporal lobe. Although complex variants represented a higher diagnostic challenge, misdiagnoses also occurred in simple variants. One of five of DNTs showed contrast enhancement, which varied on follow-up studies with enhancing parts becoming nonenhancing and vice versa. The glioneuronal element is readily identifiable on MRI and should be considered to support the DNT diagnosis. Complex DNT variants have a different clinical profile and a more variable histopathological and MRI appearance; however, misdiagnoses occasionally also occur in simple variants. (orig.)

  2. Mutations in the paralogous human alpha-globin genes yielding identical hemoglobin variants.

    Science.gov (United States)

    Moradkhani, Kamran; Préhu, Claude; Old, John; Henderson, Shirley; Balamitsa, Vera; Luo, Hong-Yuan; Poon, Man-Chiu; Chui, David H K; Wajcman, Henri; Patrinos, George P

    2009-06-01

    The human alpha-globin genes are paralogues, sharing a high degree of DNA sequence similarity and producing an identical alpha-globin chain. Over half of the alpha-globin structural variants reported to date are only characterized at the amino acid level. It is likely that a fraction of these variants, with phenotypes differing from one observation to another, may be due to the same mutation but on a different alpha-globin gene. There have been very few previous examples of hemoglobin variants that can be found at both HBA1 and HBA2 genes. Here, we report the results of a systematic multicenter study in a large multiethnic population to identify such variants and to analyze their differences from a functional and evolutionary perspective. We identified 14 different Hb variants resulting from identical mutations on either one of the two human alpha-globin paralogue genes. We also showed that the average percentage of hemoglobin variants due to a HBA2 gene mutation (alpha2) is higher than the percentage of hemoglobin variants due to the same HBA1 gene mutation (alpha1) and that the alpha2/alpha1 ratio varied between variants. These alpha-globin chain variants have most likely occurred via recurrent mutations, gene conversion events, or both. Based on these data, we propose a nomenclature for hemoglobin variants that fall into this category.

  3. Glyco-variant library of the versatile enzyme horseradish peroxidase.

    Science.gov (United States)

    Capone, Simona; Pletzenauer, Robert; Maresch, Daniel; Metzger, Karl; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

    2014-09-01

    When the glycosylated plant enzyme horseradish peroxidase (HRP) is conjugated to specific antibodies, it presents a powerful tool for medical applications. The isolation and purification of this enzyme from plant is difficult and only gives low yields. However, HRP recombinantly produced in the yeast Pichia pastoris experiences hyperglycosylation, which impedes the use of this enzyme in medicine. Enzymatic and chemical deglycosylation are cost intensive and cumbersome and hitherto existing P. pastoris strain engineering approaches with the goal to avoid hyperglycosylation only resulted in physiologically impaired yeast strains not useful for protein production processes. Thus, the last resort to obtain less glycosylated recombinant HRP from P. pastoris is to engineer the enzyme itself. In the present study, we mutated all the eight N-glycosylation sites of HRP C1A. After determination of the most suitable mutation at each N-glycosylation site, we physiologically characterized the respective P. pastoris strains in the bioreactor and purified the produced HRP C1A glyco-variants. The biochemical characterization of the enzyme variants revealed great differences in catalytic activity and stability and allowed the combination of the most promising mutations to potentially give an unglycosylated, active HRP C1A variant useful for medical applications. Interestingly, site-directed mutagenesis proved to be a valuable strategy not only to reduce the overall glycan content of the recombinant enzyme but also to improve catalytic activity and stability. In the present study, we performed an integrated bioprocess covering strain generation, bioreactor cultivations, downstream processing and product characterization and present the biochemical data of the HRP glyco-library.

  4. Genetic susceptibility variants associated with colorectal cancer prognosis.

    Science.gov (United States)

    Abulí, Anna; Lozano, Juan José; Rodríguez-Soler, María; Jover, Rodrigo; Bessa, Xavier; Muñoz, Jenifer; Esteban-Jurado, Clara; Fernández-Rozadilla, Ceres; Carracedo, Angel; Ruiz-Ponte, Clara; Cubiella, Joaquín; Balaguer, Francesc; Bujanda, Luis; Reñé, Josep M; Clofent, Juan; Morillas, Juan Diego; Nicolás-Pérez, David; Xicola, Rosa M; Llor, Xavier; Piqué, Josep M; Andreu, Montserrat; Castells, Antoni; Castellví-Bel, Sergi

    2013-10-01

    Colorectal cancer (CRC) is the second leading cause of cancer-related death among men and women in Western countries. Once a tumour develops, a differentiated prognosis could be determined by lifestyle habits or inherited and somatic genetic factors. Finding such prognostic factors will be helpful in order to identify cases with a shorter survival or at a higher risk of recurrence that may benefit from more intensive treatment and follow-up surveillance. Sixteen CRC genetic susceptibility variants were directly genotyped in a cohort of 1235 CRC patients recruited by the EPICOLON Spanish consortium. Univariate Cox and multivariate regression analyses were performed taking as primary outcomes overall survival (OS), disease-free survival and recurrence-free interval. Genetic variants rs9929218 at 16q22.1 and rs10795668 at 10p14 may have an effect on OS. The G allele of rs9929218 was linked with a better OS [GG genotype, genotypic model: hazard ratio (HR) = 0.65, 95% confidence interval (CI) 0.45-0.93, P = 0.0179; GG/GA genotypes, dominant model: HR = 0.66, 95% CI 0.47-0.94, P = 0.0202]. Likewise, the G allele of rs10795668 was associated with better clinical outcome (GG genotype, genotypic model: HR = 0.73, 95% CI 0.53-1.01, P = 0.0570; GA genotype, genotypic model: HR = 0.66, 95% CI 0.47-0.92, P = 0.0137; GG/GA genotypes, dominant model: HR = 0.68, 95% CI 0.50-0.94, P = 0.0194). In conclusion, CRC susceptibility variants rs9929218 and rs10795668 may exert some influence in modulating patient's survival and they deserve to be further tested in additional CRC cohorts in order to confirm their potential as prognosis or predictive biomarkers.

  5. Novel associations of VKORC1 variants with higher acenocoumarol requirements.

    Directory of Open Access Journals (Sweden)

    Ana Isabel Anton

    Full Text Available BACKGROUND: Algorithms combining both clinical and genetic data have been developed to improve oral anticoagulant therapy. Three polymorphisms in two genes, VKORC1 and CYP2C9, are the main coumarin dose determinants and no additional polymorphisms of any relevant pharmacogenetic importance have been identified. OBJECTIVES: To identify new genetic variations in VKORC1 with relevance for oral anticoagulant therapy. METHODS AND RESULTS: 3949 consecutive patients taking acenocoumarol were genotyped for the VKORC1 rs9923231 and CY2C9* polymorphisms. Of these, 145 patients with a dose outside the expected range for the genetic profile determined by these polymorphisms were selected. Clinical factors explained the phenotype in 88 patients. In the remaining 57 patients, all with higher doses than expected, we sequenced the VKORC1 gene and genetic changes were identified in 14 patients. Four patients carried VKORC1 variants previously related to high coumarin doses (L128R, N = 1 and D36Y, N = 3.Three polymorphisms were also detected: rs17878544 (N = 5, rs55894764 (N = 4 and rs7200749 (N = 2 which was in linkage disequilibrium with rs17878544. Finally, 2 patients had lost the rs9923231/rs9934438 linkage. The prevalence of these variations was higher in these patients than in the whole sample. Multivariate linear regression analysis revealed that only D36Y and rs55894764 variants significantly affect the dose, although the improvement in the prediction model is small (from 39% to 40%. CONCLUSION: Our strategy identified novel associations of VKORC1 variants with higher acenocoumarol doses albeit with a low effect size. Further studies are necessary to test their influence on the VKORC1 function and the cost/benefit of their inclusion in pharmacogenetic algorithms.

  6. Mitochondrial DNA polymerase gamma variants in idiopathic sporadic Parkinson disease.

    Science.gov (United States)

    Luoma, P T; Eerola, J; Ahola, S; Hakonen, A H; Hellström, O; Kivistö, K T; Tienari, P J; Suomalainen, A

    2007-09-11

    Dysfunction of mitochondrial DNA polymerase gamma (POLG) has been recently recognized as an important cause of inherited neurodegenerative diseases. We have reported dominant and recessive inheritance of parkinsonism, mitochondrial myopathy, and premature amenorrhea in five ethnically distinct families with POLG1 mutations. This prompted us to carry out a detailed analysis of the coding region and intron-exon boundaries of POLG1 in Finnish patients with idiopathic sporadic Parkinson disease (PD) and in nonparkinsonian controls. The coding region of POLG1 was analyzed in 140 Finnish patients with PD and their 127 spouses as age- and ethnically matched controls. Further, we analyzed the intragenic CAG-repeat region of POLG1 in 126 additional patients with nonparkinsonian neurologic disorders and in 516 Finnish population controls. We found clustering of rare variants of the POLG1 CAG-repeat, encoding a polyglutamine tract, in Finnish patients with idiopathic PD as compared to their spouses (p = 0.003; OR 3.01, 95% CI 1.35 to 6.71), population controls (p = 0.001; OR 2.45, 95% CI 1.45 to 4.14), and patients with nonparkinsonian neurologic disorders (p = 0.05, OR 1.98, 95% CI 0.97 to 4.05). We found several amino acid substitutions, none of them associating with PD. These included a previously parkinsonism-associated POLG variant Y831C, found in one patient with PD, but also in five controls, suggesting that it is a neutral amino acid polymorphism. Our results suggest that POLG polyglutamine tract variants should be considered as a predisposing genetic factor in idiopathic sporadic Parkinson disease.

  7. A Galeazzi-variant type fracture-dislocation in adults

    Institute of Scientific and Technical Information of China (English)

    Raju Vaishya; Sundar Kumar Shrestha; Abhishek Vaish

    2013-01-01

    Objective:Fracture of either radius or ulna with a dislocation either at the proximal or distal radioulnar joint (DRUJ) is not a common injury and is inherently unstable.Here we report a case series,with both-bone forearm fractures associated with dislocation of DRUJ,as a Galeazzi-variant type fracture-dislocation,and try to analyze this injury pattern.Methods:The study was based on 6 patients having Galeazzi-variant type fracture-dislocation of different age (20 to 45 years).All fractures were closed type.Two fractures involved the same level and three fractures were at different levels of radius and ulna shaft.After thorough examination and investigations they were treated with limited contact dynamic compression plate without additional fixation for DRUJ.Results:All cases were followed up for 24 weeks.The maximum incidence occurred in age group between 31 and 40 years.All the fractures of both radius and ulna were united in average time of 12 weeks.Range of motion of wrist and elbow,supination and pronation at final follow-up were normal.There was no subsequent re-subluxation or dislocation of the DRUJ in any of the cases.Conclusion:Galeazzi variant in adult is a new undescribed pattern of forearm with wrist injury.Stable open reduction and internal fixation of both-bone forearm fractures is mandatory,followed by 3 to 4 weeks of immobilization in a cast for the healing of disrupted DRUJ.

  8. Inferior patellar pole fragmentation in children: just a normal variant?

    Energy Technology Data Exchange (ETDEWEB)

    Kan, J.H.; Vogelius, Esben S.; Orth, Robert C.; Guillerman, R.P.; Jadhav, Siddharth P. [Texas Children' s Hospital, E.B. Singleton Pediatric Radiology, Houston, TX (United States)

    2015-06-15

    Fragmentary ossification of the inferior patella is often dismissed as a normal variant in children younger than 10 years of age. The purpose of this study was to determine whether fragmentary inferior patellar pole ossification is a normal variant or is associated with symptoms or signs of pathology using MRI and clinical exam findings as reference. A retrospective review was performed on 150 patients ages 5-10 years who underwent 164 knee radiography and MRI exams (45.1% male, mean age: 7.8 years). The presence or absence of inferior patellar pole fragmentation on radiography was correlated with the presence or absence of edema-like signal on MR images. Clinical notes were reviewed for the presence of symptoms or signs referable to the inferior patellar pole. These data were compared with a 1:1 age- and sex-matched control group without inferior pole fragmentation. Statistical analysis was performed using two-tailed t-tests. Forty of 164 (24.4%) knee radiographs showed fragmentary ossification of the inferior patella. Of these 40 knees, 62.5% (25/40) had edema-like signal of the inferior patellar bone marrow compared with 7.5% (3/40) of controls (P = 0.035). Patients with fragmentary ossification at the inferior patella had a significantly higher incidence of documented focal inferior patellar pain compared with controls (20% vs. 2.5%, P = 0.015). Inferior patellar pole fragmentation in children 5 to 10 years of age may be associated with localized symptoms and bone marrow edema-like signal and should not be routinely dismissed as a normal variant of ossification. (orig.)

  9. Classical estrogen receptors and ERα splice variants in the mouse.

    Directory of Open Access Journals (Sweden)

    Debra L Irsik

    Full Text Available Estrogens exert a variety of effects in both reproductive and non-reproductive tissues. With the discovery of ERα splice variants, prior assumptions concerning tissue-specific estrogen signaling need to be re-evaluated. Accordingly, we sought to determine the expression of the classical estrogen receptors and ERα splice variants across reproductive and non-reproductive tissues of male and female mice. Western blotting revealed that the full-length ERα66 was mainly present in female reproductive tissues but was also found in non-reproductive tissues at lower levels. ERα46 was most highly expressed in the heart of both sexes. ERα36 was highly expressed in the kidneys and liver of female mice but not in the kidneys of males. ERβ was most abundant in non-reproductive tissues and in the ovaries. Because the kidney has been reported to be the most estrogenic non-reproductive organ, we sought to elucidate ER renal expression and localization. Immunofluorescence studies revealed ERα66 in the vasculature and the glomerulus. It was also found in the brush border of the proximal tubule and in the cortical collecting duct of female mice. ERα36 was evident in mesangial cells and tubular epithelial cells of both sexes, as well as podocytes of females but not males. ERβ was found primarily in the podocytes in female mice but was also present in the mesangial cells in both sexes. Within the renal cortex, ERα46 and ERα36 were mainly located in the membrane fraction although they were also present in the cytosolic fraction. Given the variability of expression patterns demonstrated herein, identification of the specific estrogen receptors expressed in a tissue is necessary for interpreting estrogenic effects. As this study revealed expression of the ERα splice variants at multiple sites within the kidney, further studies are warranted in order to elucidate the contribution of these receptors to renal estrogen responsiveness.

  10. Efficiency of the bicycle operation under various tactical variants

    Directory of Open Access Journals (Sweden)

    A.N. Kolumbet

    2017-10-01

    Full Text Available Aim: to determine the efficiency of the cyclist in various tactical options. Material: In the experiments participated athletes (n = 6 of high qualification (mean age - 19.8 ± 1.3 years, mean weight - 71.4 ± 3.5 kg. As a model of the individual pursuit race at 4 km, a five-minute pedaling on the bicycle ergometer was used. Series of loads was set on the modernized mechanical bicycle ergometer “Monark” . The five-minute bicycle ergometer test is similar to the individual pursuit race at 4 km: according to the time of the exercise; on the frequency of pedaling (110-120 rpm; on the frequency of heartbeats. Results: Tactical variants in the pursuit race at 4 km are considered. The total work in a free test was on average 106.38 ± 3.57 kJ. The operating energy consumption is on average for 379.0±16.1 kJ. The operating efficiency (economy of the exercise attained on average for 28.0 ± 0.75%. This corresponds to the effectiveness of aerobic work of moderate power. The ratio of aerobic and anaerobic contributions to the provision of work was 77.3 and 22.7%. The smallest work was done in a test with step-increasing power. The athletes performed the closest work to the given job in the test with a variable (±15% operating mode. The shortfall in it was on average for 0.46%. The absence of reliable differences in the economics of the work did not allow us to identify a rational variant of power distribution for an exercise lasting 5 minutes. Conclusions: Tactical options in the pursuit race for 4 km depend on the features of the power systems of the rider. When optimizing tactics, it is necessary to select an individually optimal variant of the distribution of forces at a distance.

  11. Novel genetic risk variants for pediatric celiac disease.

    Science.gov (United States)

    Balasopoulou, Angeliki; Stanković, Biljana; Panagiotara, Angeliki; Nikčevic, Gordana; Peters, Brock A; John, Anne; Mendrinou, Effrosyni; Stratopoulos, Apostolos; Legaki, Aigli Ioanna; Stathakopoulou, Vasiliki; Tsolia, Aristoniki; Govaris, Nikolaos; Govari, Sofia; Zagoriti, Zoi; Poulas, Konstantinos; Kanariou, Maria; Constantinidou, Nikki; Krini, Maro; Spanou, Kleopatra; Radlovic, Nedeljko; Ali, Bassam R; Borg, Joseph; Drmanac, Radoje; Chrousos, George; Pavlovic, Sonja; Roma, Eleftheria; Zukic, Branka; Patrinos, George P; Katsila, Theodora

    2016-10-24

    Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G>A, KIAA1109 c.2933T>C and c.4268_4269delCCinsTA, HoxB6 c.668C>A, HoxD12 c.418G>A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n = 109) and Serbian (n = 73) descent and their healthy counterparts (n = 111 and n = 32, respectively) indicated that HoxD12 c.418G>A is more prevalent in celiac disease patients in the Serbian population (P celiac disease patients rather than healthy individuals of Greek descent (P = 0.03). SLC9A4 c.1919G>A and KIAA1109 c.2933T>C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance. The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology.

  12. Collapsed methylation quantitative trait loci analysis for low frequency and rare variants.

    Science.gov (United States)

    Richardson, Tom G; Shihab, Hashem A; Hemani, Gibran; Zheng, Jie; Hannon, Eilis; Mill, Jonathan; Carnero-Montoro, Elena; Bell, Jordana T; Lyttleton, Oliver; McArdle, Wendy L; Ring, Susan M; Rodriguez, Santiago; Campbell, Colin; Smith, George Davey; Relton, Caroline L; Timpson, Nicholas J; Gaunt, Tom R

    2016-10-01

    Single variant approaches have been successful in identifying DNA methylation quantitative trait loci (mQTL), although as with complex traits they lack the statistical power to identify the effects from rare genetic variants. We have undertaken extensive analyses to identify regions of low frequency and rare variants that are associated with DNA methylation levels. We used repeated measurements of DNA methylation from five different life stages in human blood, taken from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Variants were collapsed across CpG islands and their flanking regions to identify variants collectively associated with methylation, where no single variant was individually responsible for the observed signal. All analyses were undertaken using the sequence kernel association test. For loci where no individual variant mQTL was observed based on a single variant analysis, we identified 95 unique regions where the combined effect of low frequency variants (MAF ≤ 5%) provided strong evidence of association with methylation. For loci where there was previous evidence of an individual variant mQTL, a further 3 regions provided evidence of association between multiple low frequency variants and methylation levels. Effects were observed consistently across 5 different time points in the lifecourse and evidence of replication in the TwinsUK and Exeter cohorts was also identified. We have demonstrated the potential of this novel approach to mQTL analysis by analysing the combined effect of multiple low frequency or rare variants. Future studies should benefit from applying this approach as a complementary follow up to single variant analyses. © The Author 2016. Published by Oxford University Press.

  13. Functional analysis of four LDLR 5'UTR and promoter variants in patients with familial hypercholesterolaemia.

    Science.gov (United States)

    Khamis, Amna; Palmen, Jutta; Lench, Nick; Taylor, Alison; Badmus, Ebele; Leigh, Sarah; Humphries, Steve E

    2015-06-01

    Familial hypercholesterolaemia (FH) is an autosomal dominant inherited disease characterised by increased low-density lipoprotein cholesterol (LDL-C) levels. The functionality of four novel variants within the LDLR 5'UTR and promoter located at c.-13A>G, c.-101T>C, c.-121T>C and c.-215A>G was investigated using in silico and in vitro assays, and a systemic bioinformatics analysis of all 36 reported promoter variants are presented. Bioinformatic tools predicted that all four variants occurred in sites likely to bind transcription factors and that binding was altered by the variant allele. Luciferase assay was performed for all the variants. Compared with wild type, the c.-101T>C and c.-121T>C variants showed significantly lower mean (±SD) luciferase activity (64 ± 8 and 72 ± 8%, all PG or c.-215A>G variants (96 ± 15 and 100 ± 12%), suggesting these variants are not FH causing. Similar results were seen for the c.-101T>C and c.-121T>C variants in lipid-depleted serum. However, a significant reduction in luciferase activity was seen in the c.-215A>G variant in lipid-depleted serum. Electrophoretic-mobility shift assays identified allele-specific binding of liver (hepatoma) nuclear proteins to c.-121T>C and suggestive differential binding to c.-101T>C but no binding to c.-215A>G. These data highlight the importance of in vitro testing of reported LDLR promoter variants to establish their role in FH. The functional assays performed suggest that the c.-101T>C and c.-121T>C variants are pathogenic, whereas c.-13A>G variant is benign, and the status of c.-215A>G remains unclear.

  14. Las formas del crecimiento urbano y las variantes de carretera

    OpenAIRE

    Herce, Manuel

    1995-01-01

    El objeto de la tesis fue comprobar como la continua construcción de variantes de las carreteras que anteriormente atravesaban ciudades ha afectado a la organización de éstas, a la disposición de las actividades sobre el espacio y a la evolución del precio del suelo en la ciudad.La hipótesis de partida era que la forma de la ciudad, la disposición de las actividades urbanas sobre el territorio, deriva de la organización de sus redes de infraestructuras, entre las que las más importantes son l...

  15. Evidences of abundant hemocyanin variants in shrimp Litopenaeus vannamei.

    Science.gov (United States)

    Zhao, Xianliang; Guo, Lingling; Lu, Xin; Lu, Hui; Wang, Fan; Zhong, Mingqi; Chen, Jiehui; Zhang, Yueling

    2016-09-01

    Hemocyanin (HMC) is a multifunctional immune molecule present in mollusks and arthropods and functions as an important antigen non-specific immune protein. Our previous evidences demonstrated that Litopenaeus vannamei HMC might display extensive molecular diversities. In this study, bioinformatics analysis showed dozens of variant sequences of the HMC subunit with higher molecular weight from L. vannamei (LvHMC). Three variant fragments, named as LvHMCV1-3, which shared 85-99% nucleotide identity with that of the classical form of LvHMC (AJ250830.1), were cloned and characterized. Spatial expression profiles showed that LvHMCV1-3 had different tissue-specific distribution, which were affected by stimulation with six pathogenic bacteria, including Escherichia coli K12, Vibrio parahaemolyticus, Vibrio alginolyticus, Vibrio fluvialis, Streptococcus pyogenes and Staphylococcus aureus, with each variant fragment showing a specific stress pattern to different bacterial pathogens. Full length cDNA of LvHMCV3 was further cloned and characterized. The deduced amino acid sequence shared 92% identity with that of LvHMC, possessed a conserved structure characteristic of the HMC family and could be clustered into one branch along with other arthropod HMC in a phylogenetic tree. In addition, the recombinant protein of LvHMCV3 (rLvHMCV3) showed obvious agglutination activities against three aquaculture pathogenic bacteria including E. coli K12, V. parahaemolyticus and S.aureus at concentrations ranging from 31.25-62.5g/mL. It also showed obvious antibacterial activity against V. parahaemolyticus at concentrations 0.02-0.5mg/mL, and possessed the best inhibitive effects compared with those of rLvHMCV4 and rLvHMC. Co-injection of V. parahaemolyticus and rLvHMCV3 in L. vannamei showed significant decrease of the mortality rate at 24-72h after injection. Therefore, these studies suggested that L. vannamei had abundant HMC variants, which possessed obvious resistance to pathogenic

  16. Distinct roles of PTCH2 splice variants in Hedgehog signalling.

    Science.gov (United States)

    Rahnama, Fahimeh; Toftgård, Rune; Zaphiropoulos, Peter G

    2004-03-01

    The human PTCH2 gene is highly similar to PTCH1, a tumour suppressor gene frequently mutated in basal cell carcinoma and several other tumour types. PTCH1 is a transmembrane protein believed to inhibit another transmembrane protein SMO (Smoothened), which mediates HH (Hedgehog) signalling. In this study, we analysed the biological properties of several PTCH2 splice variants. An mRNA form that lacked the last exon was abundantly expressed in all tissues examined, in contrast with the one that included it. Moreover, a transcript lacking exon 9, which is a part of a conserved sterol-sensing domain, was identified in intestine, prostate and cerebellum. In ovary, spleen, testis, cerebellum and skin, an mRNA lacking both exons 9 and 10 could also be observed. The different PTCH2 isoforms localized in the cytoplasm were capable of internalizing the N-terminal fragment of Sonic HH (Shh-N). Additionally, the PTCH2 gene was found to be a target of HH signalling. PTCH2 promoter regulation assays demonstrated that only one of the PTCH2 variants could inhibit the activity of SHH-N, whereas none was capable of inhibiting the activated form of SMO (SMO-M2) and this contrasts with PTCH1. Despite the fact that the PTCH2 isoforms lacked the ability to inhibit SMO-M2 activity, all PTCH2 variants as well as PTCH1, on co-transfection with Smo, were able to change Smo localization from being largely dispersed in the cytoplasm to the juxtanuclear region. Furthermore, the PTCH2 isoforms and PTCH1 co-localized in doubly transfected cells and an interaction between them was confirmed using immunoprecipitation assays. Using Ptch1-/- mouse cells, it was shown that the PTCH2 variants and PTCH1 differentially act to reconstitute not only the SHH but also the Desert HH-dependent transcriptional response. We conclude that in spite of their structural similarities, the PTCH2 isoforms have distinct functional properties when compared with PTCH1.

  17. Copy-number variants in neurodevelopmental disorders: promises and challenges.

    LENUS (Irish Health Repository)

    Merikangas, Alison K

    2012-02-01

    Copy-number variation (CNV) is the most prevalent type of structural variation in the human genome. There is emerging evidence that copy-number variants (CNVs) provide a new vista on understanding susceptibility to neuropsychiatric disorders. Some challenges in the interpretation of current CNV studies include the use of overlapping samples, differing phenotypic definitions, an absence of population norms for CNVs and a lack of consensus in methods for CNV detection and analysis. Here, we review current CNV association study methods and results in autism spectrum disorders (ASD) and schizophrenia, and provide suggestions for design approaches to future studies that might maximize the translation of this work to etiological understanding.

  18. Constitutively active UVR8 photoreceptor variant in Arabidopsis

    OpenAIRE

    2013-01-01

    Sunlight is an essential environmental factor for photosynthetic plants and ultimately for life on Earth, which is sustained through plants as fundamental source of food. However, plants have a love/hate relationship with sunlight and must be protected from potentially harmful UV-B radiation. The UV-B photoreceptor UVR8 is of great importance in mounting UV-protective responses and thus for survival in sunlight. Based on our understanding of UVR8 signaling, we have engineered a UVR8 variant t...

  19. Deep penetrating nevus: A distinct variant of melanocytic nevus

    Directory of Open Access Journals (Sweden)

    Aparna Gupta

    2011-01-01

    Full Text Available Deep penetrating nevus (DPN is a variant of melanocytic nevus which goes unrecognized due to its relative rarity and may be misinterpreted as malignant melanoma. It commonly presents in young adults as a dark pigmented lesion on the face, neck, or shoulder. A 60-year-old lady presented with a mole over the left arm of 8 years duration. A biopsy of the lesion was performed under the clinical impression of a compound nevus with suspicion of malignancy. Based on the histologic features, a diagnosis of DPN was put forward.

  20. Progressive Concept Evaluation Method for Automatically Generated Concept Variants

    Directory of Open Access Journals (Sweden)

    Woldemichael Dereje Engida

    2014-07-01

    Full Text Available Conceptual design is one of the most critical and important phases of design process with least computer support system. Conceptual design support tool (CDST is a conceptual design support system developed to automatically generate concepts for each subfunction in functional structure. The automated concept generation process results in large number of concept variants which require a thorough evaluation process to select the best design. To address this, a progressive concept evaluation technique consisting of absolute comparison, concept screening and weighted decision matrix using analytical hierarchy process (AHP is proposed to eliminate infeasible concepts at each stage. The software implementation of the proposed method is demonstrated.

  1. Unrecorded origin of external pudendal artery with variant obturator vessels

    Directory of Open Access Journals (Sweden)

    El-Sawaf ME

    2010-08-01

    Full Text Available During routine dissection of a female cadaver for teaching purposes, the vessels in the ilioinguinal region in both sides showed some anatomical variations. In the right side, the external iliac artery gave off the obturator artery and a common trunk for both external pudendal artery and inferior epigastric artery. The obturator vein followed the variant obturator artery while the external pudendal vein showed a normal course. Meanwhile, the obturator artery in the left side originated from the inferior epigastric artery and the obturator vein drained into the external iliac vein. These anatomical findings may have important clinical implications.

  2. Susceptibility genetic variants associated with early-onset colorectal cancer.

    Science.gov (United States)

    Giráldez, María Dolores; López-Dóriga, Adriana; Bujanda, Luis; Abulí, Anna; Bessa, Xavier; Fernández-Rozadilla, Ceres; Muñoz, Jenifer; Cuatrecasas, Miriam; Jover, Rodrigo; Xicola, Rosa M; Llor, Xavier; Piqué, Josep M; Carracedo, Angel; Ruiz-Ponte, Clara; Cosme, Angel; Enríquez-Navascués, José María; Moreno, Victor; Andreu, Montserrat; Castells, Antoni; Balaguer, Francesc; Castellví-Bel, Sergi

    2012-03-01

    Colorectal cancer (CRC) is the second most common cancer in Western countries. Hereditary forms only correspond to 5% of CRC burden. Recently, genome-wide association studies have identified common low-penetrant CRC genetic susceptibility loci. Early-onset CRC (CRC65 years old) (n = 1264). CRC susceptibility variants at 8q23.3 (rs16892766), 8q24.21 (rs6983267), 10p14 (rs10795668), 11q23.1 (rs3802842), 15q13.3 (rs4779584), 18q21 (rs4939827), 14q22.2 (rs4444235), 16q22.1 (rs9929218), 19q13.1 (rs10411210) and 20p12.3 (rs961253) were genotyped in all DNA samples. A genotype-phenotype correlation with clinical and pathological characteristics in both groups was performed. Risk allele carriers for rs3802842 [Odds ratio (OR) = 1.5, 95% confidence interval (CI) 1.1-2.05, P = 0.0096, dominant model) and rs4779584 (OR = 1.39, 95% CI 1.02-1.9, P = 0.0396, dominant model) were more frequent in the CRC<50 group, whereas homozygotes for rs10795668 risk allele were also more frequent in the early-onset CRC (P = 0.02, codominant model). Regarding early-onset cases, 14q22 (rs4444235), 11q23 (rs3802842) and 20p12 (rs961253) variants were more associated with family history of CRC or tumors of the Lynch syndrome spectrum excluding CRC. In our entire cohort, sum of risk alleles was significantly higher in patients with a CRC family history (OR = 1.40, 95% CI 1.06-1.85, P = 0.01). In conclusion, variants at 10p14 (rs10795668), 11q23.1 (rs3802842) and 15q13.3 (rs4779584) may have a predominant role in predisposition to early-onset CRC. Association of CRC susceptibility variants with some patient's familiar and personal features could be relevant for screening and surveillance strategies in this high-risk group and it should be explored in further studies.

  3. Una variante del carácter cultural

    OpenAIRE

    Efraín Aguilar Jiménez

    2005-01-01

    Este artículo trata de la construcción de una variante del carácter cultural con base en la teoría de las necesidades psicológicas de Erich Fromm y en el carácter social por él desarrollado. Se describen algunas diferencias entre carácter y personalidad y, luego de revisar brevemente la teoría frommiana sobre el tema, se mencionan los fundamentos teóricos y conceptuales necesarios para la elaboración del carácter cultural. Este será una herramienta para estudiar las necesida...

  4. Genetic variants associated with neurodegenerative Alzheimer disease in natural models.

    Science.gov (United States)

    Salazar, Claudia; Valdivia, Gonzalo; Ardiles, Álvaro O; Ewer, John; Palacios, Adrián G

    2016-02-26

    The use of transgenic models for the study of neurodegenerative diseases has made valuable contributions to the field. However, some important limitations, including protein overexpression and general systemic compensation for the missing genes, has caused researchers to seek natural models that show the main biomarkers of neurodegenerative diseases during aging. Here we review some of these models-most of them rodents, focusing especially on the genetic variations in biomarkers for Alzheimer diseases, in order to explain their relationships with variants associated with the occurrence of the disease in humans.

  5. Functional relevance for associations between osteoporosis and genetic variants

    Science.gov (United States)

    Tan, Li-Jun; Wang, Peng; Chen, Xiang-Ding; Zhu, Li-Hua; Zeng, Qin; Hu, Yuan; Deng, Hong-Wen

    2017-01-01

    Osteoporosis is characterized by increased bone loss and deterioration of bone microarchitecture, which will lead to reduced bone strength and increased risk of fragility fractures. Previous studies have identified many genetic loci associated with osteoporosis, but functional mechanisms underlying the associations have rarely been explored. In order to explore the potential molecular functional mechanisms underlying the associations for osteoporosis, we performed integrative analyses by using the publically available datasets and resources. We searched 128 identified osteoporosis associated SNPs (Posteoporosis. This study may provide novel insights into the functional mechanisms underlying the osteoporosis associated genetic variants, which will help us to comprehend the potential mechanisms underlying the genetic association for osteoporosis. PMID:28369098

  6. Interpolated spatially variant apodization in synthetic aperture radar imagery.

    Science.gov (United States)

    Yocky, D A; Jakowatz, C V; Eichel, P H

    2000-05-10

    The original formulation of spatially variant apodization for complex synthetic aperture radar imagery concentrated on integer-oversampled data. Noninteger-oversampled data presented previously [IEEE Trans. Aerosp. Electron. Syst. 31, 267 (1995)] suggested use of different weightings in the algorithm. An alternative noninteger-oversampled approach that employs the same apodization concept but uses local spatial interpolation is presented. With this approach the combined image formation, apodization, and detection of 1.3x-versus-2.0x oversampled data can be performed in half the time without loss of image quality.

  7. No association of common VCP variants with sporadic frontotemporal dementia.

    Science.gov (United States)

    Schumacher, Axel; Friedrich, Patricia; Diehl, Janine; Ibach, Bernd; Schoepfer-Wendels, Andreas; Mueller, Jakob C; Konta, Lidija; Laws, Simon M; Kurz, Alexander; Foerstl, Hans; Riemenschneider, Matthias

    2009-02-01

    Mutations in the gene for valosin containing protein (VCP) cause autosomal dominant inclusion body myopathy associated with Paget disease and frontotemporal dementia (IBMPFD). To investigate the role of this novel gene in sporadic forms of frontotemporal dementia (FTD), we genotyped 27 single nucleotide polymorphisms covering the entire VCP genomic region in 198 patients with sporadic FTD and 184 matched controls from Germany. No significant association could be demonstrated. There is no evidence, that common variants in VCP confer a strong risk to the development of sporadic FTD.

  8. BILATERAL PECTORALIS MINOR MUSCLE VARIANT: A CASE REPORT

    Directory of Open Access Journals (Sweden)

    David R Terfera

    2015-03-01

    Full Text Available During a routine anatomical dissection we discovered an aberrant muscle slip associated with the pectoralis minor muscle that occurred bilaterally. The muscle slips originated from ribs five or six and inserted into the tendon of the coracobrachialis in close proximity the coracoid process of the scapula. Fibers of the muscle slip also blended with the pectoralis minor muscle on its lateral border. The muscle slips were innervated by the medial pectoral nerve. Reports and documentation of anatomical variants such as this provide an important resource for both researchers and clinicians.

  9. A high-rising epiglottis: a benign anatomical variant.

    Science.gov (United States)

    Alamri, Yassar; Stringer, Mark D

    2011-07-01

    We report an asymptomatic 10-year-old boy who was found to have a high-rising epiglottis visible in his pharynx. This benign anatomical variant is not widely recognized yet may cause anxiety to patients and their families. The prevalence of this finding is controversial, and it is uncertain whether it reflects an abnormal position, size, and/or shape of the epiglottis. It is probably more common in children, which is to be expected considering the normal descent of the larynx with postnatal growth. To date, the condition has not been associated with any significant clinical sequelae.

  10. A variant of special relativity and long-distance astronomy.

    Science.gov (United States)

    Segal, I E

    1974-03-01

    THE REDSHIFT, MICROWAVE BACKGROUND, AND OTHER OBSERVABLE ASTRONOMICAL FEATURES ARE DEDUCED FROM TWO THEORETICAL ASSUMPTIONS: (1) global space-time is a certain variant of Minkowski space, locally indistinguishable in causality and covariance features but globally admitting the full conformal group as symmetries although having a spherical space component; (2) the true energy operator corresponds to a certain generator of this group which is not globally scale-covariant, whereas laboratory frequency measurements are inevitably such and correspond to the conventional energy operator [unk]/i[unk]/[unk]t.

  11. Motor variant of chronic inflammatory demyelinating polyneuropathy in a child.

    Science.gov (United States)

    Sinno, Durriyah D; Darras, Basil T; Yamout, Bassem I; Rebeiz, Jean G; Mikati, Mohamad A

    2008-06-01

    Only 2 cases of pure motor chronic demyelinating inflammatory polyneuropathy in the pediatric age group have been reported in the literature. We report on a motor variant of chronic demyelinating inflammatory polyneuropathy with anti-ganglioside antibodies, diagnosed in a 5-year-old girl who presented with progressive motor weakness over a period of 12 months with no sensory involvement. She initially responded partially to intravenous immunoglobulin therapy (1 gm/kg/month for 6 months), and then demonstrated sustained but incomplete improvement on chronic prednisone therapy (1-2 mg/kg/day), on which she has continued since 1 year and 4 months after her initial presentation 3 years ago.

  12. Emotional evaluation and memory in behavioral variant frontotemporal dementia.

    Science.gov (United States)

    St Jacques, Peggy L; Grady, Cheryl; Davidson, Patrick S R; Chow, Tiffany W

    2015-01-01

    Behavioral variant frontotemporal dementia (bvFTD) affects emotional evaluation, but less is known regarding the patients' ability to remember emotional stimuli. Here, bvFTD patients and age-matched controls studied positive, negative, and neutral pictures followed by a recognition memory test. Compared to controls, bvFTD patients showed a reduction in emotional evaluation of negative scenes, but not of positive or neutral scenes. Additionally, the patients showed an overall reduction in recognition memory accuracy, due to impaired recollection in the face of relatively preserved familiarity. These results show that bvFTD reduces the emotional evaluation of negative scenes and impairs overall recognition memory accuracy and recollection.

  13. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants.

    Science.gov (United States)

    Yoshida, Masa-aki; Yura, Kei; Ogura, Atsushi

    2014-03-05

    Previous studies have reported that the developmental processes of vertebrate eyes are controlled by four Pax-6 splicing variants, each modulating different downstream genes, whereas those of insect eyes are controlled by duplicated Pax-6 genes. Cephalopods belong to the Protostomes but possess a camera-type eye similar to those in vertebrates. We examined Pax-6 variations in the squid and found five types of Pax-6 splicing variants but no duplication of the Pax-6 gene. In the five splicing variants, the splicing patterns were produced by the combination of two additional exons to the ortholog and one jettisoned exon containing most of the Homeobox domain (HD). These five variants show spatio-temporal patterns of gene expression during development in the squid. Our study suggests that cephalopods acquired Pax-6 splicing variants independent of those in vertebrates and that these variants were similarly utilized in the development of the squid eye.

  14. A novel variant of androgen receptor is associated with idiopathic azoospermia.

    Science.gov (United States)

    Mou, Lisha; Gui, Yaoting

    2016-10-01

    A variety of genetic variants can lead to abnormal human spermatogenesis. The androgen receptor (AR) is an important steroid hormone receptor that is critical for male sexual differentiation and the maintenance of normal spermatogenesis. In the present study, each exon of AR in 776 patients diagnosed with idiopathic azoospermia (IA) and 709 proven fertile men were sequenced using use panel re‑sequencing methods to examine whether AR is involved in the pathogenesis of IA. Two synonymous variants and seven missense variants were detected. Of the missense variants, a luciferase assay demonstrated that the R630W variant reduced the transcriptional regulatory function of AR. This novel variant (p. R630W) of AR is the first to be identified in association with IA, thereby highlighting the importance of AR during spermatogenesis.

  15. PERFORMANCE ANALYSIS OF ROUTING PROTOCOLS AND TCP VARIANTS UNDER HTTP AND FTP TRAFFIC IN MANETS

    Directory of Open Access Journals (Sweden)

    Ghassan A. QasMarrogy

    2014-12-01

    Full Text Available MANET stands for mobile ad-hoc network that has multi-hop and dynamic nature, where each station changes its location frequently and automatically configures itself. In this paper, four routing protocols that are OLSR, GRP, DSR, and AODV are discussed along with three TCP variants that are SACK, New Reno and Reno. The main focus of this paper is to study the impact scalability, mobility and traffic loads on routing protocols and TCP variants. The paper results shows that the proactive protocols OLSR and GRP outperform the reactive protocols AODV and DSR with the same nodes size, nodes speed, and traffic load. On the other hand, the TCP variants research reveal the superiority of the TCP SACK variant over the other two variants in case of adapting to varying network size, while the TCP Reno variant acts more robustly in varying mobility speeds and traffic loads

  16. Fat-forming variant of solitary fibrous tumor of the mediastinum

    Institute of Scientific and Technical Information of China (English)

    LIU Xi; ZHANG Hong-ying; BU Hong; MENG Guo-zhao; ZHANG Zhang; KE Qi

    2007-01-01

    @@ Fat-forming variant of solitary fibrous tumor (fat-forming variant of SFT), previously called lipomatous hemangiopericytoma (L-HPC), is a recently recognized rare variant of solitary fibrous tumor (SFT)with unpredictable biologic behavior. Fat-forming variant of SFT occurs predominately in the deep soft tissues of the lower extremities. Histologically, it is composed of an admixture of benign hemangiopericytomatous and lipomatous components. Up to now, only 37 cases have been reported in the English literature worldwide1-7 and the molecular analyses are sparse. Reported herein is the first Chinese case of fat-forming variant of SFT. Although one case of fat-forming variant of SFT in the mediastinum was briefly reported, this is the first case in the region with detailed histologic, immunohistochemical features and flow cytometric DNA analysis.

  17. Neuronal fast activating and meningeal silent modulatory BK channel splice variants cloned from rat

    DEFF Research Database (Denmark)

    Poulsen, Asser Nyander; Jansen-Olesen, Inger; Olesen, Jes

    2011-01-01

    The big conductance calcium-activated K(+) channel (BK) is involved in regulating neuron and smooth muscle cell excitability. Functional diversity of BK is generated by alpha-subunit splice variation and co-expression with beta subunits. Here, we present six different splice combinations cloned...... from rat brain or cerebral vascular/meningeal tissues, of which at least three variants were previously uncharacterized (X1, X2(92), and X2(188)). An additional variant was identified by polymerase chain reaction but not cloned. Expression in Xenopus oocytes showed that the brain-specific X1 variant...... displays reduced current, faster activation, and less voltage sensitivity than the insert-less Zero variant. Other cloned variants Strex and Slo27,3 showed slower activation than Zero. The X1 variant contains sequence inserts in the S1-S2 extracellular loop (8 aa), between intracellular domains RCK1...

  18. Dominant transmission of de novo KIF1A motor domain variant underlying pure spastic paraplegia.

    Science.gov (United States)

    Ylikallio, Emil; Kim, Doyoun; Isohanni, Pirjo; Auranen, Mari; Kim, Eunjoon; Lönnqvist, Tuula; Tyynismaa, Henna

    2015-10-01

    Variants in family 1 kinesin (KIF1A), which encodes a kinesin axonal motor protein, have been described to cause variable neurological manifestations. Recessive missense variants have led to spastic paraplegia, and recessive truncations to sensory and autonomic neuropathy. De novo missense variants cause developmental delay or intellectual disability, cerebellar atrophy and variable spasticity. We describe a family with father-to-son transmission of de novo variant in the KIF1A motor domain, in a phenotype of pure spastic paraplegia. Structural modeling of the predicted p.(Ser69Leu) amino acid change suggested that it impairs the stable binding of ATP to the KIF1A protein. Our study reports the first dominantly inherited KIF1A variant and expands the spectrum of phenotypes caused by heterozygous KIF1A motor domain variants to include pure spastic paraplegia. We conclude that KIF1A should be considered a candidate gene for hereditary paraplegias regardless of inheritance pattern.

  19. Construction and Characterization of Novel Staphylokinase Variants with Antiplatelet Aggregation Activity and Reduced Immunogenecity

    Institute of Scientific and Technical Information of China (English)

    Hua-Bo SU; Yu-Gao ZHANG; Jin-Tian HE; Wei MO; Yan-Ling ZHANG; Xian-Mei TAO; Hou-Yan SONG

    2004-01-01

    To develop target thrombolytic agents with fibrinolytic activity, antiplatelet aggregation activity and reduced immunogenicity, two staphylokinase variants containing Arg-Gly-Asp (RGD) motif were constructed. Gene expression was induced in E. coli JF1125 and the variants, designated DGR and RL1, were purified with gel filtration and ion-exchange chromatography and the purity was over 95%. The fibrinolytic activity and kinetic constants of the two variants were comparable to those of recombinant wild-type staphylokinase. Both the variants can inhibit the platelet aggregation at a final concentration of 2 μM. Thetiters of antibodies against variants were much lower than those against recombinant staphylokinase in guineapigs, which indicated that the immunogenicity of the variants was greatly reduced. These results confirm thatit is possible to design and produce a bifunctional protein that possesses fibrinolytic and antiplatelet aggregation activities.

  20. Asian-variant intravascular lymphoma in the African race

    Directory of Open Access Journals (Sweden)

    Holly Geyer

    2012-03-01

    Full Text Available Intravascular large B-cell lymphoma (IVLBCL is an exceptionally rare form of non- Hodgkin lymphoma (NHL distinguished by the preferential growth of neoplastic cells within blood vessel lumen. Challenging to detect and deemed disseminated at diagnosis, this condition is characterized by a highly aggressive, inconspicuous course with a high mortality rate. We describe the case of a 48 year-old African-American female presenting with a two month history of low-grade fevers and malaise. Laboratory data was notable for anemia, thrombocytopenia, elevated liver function tests, and hematuria. An extensive workup for infectious, rheumatologic and malignant causes was negative. Her symptoms progressed and within two weeks, she was admitted for disseminated intravascular coagulation (DIC. Her course was complicated by diffuse pulmonary hemorrhage and ultimately, care was withdrawn. Autopsy identified widespread CD-20 positive intravascular large B-cell lymphoma with significant hepatosplenic involvement, characteristic of the Asian variant IVLBCL. This case uniquely highlights development of the Asian variant IVLBVL in a previously undescribed race. Identified by its intraluminal vascular growth pattern, IVLBCL generally spares lymphatic channels. Diagnosis and differentiation of this condition from other hematological malignancies via skin, visceral and bone marrow biopsy is imperative as anthracycline-containing chemotherapies may significantly improve clinical outcomes. This article outlines the common presentation, natural course, and treatment options of IVLBCL, along with the histopathology, immunohistochemistry, and chromosomal aberrations common to this condition.

  1. Confirmed rare copy number variants implicate novel genes in schizophrenia.

    Science.gov (United States)

    Tam, Gloria W C; van de Lagemaat, Louie N; Redon, Richard; Strathdee, Karen E; Croning, Mike D R; Malloy, Mary P; Muir, Walter J; Pickard, Ben S; Deary, Ian J; Blackwood, Douglas H R; Carter, Nigel P; Grant, Seth G N

    2010-04-01

    Understanding how cognitive processes including learning, memory, decision making and ideation are encoded by the genome is a key question in biology. Identification of sets of genes underlying human mental disorders is a path towards this objective. Schizophrenia is a common disease with cognitive symptoms, high heritability and complex genetics. We have identified genes involved with schizophrenia by measuring differences in DNA copy number across the entire genome in 91 schizophrenia cases and 92 controls in the Scottish population. Our data reproduce rare and common variants observed in public domain data from >3000 schizophrenia cases, confirming known disease loci as well as identifying novel loci. We found copy number variants in PDE10A (phosphodiesterase 10A), CYFIP1 [cytoplasmic FMR1 (Fragile X mental retardation 1)-interacting protein 1], K(+) channel genes KCNE1 and KCNE2, the Down's syndrome critical region 1 gene RCAN1 (regulator of calcineurin 1), cell-recognition protein CHL1 (cell adhesion molecule with homology with L1CAM), the transcription factor SP4 (specificity protein 4) and histone deacetylase HDAC9, among others (see http://www.genes2cognition.org/SCZ-CNV). Integrating the function of these many genes into a coherent model of schizophrenia and cognition is a major unanswered challenge.

  2. Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

    Energy Technology Data Exchange (ETDEWEB)

    Milacic, Marija; Haw, Robin, E-mail: robin.haw@oicr.on.ca; Rothfels, Karen; Wu, Guanming [Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON, M5G0A3 (Canada); Croft, David; Hermjakob, Henning [European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD (United Kingdom); D’Eustachio, Peter [Department of Biochemistry, NYU School of Medicine, New York, NY 10016 (United States); Stein, Lincoln [Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON, M5G0A3 (Canada)

    2012-11-08

    Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics.

  3. A comparative analysis of VIKOR method and its variants

    Directory of Open Access Journals (Sweden)

    Prasenjit Chatterjee

    2016-09-01

    Full Text Available The VIKOR (Vlse Kriterijumska Optimizacija Kompromisno Resenje which means multi-criteria optimization and compromise solution, in Serbian method has already become a quite popular multi-criteria decision making tool for its computational simplicity and solution accuracy. This method focuses on selecting and ranking from a set of feasible alternatives, and determines compromise solution for a problem with conflicting criteria to help the decision maker in reaching a final course of action. It determines the compromise ranking list based on the particular measure of closeness to the ideal solution. Depending upon the type of decision problem and necessity of the decision maker, apart from VIKOR method, different variants of it, like comprehensive VIKOR, fuzzy VIKOR, regret theory-based VIKOR, modified VIKOR and interval VIKOR methods have also been subsequently developed. In this paper, the ranking performance of original VIKOR method and its five variants is analyzed based on two demonstrative examples. It is observed that interval VIKOR method performs unsatisfactorily and when the information in a decision problem is imprecise, fuzzy VIKOR method should always be preferred. But, for any decision problem, original VIKOR is the best method for solution without unnecessarily complicating the related mathematical computations.

  4. Predicting enhancer activity and variant impact using gkm-SVM.

    Science.gov (United States)

    Beer, Michael A

    2017-01-25

    We participated in the Critical Assessment of Genome Interpretation eQTL challenge to further test computational models of regulatory variant impact and their association with human disease. Our prediction model is based on a discriminative gapped-kmer SVM (gkm-SVM) trained on genome-wide chromatin accessibility data in the cell type of interest. The comparisons with massively parallel reporter assays (MPRA) in lymphoblasts show that gkm-SVM is among the most accurate prediction models even though all other models used the MPRA data for model training, and gkm-SVM did not. In addition, we compare gkm-SVM with other MPRA datasets and show that gkm-SVM is a reliable predictor of expression and that deltaSVM is a reliable predictor of variant impact in K562 cells and mouse retina. We further show that DHS (DNase-I hypersensitive sites) and ATAC-seq (assay for transposase-accessible chromatin using sequencing) data are equally predictive substrates for training gkm-SVM, and that DHS regions flanked by H3K27Ac and H3K4me1 marks are more predictive than DHS regions alone.

  5. Schizophrenia genetic variants are not associated with intelligence

    DEFF Research Database (Denmark)

    Van Scheltinga, A.F.T.; Bakker, S.C.; Van Haren, N.E.M.

    2013-01-01

    BACKGROUND: Schizophrenia is associated with lower pre-morbid intelligence (IQ) in addition to (pre-morbid) cognitive decline. Both schizophrenia and IQ are highly heritable traits. Therefore, we hypothesized that genetic variants associated with schizophrenia, including copy number variants (CNVs......) and a polygenic schizophrenia (risk) score (PSS), may influence intelligence. Method IQ was estimated with the Wechsler Adult Intelligence Scale (WAIS). CNVs were determined from single nucleotide polymorphism (SNP) data using the QuantiSNP and PennCNV algorithms. For the PSS, odds ratios for genome-wide SNP data...... significantly more genes were disrupted by deletions in schizophrenia patients compared to controls (p = 0.009), there was no effect of CNV measures on IQ. The PSS was associated with disease status (R 2 = 0.055, p = 2.1 × 10-7) and with IQ in the entire sample (R 2 = 0.018, p = 0.0008) but the effect on IQ...

  6. Processing morphological variants in searches of Latin text

    Directory of Open Access Journals (Sweden)

    Mark Greengrass

    1996-01-01

    Full Text Available A characteristic of natural-language text databases is that a user must be able to specify all of the variant forms of each query word if high recall is to be achieved. The most common type of word variants are those arising from morphology and thus most retrieval systems provide facilities for user-controlled right-hand (and occasionally left-hand truncation to allow the retrieval of all words with the same root. A stemming algorithm, or stemmer, is a computational procedure that reduces all words with the same root to a single form by stripping the root of its derivational and inflectional affixes. In most cases, only suffixes are stripped so that a stemmer provides an automatic equivalent of manual, right-hand truncation. Thus far, most work on stemmers has focused on present-day languages, but the increasing user of computers in the humanities has resulted in a need for comparable tools to facilitate searching in historical text databases. This paper summarises some of the initial results of a project here in Sheffield to develop such tools for databases of Latin text.

  7. DESARROLLO DE LA VARIANTE CAMBIAL EN SERJANIA MERIDIONALIS (SAPINDACEAE, PAULLINIEAE

    Directory of Open Access Journals (Sweden)

    M. Lucía Borniego

    2014-01-01

    Full Text Available La familia Sapindaceae representa uno de los grupos de plantas trepadoras más importante del Neo - trópico y presenta diversas variantes cambiales, algunas exclusivas. En esta contribución se describe el desarrollo del leño de Serjania meridionalis , la especie más austral del género, estudiado mediante técnicas anatómicas convencionales sobre la base de material proveniente de Isla Martín García (Buenos Aires, Argentina. El sistema vascular primario es eustélico. El crecimiento secundario se inicia con un cambium típico; sin embargo, con posterioridad, se desdiferencian meristemas de engrosamiento secun - dario supernumerarios. Estos meristemas producen nuevos cilindros vasculares (xilema y floema secun - darios en la periferia del cilindro vascular original. La presencia de cilindros vasculares cordados en los tallos añosos de S. meridionalis es novedad para la especie y plantea la necesidad de rever la dicotomía presencia-ausencia de variantes cambiales en muchas claves de identificación.

  8. Progressive supranuclear palsy (PSP): Richardson syndrome and other PSP variants.

    Science.gov (United States)

    Lopez, G; Bayulkem, K; Hallett, M

    2016-10-01

    Phenotypic heterogeneity of progressive supranuclear palsy (PSP) has been increasingly reported in the literature and can be the source of incorrect clinical diagnosis particularly in the early stages of the disease when the classically associated symptoms of early falls and supranuclear gaze palsy may not be apparent. In addition to Richardson syndrome (RS), several atypical clinical phenotypes have been described. Advances in genetic, neuroimaging, and biochemical/molecular technologies contribute to the identification of these clinical subtypes in the context of typical PSP pathological findings. Our goal is to review the phenomenology reported in the literature that is associated with confirmed histopathological changes consistent with a PSP diagnosis and to highlight the clinical spectrum of PSP. A systematic review of the literature in PubMed through July 2015 using MeSH terms and key words related to PSP was conducted. Articles describing PSP classifications, diagnostic criteria, and case reports were reviewed and summarized. Additional PSP phenotypes not seen in recent clinicopathological studies are included. These include primary lateral sclerosis, pallido-nigro-luysian degeneration, axonal dystrophy, and multiple system atrophy in the spectrum of atypical PSP variants beyond the traditionally classified PSP subtypes. This review is intended to help with the diagnostic challenges of atypical PSP variants. We believe that large multicenter clinicopathological studies will help expand our understanding of etiology and specific mechanisms of neurodegeneration and will aid in the appropriate interpretation of outcomes when conducting clinical and basic science research.

  9. Emerging tumor entities and variants of CNS neoplasms.

    Science.gov (United States)

    Cenacchi, Giovanna; Giangaspero, Felice

    2004-03-01

    Since the appearance in 2000 of the World Health Organization (WHO) classification for central nervous system (CNS) neoplasms, numerous descriptions of new entities or variants have appeared in the literature. In the group of neuronal and mixed glioneuronal neoplasms are lesions with distinctive morphological features that are still not included in a precise classification, including extraventricular neurocytoma, papillary glioneuronal tumor, rosette-forming glioneuronal of the fourth ventricle, glioneuronal with neuropil-like rosette, and DNT-like tumor of the septum pellucidum. The glioneuronal tumor with neuropil-like rosette and oligodendroglioma with neurocytic differentiation represent morphological variants of genetically proven diffuse gliomas. The lipoastrocytoma and the pilomixoid astrocytoma enlarge the group of astrocytic lesions. Rare, low-grade gliomas of the spinal cord with extensive leptomeningeal dissemination associated with unusual neuroimaging are described. The chordoid glioma of the third ventricle and the papillary tumor of the pineal region seem to be correlated by a common histogenesis from the specialized ependyma of the subcommissural organ. An embryonal tumor with neuropil and true rosettes combining features of neuroblastoma and ependymoblastoma is discussed. These new, recently described lesions indicate that the complex morphologic spectrum of CNS tumors is far from being completely delineated.

  10. Screening for Structural Hemoglobin Variants in Bahia, Brazil

    Directory of Open Access Journals (Sweden)

    Wellington Santos Silva

    2016-02-01

    Full Text Available Brazil was the country that received the largest number of Africans during the time of colonization, and Bahia was the Brazilian state that received the largest number of slaves from Africa. The purpose of this study was to evaluate the coverage of the newborn screening program for sickle cell disease in the Recôncavo Baiano region of the state of Bahia, and to show the frequency of the subjects with hemoglobin variants in the 2006–2009 period. Blood samples from neonates in twelve cities in the Recôncavo Baiano region were analyzed by High Performance Liquid Chromatography. A total of 16,402 children were born in this period, 14,773 of which underwent newborn screening. In this period 1416 children were born carrying hemoglobin variants HbS and HbC. Forty-seven patients—20 HbSS genotype and 27 HbSC genotype—were diagnosed in eleven of the twelve cities surveyed. The proportion of children born with sickle cell disease in the Recôncavo Baiano region was 1/314, which was higher than the 1/650 rate for the state of Bahia. The data presented in this study confirm the high frequency of sickle cell disease in Recôncavo Baiano, demonstrating the need to create a referral center for the care of patients with sickle cell diseases in the region.

  11. Super Spy variants implicate flexibility in chaperone action.

    Science.gov (United States)

    Quan, Shu; Wang, Lili; Petrotchenko, Evgeniy V; Makepeace, Karl At; Horowitz, Scott; Yang, Jianyi; Zhang, Yang; Borchers, Christoph H; Bardwell, James Ca

    2014-01-01

    Experimental study of the role of disorder in protein function is challenging. It has been proposed that proteins utilize disordered regions in the adaptive recognition of their various binding partners. However apart from a few exceptions, defining the importance of disorder in promiscuous binding interactions has proven to be difficult. In this paper, we have utilized a genetic selection that links protein stability to antibiotic resistance to isolate variants of the newly discovered chaperone Spy that show an up to 7 fold improved chaperone activity against a variety of substrates. These "Super Spy" variants show tighter binding to client proteins and are generally more unstable than is wild type Spy and show increases in apparent flexibility. We establish a good relationship between the degree of their instability and the improvement they show in their chaperone activity. Our results provide evidence for the importance of disorder and flexibility in chaperone function. DOI: http://dx.doi.org/10.7554/eLife.01584.001.

  12. Phylogenetic interrelations between serological variants of Bacillus thuringiensis

    Directory of Open Access Journals (Sweden)

    Patyka N. V.

    2009-06-01

    Full Text Available Aim. B. thuringiensis (Bt are gram-positive spore-forming aerobic or facultative anaerobic bacteria able to form during sporulation species specific crystal-like inclusions of protein nature, consisting of particular thermolabile d-endotoxins. Serological Bt variants produce different entomotoxins; their synthesis in many respects depends on the conditions of cultivation. There was accumulated a vast information on the entomotoxins, their origin, synthesis, structure, toxic properties and mechanisms of action on insects. These bacteria are dominating in the microbiomethods of pest control in plants and animals. There are more than 70 serovariants of Bt selectively specific to the definite groups of host insects. However, the description of new variants not always looks justified considering the phylogenetic systematization based on phenotype signs. Methods. A comparative phylogenetic analysis of the Bt intraspecific interrelations was performed on the basis of the cloned 16S rRNA genes of entomopathogenic bacteria BtH1, BtH10, BtH14. Results. The phylogenetically homogeneous lines were investigated – a homology of 16S rRNA of the strains 1 and 10 ranged from 90,0 to 94,0 %; no distinct genetic isolation among the strains of 14th and 10th serovars was revealed. Conclusions. The comparison of nucleotides sequences of 16S rRNA has shown the existence of strains polymorphism within the group of entomopathogens BtH1, BtH10, BtH14, connected with their entomocide activity

  13. [Numerical variants and congenital fusions of carpal bones].

    Science.gov (United States)

    Senecail, B; Perruez, H; Colin, D

    2007-03-01

    The number of carpal bones may be increased or decreased by the fact of anatomical variants or true congenital anomalies. Numerical increment arises from additional or from split bones. Over twenty accessory carpal bones have been described but the commonest are the os centrale carpi, the os radiale externum, the triangular bone and the styloideum bone. Additional carpal bones usually result from a failure of fusion of their ossification centers. A congenital origin is not clearly established for all these ossicles. The scaphoid and lunate may split into two or three bones and several cases of bipartite hamulus of the hamatum have been reported. A carpus with only seven bones results from the congenital absence of a normal bone, which mainly affects the scaphoid, lunate and triquetrum, or from a synostosis between two carpal bones, usually the lunate and triquetrum. Congenital fusions originate from an absence of joint cavitation into the embryo and chondrification of the joint interzone. Numerical carpal variants are uncommon as independent entities but occur with a relative high frequency in association with complex malformations of the hand. These anomalies are detectable on plain radiographs of the wrist, but CT-scan and MR-Imaging are useful to differentiate bipartite and accessory bones from carpal fractures or posttraumatic injuries, carpal fusions having to be distinguished from bony ankylosis.

  14. A nontumorigenic variant of FGF19 treats cholestatic liver diseases.

    Science.gov (United States)

    Luo, Jian; Ko, Brian; Elliott, Michael; Zhou, Mei; Lindhout, Darrin A; Phung, Van; To, Carmen; Learned, R Marc; Tian, Hui; DePaoli, Alex M; Ling, Lei

    2014-07-30

    Hepatic accumulation of bile acids is central to the pathogenesis of cholestatic liver diseases. Endocrine hormone fibroblast growth factor 19 (FGF19) may reduce hepatic bile acid levels through modulation of bile acid synthesis and prevent subsequent liver damage. However, FGF19 has also been implicated in hepatocellular carcinogenesis, and consequently, the potential risk from prolonged exposure to supraphysiological levels of the hormone represents a major hurdle for developing an FGF19-based therapy. We describe a nontumorigenic FGF19 variant, M70, which regulates bile acid metabolism and, through inhibition of bile acid synthesis and reduction of excess hepatic bile acid accumulation, protects mice from liver injury induced by either extrahepatic or intrahepatic cholestasis. Administration of M70 in healthy human volunteers potently reduces serum levels of 7α-hydroxy-4-cholesten-3-one, a surrogate marker for the hepatic activity of cholesterol 7α-hydroxylase (CYP7A1), the enzyme responsible for catalyzing the first and rate-limiting step in the classical bile acid synthetic pathway. This study provides direct evidence for the regulation of bile acid metabolism by FGF19 pathway in humans. On the basis of these results, the development of nontumorigenic FGF19 variants capable of modulating CYP7A1 expression represents an effective approach for the prevention and treatment of cholestatic liver diseases as well as potentially for other disorders associated with bile acid dysregulation.

  15. Design of non-aggregating variants of Aβ peptide

    Energy Technology Data Exchange (ETDEWEB)

    Caine, Joanne M., E-mail: jo.caine@csiro.au [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Churches, Quentin; Waddington, Lynne [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Nigro, Julie; Breheney, Kerry [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Masters, Colin L. [CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria 3052 (Australia); Nuttall, Stewart D. [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia); Streltsov, Victor A., E-mail: victor.streltsov@csiro.au [CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Preventative Health Flagship, 343 Royal Parade, Parkville, Victoria 3052 (Australia); CRC for Mental Health, Level 2, 161 Barry Street, Carlton South, Victoria 3053 (Australia)

    2014-10-24

    Highlights: • Non-aggregating, non-toxic variants of Aβ peptide were designed using Aβ structure. • Mutations reduce aggregation by stabilising Aβ into small non-toxic oligomers. • Identification of these residues will assist the design of future therapeutic peptides. - Abstract: Self association of the amyloid-β (Aβ{sub 42}) peptide into oligomers, high molecular weight forms, fibrils and ultimately neuritic plaques, has been correlated with progressive cognitive decline in Alzheimer’s disease. Thus, insights into the drivers of the aggregation pathway have the capacity to significantly contribute to our understanding of disease mechanism. Functional assays and a three-dimensional crystal structure of the P3 amyloidogenic region 18–41 of Aβ were used to identify residues important in self-association and to design novel non-aggregating variants of the peptide. Biophysical studies (gel filtration, SDS–PAGE, dynamic light scattering, thioflavin T assay, and electron microscopy) demonstrate that in contrast to wild type Aβ these targeted mutations lose the ability to self-associate. Loss of aggregation also correlates with reduced neuronal toxicity. Our results highlight residues and regions of the Aβ peptide important for future targeting agents aimed at the amelioration of Alzheimer’s disease.

  16. An Overview on Primary Progressive Aphasia and Its Variants

    Directory of Open Access Journals (Sweden)

    Serena Amici

    2006-01-01

    Full Text Available We present a review of the literature on Primary Progressive Aphasia (PPA together with the analysis of neuropschychological and neuroradiologic profiles of 42 PPA patients. Mesulam originally defined PPA as a progressive degenerative disorder characterized by isolated language impairment for at least two years. The most common variants of PPA are: (1 Progressive nonfluent aphasia (PNFA, (2 semantic dementia (SD, (3 logopenic progressive aphasia (LPA. PNFA is characterized by labored speech, agrammatism in production, and/or comprehension. In some cases the syndrome begins with isolated deficits in speech. SD patients typically present with loss of word and object meaning and surface dyslexia. LPA patients have word-finding difficulties, syntactically simple but accurate language output and impaired sentence comprehension. The neuropsychological data demonstrated that SD patients show the most characteristic pattern of impairment, while PNFA and LPA overlap within many cognitive domains. The neuroimaging analysis showed left perisylvian region involvement. A comprehensive cognitive, neuroimaging and pathological approach is necessary to identify the clinical and pathogenetic features of different PPA variants.

  17. [VARIANT ANATOMY OF SPLENIC LIGAMENTS AND ARTERIES PASSING THROUGH THEM].

    Science.gov (United States)

    Gaivoronskiy, I V; Kotiv, B N; Alekseyev, V S; Nichiporuk, G I

    2015-01-01

    The research was performed on 15 non embalmed bodies and 32 abdominal complexes of adult individuals. The comparative study of variant anatomy of splenic ligaments and architectonics of arteries passing through them was carried out to substantiate the mobilization of splenopancreatic complex. Anatomical and angiographic restudied were carried out using preparation, morphometry, injection of gastric, pancreatic and splenic vascular bed with red lead suspension. It was established that the form and sizes of splenic ligaments and their interrelation with the branches of the splenic artery were variable. The minimal and maximal sizes of gastrolienal, phrenicosplenic and splenocolic ligaments differed 2-3 times. In most cases, spleen was fixed in abdominal cavity by many short ligaments. It was shown that architectonics and topography of main branches of spleen artery were determined by morphometric characteristics of the spleen proper and its ligaments. The knowledge of splenic ligament variant anatomy allows a new perspective to approach to substantiate different methods of the mobilization of spleno-pancreatic complex during surgical operations on organs of the upper part of the peritoneal cavity and organ-preserving surgery of the spleen.

  18. Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder.

    Directory of Open Access Journals (Sweden)

    Brandi Rollins

    Full Text Available BACKGROUND: Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ, bipolar disorder (BD, and major depressive disorder (MDD in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA sequence have been reported in SZ and BD patients. METHODOLOGY/PRINCIPAL FINDINGS: Dorsolateral prefrontal cortex (DLPFC from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017 in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK was significant (p = 0.004 and independent of postmortem interval time. CONCLUSIONS: Focusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.

  19. New polymorphic variants of human blood clotting factor IX

    Energy Technology Data Exchange (ETDEWEB)

    Surin, V.L.; Luk`yanenko, A.V.; Tagiev, A.F.; Smirnova, O.V. [Hematological Research Center, Moscow (Russian Federation); Plutalov, O.V.; Berlin, Yu.A. [Shemyakin Institute of Bioorganic Chemistry, Moscow (Russian Federation)

    1995-04-01

    The polymorphism of Alu-repeats, which are located in the introns of the human factor IX gene (copies 1-3), was studied. To identify polymorphic variants, direct sequencing of PCR products that contained appropriate repeats was used. In each case, 20 unrelated X chromosomes were studied. A polymorphic Dra I site was found near the 3{prime}-end of Alu copy 3 within the region of the polyA tract. A PCR-based testing system with internal control of restriction hydrolysis was suggested. Testing 81 unrelated X chromosomes revealed that the frequency of the polymorphic Dra I site is 0.23. Taq I polymorphism, which was revealed in Alu copy 4 of factor IX gene in our previous work, was found to be closely linked to Dra I polymorphism. Studies in linkage between different types of polymorphisms of the factor IX gene revealed the presence of a rare polymorphism in intron a that was located within the same minisatellite region as the known polymorphic insertion 50 bp/Dde I. However, the size of the insertion in our case was 26 bp. Only one polymorphic variant was found among over 150 unrelated X chromosomes derived from humans from Moscow and its vicinity. 10 refs., 4 figs., 1 tab.

  20. Cytochrome allelic variants and clopidogrel metabolism in cardiovascular diseases therapy.

    Science.gov (United States)

    Jarrar, Mohammed; Behl, Shalini; Manyam, Ganiraju; Ganah, Hany; Nazir, Mohammed; Nasab, Reem; Moustafa, Khaled

    2016-06-01

    Clopidogrel and aspirin are among the most prescribed dual antiplatelet therapies to treat the acute coronary syndrome and heart attacks. However, their potential clinical impacts are a subject of intense debates. The therapeutic efficiency of clopidogrel is controlled by the actions of hepatic cytochrome P450 (CYPs) enzymes and impacted by individual genetic variations. Inter-individual polymorphisms in CYPs enzymes affect the metabolism of clopidogrel into its active metabolites and, therefore, modify its turnover and clinical outcome. So far, clinical trials fail to confirm higher or lower adverse cardiovascular effects in patients treated with combinations of clopidogrel and proton pump inhibitors, compared with clopidogrel alone. Such inconclusive findings may be due to genetic variations in the cytochromes CYP2C19 and CYP3A4/5. To investigate potential interactions/effects of these cytochromes and their allele variants on the treatment of acute coronary syndrome with clopidogrel alone or in combination with proton pump inhibitors, we analyze recent literature and discuss the potential impact of the cytochrome allelic variants on cardiovascular events and stent thrombosis treated with clopidogrel. The diversity of CYP2C19 polymorphisms and prevalence span within various ethnic groups, subpopulations and demographic areas are also debated.

  1. Fast space-variant elliptical filtering using box splines.

    Science.gov (United States)

    Chaudhury, Kunal Narayan; Munoz-Barrutia, Arrate; Unser, Michael

    2010-09-01

    The efficient realization of linear space-variant (non-convolution) filters is a challenging computational problem in image processing. In this paper, we demonstrate that it is possible to filter an image with a Gaussian-like elliptic window of varying size, elongation and orientation using a fixed number of computations per pixel. The associated algorithm, which is based upon a family of smooth compactly supported piecewise polynomials, the radially-uniform box splines, is realized using preintegration and local finite-differences. The radially-uniform box splines are constructed through the repeated convolution of a fixed number of box distributions, which have been suitably scaled and distributed radially in an uniform fashion. The attractive features of these box splines are their asymptotic behavior, their simple covariance structure, and their quasi-separability. They converge to Gaussians with the increase of their order, and are used to approximate anisotropic Gaussians of varying covariance simply by controlling the scales of the constituent box distributions. Based upon the second feature, we develop a technique for continuously controlling the size, elongation and orientation of these Gaussian-like functions. Finally, the quasi-separable structure, along with a certain scaling property of box distributions, is used to efficiently realize the associated space-variant elliptical filtering, which requires O(1) computations per pixel irrespective of the shape and size of the filter.

  2. HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants.

    Science.gov (United States)

    Draizen, Eli J; Shaytan, Alexey K; Mariño-Ramírez, Leonardo; Talbert, Paul B; Landsman, David; Panchenko, Anna R

    2016-01-01

    Compaction of DNA into chromatin is a characteristic feature of eukaryotic organisms. The core (H2A, H2B, H3, H4) and linker (H1) histone proteins are responsible for this compaction through the formation of nucleosomes and higher order chromatin aggregates. Moreover, histones are intricately involved in chromatin functioning and provide a means for genome dynamic regulation through specific histone variants and histone post-translational modifications. 'HistoneDB 2.0--with variants' is a comprehensive database of histone protein sequences, classified by histone types and variants. All entries in the database are supplemented by rich sequence and structural annotations with many interactive tools to explore and compare sequences of different variants from various organisms. The core of the database is a manually curated set of histone sequences grouped into 30 different variant subsets with variant-specific annotations. The curated set is supplemented by an automatically extracted set of histone sequences from the non-redundant protein database using algorithms trained on the curated set. The interactive web site supports various searching strategies in both datasets: browsing of phylogenetic trees; on-demand generation of multiple sequence alignments with feature annotations; classification of histone-like sequences and browsing of the taxonomic diversity for every histone variant. HistoneDB 2.0 is a resource for the interactive comparative analysis of histone protein sequences and their implications for chromatin function. Database URL: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0.

  3. Far-Field Tunable Nano-focusing Based on Metallic Slits Surrounded with Nonlinear-Variant Widths and Linear-Variant Depths of Circular Dielectric Grating

    CERN Document Server

    Cao, Peng-Fei; Zhang, Xiao-Ping; Lu, Wei-Ping; Kong, Wei-Jie; Liang, Xue-Wu

    2013-01-01

    In this work, we design a new tunable nanofocusing lens by the linear-variant depths and nonlinear-variant widths of circular grating for far field practical applications. The constructively interference of cylindrical surface plasmon launched by the subwavelength metallic structure can form a subdiffraction-limited focus, and the focal length of the this structures can be adjusted if the each groove depth and width of circular grating are arranged in traced profile. According to the numerical calculation, the range of focusing points shift is much more than other plasmonic lens, and the relative phase of emitting light scattered by surface plasmon coupling circular grating can be modulated by the nonlinear-variant width and linear-variant depth. The simulation result indicates that the different relative phase of emitting light lead to variant focal length. We firstly show a unique phenomenon for the linear-variant depths and nonlinear-variant widths of circular grating that the positive change and negative ...

  4. 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.

  5. 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.

  6. Variants of glycerol dehydrogenase having D-lactate dehydrogenase activity and uses thereof

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qingzhao; Shanmugam, Keelnatham T.; Ingram, Lonnie O' Neal

    2017-08-29

    The present invention provides methods of designing and generating glycerol dehydrogenase (GlyDH) variants that have altered function as compared to a parent polypeptide. The present invention further provides nucleic acids encoding GlyDH polypeptide variants having altered function as compared to the parent polypeptide. Host cells comprising polynucleotides encoding GlyDH variants and methods of producing lactic acids are also provided in various aspects of the invention.

  7. A massive sinonasal psammomatoid variant of juvenile ossifying fibroma: Report of a rare entity

    OpenAIRE

    VR Guttikonda; Taneeru, S; Gaddipati, R; Madala, J

    2013-01-01

    Juvenile ossifying fibroma (JOF) is an uncommon, benign, bone-forming neoplasm with an aggressive local growth that is distinguished from other fibro-osseous lesions primarily by its age of onset, clinical presentation and aggressive behaviour. JOF is considered as a variant of the ossifying fibroma (OF) and the former includes psammomatoid JOF (PsJOF) and Trabecular JOF (TrJOF). Both variants involve the craniofacial bones with the trabecular variant being more common in the jaws and the psa...

  8. High prevalence of genetic variants previously associated with LQT syndrome in new exome data

    DEFF Research Database (Denmark)

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz

    2012-01-01

    variants KCNH2 P347S; SCN5A: S216L, V1951L; and CAV3 T78M in the control population (n=704) revealed prevalences comparable to those of ESP. Thus, we identified a much higher prevalence of previously LQTS-associated variants than expected in exome data from population studies. Great caution regarding...... the possible disease causation of some of these variants has to be taken, especially when used for risk stratification in family members....

  9. RNA Populations in Immunocompromised Patients as Reservoirs for Novel Norovirus Variants

    OpenAIRE

    Vega, Everardo; Donaldson, Eric; Huynh, Jeremy; Barclay, Leslie; Lopman, Ben; Baric, Ralph; Luke F Chen; Vinjé, Jan

    2014-01-01

    Noroviruses are the leading cause of acute gastroenteritis outbreaks worldwide. The majority of norovirus outbreaks are caused by genogroup II.4 (GII.4). Novel GII.4 strains emerge every 2 to 4 years and replace older variants as the dominant norovirus. Novel variants emerge through a combination of recombination, genetic drift, and selection driven by population immunity, but the exact mechanism of how or where is not known. We detected two previously unknown novel GII.4 variants, termed GII...

  10. Challenges in the Diagnosis of Urothelial Carcinoma Variants: Can Emerging Molecular Data Complement Pathology Review?

    Science.gov (United States)

    Solomon, James P; Lowenthal, Brett M; Kader, A Karim; Parsons, J Kellogg; Flaig, Thomas W; Siefker-Radtke, Arlene O; Dyrskjøt, Lars; Hansel, Donna E

    2016-10-18

    Urothelial carcinoma can exhibit a wide variety of histopathologic phenotypes or variant morphologies, classifications of which have recently been revised in the 2016 World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs. Many of these variants not only present diagnostic challenges, but also have clinical implications that affect patient prognosis and treatment strategies. This review will discuss these variant morphologies and their relationship to current understanding of the underlying biology of urothelial carcinoma and molecular classification paradigms.

  11. Variants in microRNA genes in familial papillary thyroid carcinoma.

    Science.gov (United States)

    Tomsic, Jerneja; Fultz, Rebecca; Liyanarachchi, Sandya; Genutis, Luke K; Wang, Yanqiang; Li, Wei; Volinia, Stefano; Jazdzewski, Krystian; He, Huiling; Wakely, Paul E; Senter, Leigha; de la Chapelle, Albert

    2017-01-24

    Papillary Thyroid Carcinoma (PTC) displays one of the highest familiality scores of all cancers as measured by case-control studies, yet only a handful of genes have been implicated until now. Variants in microRNAs have been associated with the risk of several cancers including PTC but the magnitude of this involvement is unclear. This study was designed to test to what extent genomic variants in microRNAs contribute to PTC risk. We used SOLiD technology to sequence 321 genomic regions encoding 427 miRNAs in one affected individual from each of 80 PTC families. After excluding variants with frequency ≥ 1% in 1000 Genomes Phase 1 (n = 1092) we detected 1978 variants. After further functional filtering steps 25 variants in pre-miRs remained. Co-segregation was observed for six out of 16 tested miRNA variants with PTC in the families, namely let-7e, miR-181b, miR-135a, miR-15b, miR-320, and miR-484. Expression of miR-135a and miR-181b was tested in normal thyroid and tumor tissue from patients that carry the variants and a decrease in expression was observed. In vitro assays were applied to measure the effect of the variants on microRNAs' maturation. Four out of six variants were tested. Only the let-7e and miR-181b variants showed an effect on processing leading to lower levels of mature miRNA. These two variants were not detected in 1170 sporadic PTC cases nor in 1404 controls. Taken together, our data show that high penetrance germline sequence variants of miRNAs potentially predispose to a fraction of all PTC but are not common.

  12. Initial Comparisons between the Advanced Technology Development Gen 2 Baseline Cells and Variant C Cells

    Energy Technology Data Exchange (ETDEWEB)

    Christophersen, Jon Petter; Motloch, Chester George; Wright, Randy Ben; Murphy, Timothy Collins; Belt, Jeffrey R; Ho, Chinh Dac; Bloom, Ira D.; Jones, S. A.; Battaglia, Vincent S.; Jungst, Rudy G.; Case, Herb L.; Sutula, Raymond A.; Barnes, James A.; Duong, Tien Q.

    2002-06-01

    The Advanced Technology Development Program is testing a second generation of lithium-ion cells, consisting of a baseline and three variant chemistries. The cathode composition of the Variant C chemistry was altered with an increase to the aluminum dopant and a decrease to the cobalt dopant to explore the impact on performance. However, it resulted in a 20% drop in rated capacity. Also, the Variant C average power fade is higher, but capacity fade is higher for the Baseline cell chemistry. Initial results indicate that the Variant C chemistry will reach end of life sooner than the Baseline chemistry.

  13. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

    Science.gov (United States)

    Shameer, Khader; Tripathi, Lokesh P; Kalari, Krishna R; Dudley, Joel T; Sowdhamini, Ramanathan

    2016-09-01

    Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.

  14. APOL1 risk variants and death among African American hemodialysis patients: survival of the fittest?

    Science.gov (United States)

    Chen, Teresa K; Estrella, Michelle M

    2016-08-01

    Recent studies have focused on associations of the APOL1 risk variants with outcomes beyond kidney disease, including cardiovascular disease and mortality. Ma and colleagues now expand on this growing but contradicting body of work. Their analysis of a prevalent cohort of African American hemodialysis patients shows that the risk variants are associated with a survival benefit among nondiabetics. Whether this simply reflects a healthier status at hemodialysis initiation among those carrying 2 risk variants or whether these variants truly confer a survival advantage is unclear.

  15. Variants of Aspergillus alutaceus var. alutaceus (formerly Aspergillus ochraceus) with altered ochratoxin a production

    Energy Technology Data Exchange (ETDEWEB)

    Chelack, W.S.; Borsa, J.; Szekely, J.G. (Whiteshell Labs., Pinawa, Manitoba (Canada)); Marquardt, R.R.; Frohlich, A.A. (Univ. of Manitoba, Winnipeg (Canada))

    1991-09-01

    The present studies, using Asperigillus alutaceus var. alutaceus Berkeley et Curtis (formerly A. ochraceus Wilhelm) NRRL 3174 along with three other wild-type strains, were undertaken in an attempt to understand the effects of irradiation and other treatments on mycotoxin production in grain. Bedford barley was inoculated with spores of NRRL 3174, gamma irradiated, and incubated at 28C and 25% moisture. After 10 days of incubation, two colony types, ocher (parental) and yellow (variant), were isolated from the grain. Further culturing of the yellow variant resulted in the spontaneous appearance of a white variant that exhibited greatly enhanced fluorescence under UV light. In subsequent work, we have also isolated variants producing a soluble red pigment. In addition, in model experiments involving irradiation (1 kGy) of pure cultures, induction frequencies ranging between 2 and 4% (survival basis) were observed for the yellow and red variants. Inoculation of these variants into wheat and incubation for 14 days at 28C and 32% moisture resulted in ochratoxin A production in the relative amounts of 0.09:1:4.6:9.3 for the red, ocher (parental), yellow, and white variants, respectively. Additional characteristics of these isolates are described. Confirmation that the white high-ochratoxin-A-producing variants were derived from the parental strain was demonstrated by obtaining revertant sectors in monoclonal cultures of the variants.

  16. Overlap between Parkinson disease and Alzheimer disease in ABCA7 functional variants.

    Science.gov (United States)

    Nuytemans, Karen; Maldonado, Lizmarie; Ali, Aleena; John-Williams, Krista; Beecham, Gary W; Martin, Eden; Scott, William K; Vance, Jeffery M

    2016-02-01

    Given their reported function in phagocytosis and clearance of protein aggregates in Alzheimer disease (AD), we hypothesized that variants in ATP-binding cassette transporter A7 (ABCA7) might be involved in Parkinson disease (PD). ABCA7 variants were identified using whole-exome sequencing (WES) on 396 unrelated patients with PD and 222 healthy controls. In addition, we used the publicly available WES data from the Parkinson's Progression Markers Initiative (444 patients and 153 healthy controls) as a second, independent data set. We observed a higher frequency of loss-of-function (LOF) variants and rare putative highly functional variants (Combined Annotation Dependent Depletion [CADD] >20) in clinically diagnosed patients with PD than in healthy controls in both data sets. Overall, we identified LOF variants in 11 patients and 1 healthy control (odds ratio [OR] 4.94, Fisher exact p = 0.07). Four of these variants have been previously implicated in AD risk (p.E709AfsX86, p.W1214X, p.L1403RfsX7, and rs113809142). In addition, rare variants with CADD >20 were observed in 19 patients vs 3 healthy controls (OR 2.85, Fisher exact p = 0.06). The presence of ABCA7 LOF variants in clinically defined PD suggests that they might be risk factors for neurodegeneration in general, especially those variants hallmarked by protein aggregation. More studies will be needed to evaluate the overall impact of this transporter in neurodegenerative disease.

  17. 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.

  18. Riñón en herradura asociado a variantes anatómicas

    OpenAIRE

    David Rodríguez Palomo

    2009-01-01

    El riñón en herradura es una variante anatómica frecuente del sistema renal que normalmente cursa asintomático, sin embargo, la concomitancia de anormalidades congénitas en los pacientes portadores de esta variante puede desencadenar síntomas producto de complicaciones renales, cardiocirculatorias y varios tipos de neoplasias que tienden a la malignidad. Este trabajo describe la variante anatómica del riñón en herradura asociado a tres uréteres independientes con variante arteriovenosa de su ...

  19. Rare Titin (TTN Variants in Diseases Associated with Sudden Cardiac Death

    Directory of Open Access Journals (Sweden)

    Oscar Campuzano

    2015-10-01

    Full Text Available A leading cause of death in western countries is sudden cardiac death, and can be associated with genetic disease. Next-generation sequencing has allowed thorough analysis of genes associated with this entity, including, most recently, titin. We aimed to identify potentially pathogenic genetic variants in titin. A total of 1126 samples were analyzed using a custom sequencing panel including major genes related to sudden cardiac death. Our cohort was divided into three groups: 432 cases from patients with cardiomyopathies, 130 cases from patients with channelopathies, and 564 post-mortem samples from individuals showing anatomical healthy hearts and non-conclusive causes of death after comprehensive autopsy. None of the patients included had definite pathogenic variants in the genes analyzed by our custom cardio-panel. Retrospective analysis comparing the in-house database and available public databases also was performed. We identified 554 rare variants in titin, 282 of which were novel. Seven were previously reported as pathogenic. Of these 554 variants, 493 were missense variants, 233 of which were novel. Of all variants identified, 399 were unique and 155 were identified at least twice. No definite pathogenic variants were identified in any of genes analyzed. We identified rare, mostly novel, titin variants that seem to play a potentially pathogenic role in sudden cardiac death. Additional studies should be performed to clarify the role of these variants in sudden cardiac death.

  20. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants

    National Research Council Canada - National Science Library

    Yoshida, Masa-aki; Yura, Kei; Ogura, Atsushi

    2014-01-01

    Previous studies have reported that the developmental processes of vertebrate eyes are controlled by four Pax-6 splicing variants, each modulating different downstream genes, whereas those of insect...

  1. Direct Correlation of Cell Toxicity to Conformational Ensembles of Genetic Aβ Variants

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2015-01-01

    We report a systematic analysis of conformational ensembles generated from multiseed molecular dynamics simulations of all 15 known genetic variants of Aβ42. We show that experimentally determined variant toxicities are largely explained by random coil content of the amyloid ensembles (correlation......, are fundamentally related to neurodegeneration. The data provide molecular explanations for the high toxicity of E22 variants and for the protective features of the recently characterized A2T variant. The identified conformational features, for example, the local helix-coil-strand transitions of the C...

  2. Human thromboxane A2 receptor genetic variants: in silico, in vitro and "in platelet" analysis.

    Directory of Open Access Journals (Sweden)

    Scott Gleim

    Full Text Available Thromboxane and its receptor have emerged as key players in modulating vascular thrombotic events. Thus, a dysfunctional hTP genetic variant may protect against (hypoactivity or promote (hyperactivity vascular events, based upon its activity on platelets. After extensive in silico analysis, six hTP-α variants were selected (C(68S, V(80E, E(94V, A(160T, V(176E, and V(217I for detailed biochemical studies based on structural proximity to key regions involved in receptor function and in silico predictions. Variant biochemical profiles ranged from severe instability (C(68S to normal (V(217I, with most variants demonstrating functional alteration in binding, expression or activation (V(80E, E(94V, A(160T, and V(176E. In the absence of patient platelet samples, we developed and validated a novel megakaryocyte based system to evaluate human platelet function in the presence of detected dysfunctional genetic variants. Interestingly, variant V80E exhibited reduced platelet activation whereas A160T demonstrated platelet hyperactivity. This report provides the most comprehensive in silico, in vitro and "in platelet" evaluation of hTP variants to date and highlightscurrent inherent problems in evaluating genetic variants, with possible solutions. The study additionally provides clinical relevance to characterized dysfunctional hTP variants.

  3. Acantholytic variant of bowen′s disease with micro-invasive squamous cell carcinoma: A case report of a unique variant

    Directory of Open Access Journals (Sweden)

    Kanthilatha Pai

    2014-01-01

    Full Text Available Bowen′s disease is generally regarded as premalignant dermatoses. The disease affects both skin and the mucosa and has the potential to progress to invasive squamous cell carcinoma. There are descriptions of several histological variants of Bowen′s disease like psoriasiform, atrophic, pagetoid, etc. Acantholysis of anaplastic keratinocytes with bullae/cleft formation is described in premalignant condition like actinic keratosis and adenoid variant of squamous cell carcinoma, but there is lack of report describing this phenomena in Bowen′s disease. We present a case of unusual acantholytic variant of Bowen′s disease with focus of micro-invasive carcinoma.

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

    Directory of Open Access Journals (Sweden)

    Liu Melissa M

    2012-08-01

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

  5. Sciatic nerve high division: two different anatomical variants.

    Science.gov (United States)

    Pais, Diogo; Casal, Diogo; Bettencourt Pires, Maria Alexandre; Furtado, Andrea; Bilhim, Tiago; Angélica-Almeida, Maria; Goyri-O'Neill, João

    2013-01-01

    Introdução: As variações do nervo isquiático são relativamente comuns e frequentemente muito significativas clinicamente. O objetivo deste trabalho é apresentar duas destas variações e discutir algumas das suas implicações clínicas.Material e Métodos: Três cadáveres caucasianos sem história prévia de trauma ou cirurgia no membro inferior foram dissecados, apresentando variações anatómicas do nervo isquiático.Resultados: Em todos os casos o nervo isquiático dividia-se acima da fossa poplítea.Em dois casos (cadáveres1 e 2) a terminação deste nervo ocorria na porção inferior da região glútea nos seus dois ramos terminais: os nervos fibular comum e tibial. Num outro caso (cadáver 3), o nervo isquiático dividia-se ainda dentro da bacia antes de percorrer a incisura isquiática maior. Neste caso, o nervo fibular comum saía da pelve acima do músculo piriforme, passando em seguida ao longo de sua face posterior, enquanto que o nervo tibial corria profundamente ao músculo piriforme.Discussão: De acordo com a literatura, a variante anatómica descrita no cadáver 3 é considerada relativamente rara. Esta variante poderá predispor a síndromes compressivos do nervo isquiático. A divisão alta do nervo isquiático, de que são exemplos os cadáveres 1 e 2, pode comprometer a eficácia dos bloqueios anestésicos ao nível da fossa poplítea.Conclusão: As variantes anatómicas associadas à divisão alta do nervo isquiático devem sempre ser tidas em consideração porserem relativamente comuns e terem importantes implicações clínicas, nomeadamente nas áreas de Anestesiologia, Neurologia, Medicina do Desporto e Cirurgia.

  6. Gastrointestinal stromal tumors, somatic mutations and candidate genetic risk variants.

    Science.gov (United States)

    O'Brien, Katie M; Orlow, Irene; Antonescu, Cristina R; Ballman, Karla; McCall, Linda; DeMatteo, Ronald; Engel, Lawrence S

    2013-01-01

    Gastrointestinal stromal tumors (GISTs) are rare but treatable soft tissue sarcomas. Nearly all GISTs have somatic mutations in either the KIT or PDGFRA gene, but there are no known inherited genetic risk factors. We assessed the relationship between KIT/PDGFRA mutations and select deletions or single nucleotide polymorphisms (SNPs) in 279 participants from a clinical trial of adjuvant imatinib mesylate. Given previous evidence that certain susceptibility loci and carcinogens are associated with characteristic mutations, or "signatures" in other cancers, we hypothesized that the characteristic somatic mutations in the KIT and PDGFRA genes in GIST tumors may similarly be mutational signatures that are causally linked to specific mutagens or susceptibility loci. As previous epidemiologic studies suggest environmental risk factors such as dioxin and radiation exposure may be linked to sarcomas, we chose 208 variants in 39 candidate genes related to DNA repair and dioxin metabolism or response. We calculated adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the association between each variant and 7 categories of tumor mutation using logistic regression. We also evaluated gene-level effects using the sequence kernel association test (SKAT). Although none of the association p-values were statistically significant after adjustment for multiple comparisons, SNPs in CYP1B1 were strongly associated with KIT exon 11 codon 557-8 deletions (OR = 1.9, 95% CI: 1.3-2.9 for rs2855658 and OR = 1.8, 95% CI: 1.2-2.7 for rs1056836) and wild type GISTs (OR = 2.7, 95% CI: 1.5-4.8 for rs1800440 and OR = 0.5, 95% CI: 0.3-0.9 for rs1056836). CYP1B1 was also associated with these mutations categories in the SKAT analysis (p = 0.002 and p = 0.003, respectively). Other potential risk variants included GSTM1, RAD23B and ERCC2. This preliminary analysis of inherited genetic risk factors for GIST offers some clues about the disease's genetic origins and

  7. Gastrointestinal stromal tumors, somatic mutations and candidate genetic risk variants.

    Directory of Open Access Journals (Sweden)

    Katie M O'Brien

    Full Text Available Gastrointestinal stromal tumors (GISTs are rare but treatable soft tissue sarcomas. Nearly all GISTs have somatic mutations in either the KIT or PDGFRA gene, but there are no known inherited genetic risk factors. We assessed the relationship between KIT/PDGFRA mutations and select deletions or single nucleotide polymorphisms (SNPs in 279 participants from a clinical trial of adjuvant imatinib mesylate. Given previous evidence that certain susceptibility loci and carcinogens are associated with characteristic mutations, or "signatures" in other cancers, we hypothesized that the characteristic somatic mutations in the KIT and PDGFRA genes in GIST tumors may similarly be mutational signatures that are causally linked to specific mutagens or susceptibility loci. As previous epidemiologic studies suggest environmental risk factors such as dioxin and radiation exposure may be linked to sarcomas, we chose 208 variants in 39 candidate genes related to DNA repair and dioxin metabolism or response. We calculated adjusted odds ratios (ORs and 95% confidence intervals (CIs for the association between each variant and 7 categories of tumor mutation using logistic regression. We also evaluated gene-level effects using the sequence kernel association test (SKAT. Although none of the association p-values were statistically significant after adjustment for multiple comparisons, SNPs in CYP1B1 were strongly associated with KIT exon 11 codon 557-8 deletions (OR = 1.9, 95% CI: 1.3-2.9 for rs2855658 and OR = 1.8, 95% CI: 1.2-2.7 for rs1056836 and wild type GISTs (OR = 2.7, 95% CI: 1.5-4.8 for rs1800440 and OR = 0.5, 95% CI: 0.3-0.9 for rs1056836. CYP1B1 was also associated with these mutations categories in the SKAT analysis (p = 0.002 and p = 0.003, respectively. Other potential risk variants included GSTM1, RAD23B and ERCC2. This preliminary analysis of inherited genetic risk factors for GIST offers some clues about the disease's genetic

  8. New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants

    DEFF Research Database (Denmark)

    Andreasen, Charlotte Hartig; Nielsen, Jonas B; Refsgaard, Lena

    2013-01-01

    with these cardiomyopathies, but the disease-causing effect of reported variants is often dubious. In order to identify possible false-positive variants, we investigated the prevalence of previously reported cardiomyopathy-associated variants in recently published exome data. We searched for reported missense and nonsense...... variants in the NHLBI-Go Exome Sequencing Project (ESP) containing exome data from 6500 individuals. In ESP, we identified 94 variants out of 687 (14%) variants previously associated with HCM, 58 out of 337 (17%) variants associated with DCM, and 38 variants out of 209 (18%) associated with ARVC...... times higher than expected from the phenotype prevalences in the general population (HCM 1:500, DCM 1:2500, and ARVC 1:5000) and our data suggest that a high number of these variants are not monogenic causes of cardiomyopathy....

  9. Localization of association signal from risk and protective variants in sequencing studies.

    Science.gov (United States)

    Brisbin, Abra; Jenkins, Gregory D; Ellsworth, Katarzyna A; Wang, Liewei; Fridley, Brooke L

    2012-01-01

    Aggregating information across multiple variants in a gene or region can improve power for rare variant association testing. Power is maximized when the aggregation region contains many causal variants and few neutral variants. In this paper, we present a method for the localization of the association signal in a region using a sliding-window based approach to rare variant association testing in a region. We first introduce a novel method for analysis of rare variants, the Difference in Minor Allele Frequency test (DMAF), which allows combined analysis of common and rare variants, and makes no assumptions about the direction of effects. In whole-region analyses of simulated data with risk and protective variants, DMAF and other methods which pool data across individuals were found to outperform methods which pool data across variants. We then implement a sliding-window version of DMAF, using a step-down permutation approach to control type I error with the testing of multiple windows. In simulations, the sliding-window DMAF improved power to detect a causal sub-region, compared to applying DMAF to the whole region. Sliding-window DMAF was also effective in localizing the causal sub-region. We also applied the DMAF sliding-window approach to test for an association between response to the drug gemcitabine and variants in the gene FKBP5 sequenced in 91 lymphoblastoid cell lines derived from white non-Hispanic individuals. The application of the sliding-window test procedure detected an association in a sub-region spanning an exon and two introns, when rare and common variants were analyzed together.

  10. Genome-wide analysis of copy number variants in attention deficit hyperactivity disorder: the role of rare variants and duplications at 15q13.3.

    NARCIS (Netherlands)

    Williams, N.M.; Franke, B.; Mick, E.; Anney, R.J.; Freitag, C.M.; Gill, M.; Thapar, A.; O'Donovan, M.C.; Owen, M.J.; Holmans, P.; Kent, L.; Middleton, F.; Zhang-James, Y.; Liu, L.; Meyer, J.; Nguyen, T.T.M.; Romanos, J.; Romanos, M.; Seitz, C.; Renner, T.J.; Walitza, S.; Warnke, A.; Palmason, H.; Buitelaar, J.K.; Rommelse, N.N.; Arias Vasquez, A.; Hawi, Z.; Langley, K.; Sergeant, J.A.; Steinhausen, H.C.; Roeyers, H.; Biederman, J.; Zaharieva, I.; Hakonarson, H.; Elia, J.; Lionel, A.C.; Crosbie, J.; Marshall, C.R.; Schachar, R.; Scherer, S.W.; Todorov, A.; Smalley, S.L.; Loo, S.; Nelson, S.; Shtir, C.; Asherson, P.; Reif, A.; Lesch, K.P.; Faraone, S.V.

    2012-01-01

    OBJECTIVE: Attention deficit hyperactivity disorder (ADHD) is a common, highly heritable psychiatric disorder. Because of its multifactorial etiology, however, identifying the genes involved has been difficult. The authors followed up on recent findings suggesting that rare copy number variants (CNV

  11. Stability Analysis of a Variant of the Prony Method

    Directory of Open Access Journals (Sweden)

    Rodney Jaramillo

    2012-01-01

    Full Text Available Prony type methods are used in many engineering applications to determine the exponential fit corresponding to a dataset. In this paper we study a variant of Prony's method that was used by Martín-Landrove et al., in a process of segmentation of T2-weighted MRI brain images. We show the equivalence between that method and the classical Prony method and study the stability of the computed solutions with respect to noise in the data set. In particular, we show that the relative error in the calculation of the exponential fit parameters is linear with respect to noise in the data. Our analysis is based on classical results from linear algebra, matrix computation theory, and the theory of stability for roots of polynomials.

  12. Common variants in CASP3 confer susceptibility to Kawasaki disease.

    Science.gov (United States)

    Onouchi, Yoshihiro; Ozaki, Kouichi; Buns, Jane C; Shimizu, Chisato; Hamada, Hiromichi; Honda, Takafumi; Terai, Masaru; Honda, Akihito; Takeuchi, Takashi; Shibuta, Shoichi; Suenaga, Tomohiro; Suzuki, Hiroyuki; Higashi, Kouji; Yasukawa, Kumi; Suzuki, Yoichi; Sasago, Kumiko; Kemmotsu, Yasushi; Takatsuki, Shinichi; Saji, Tsutomu; Yoshikawa, Tetsushi; Nagai, Toshiro; Hamamoto, Kunihiro; Kishi, Fumio; Ouchi, Kazunobu; Sato, Yoshitake; Newburger, Jane W; Baker, Annette L; Shulman, Stanford T; Rowley, Anne H; Yashiro, Mayumi; Nakamura, Yoshikazu; Wakui, Keiko; Fukushima, Yoshimitsu; Fujino, Akihiro; Tsunoda, Tatsuhiko; Kawasaki, Tomisaku; Hata, Akira; Nakamura, Yusuke; Tanaka, Toshihiro

    2010-07-15

    Kawasaki disease (KD; OMIM 611775) is an acute vasculitis syndrome which predominantly affects small- and medium-sized arteries of infants and children. Epidemiological data suggest that host genetics underlie the disease pathogenesis. Here we report that multiple variants in the caspase-3 gene (CASP3) that are in linkage disequilibrium confer susceptibility to KD in both Japanese and US subjects of European ancestry. We found that a G to A substitution of one commonly associated SNP located in the 5' untranslated region of CASP3 (rs72689236; P = 4.2 x 10(-8) in the Japanese and P = 3.7 x 10(-3) in the European Americans) abolished binding of nuclear factor of activated T cells to the DNA sequence surrounding the SNP. Our findings suggest that altered CASP3 expression in immune effecter cells influences susceptibility to KD.

  13. Familial Mediterranean fever variant with repeated atypical skin eruptions.

    Science.gov (United States)

    Takahashi, Tomoko; Fujisawa, Tomomi; Kimura, Masaki; Ohnishi, Hidenori; Seishima, Mariko

    2015-09-01

    Familial Mediterranean fever (FMF) is characterized by self-limited bouts of fever and polyserositis. Skin involvement is not common in FMF, and erysipelas-like erythema is found to be the most frequent skin eruption which is often accompanied by arthritis and fever, and disappears within 12-72 h. We report a 40-year-old Japanese woman who presented with a 2-year history of recurrent fever with general fatigue, polyarthralgia and transient maculopapular eruptions on her lower extremities and trunk. The histological findings of the maculopapular eruption showed lymphocyte infiltration around the capillaries in the entire dermis. Mutation analysis showed a heterozygous E148Q-P369S mutation of MEFV. These findings suggested a diagnosis of late-onset FMF variant with atypical skin eruptions. The patient was successfully treated with colchicine. Thus, we should pay attention to repeated atypical skin eruptions for the early detection of atypical FMF. © 2015 Japanese Dermatological Association.

  14. Fast space-variant elliptical filtering using box splines

    CERN Document Server

    Chaudhury, Kunal Narayan; Unser, Michael

    2010-01-01

    The efficient realization of linear space-variant (non-convolution) filters is a challenging computational problem in image processing. In this paper, we demonstrate that it is possible to filter an image with a Gaussian-like elliptic window of varying size, elongation and orientation using a fixed number of computations per pixel. The associated algorithm, which is based on a family of smooth compactly supported piecewise polynomials, the radially-uniform box splines, is realized using pre-integration and local finite-differences. The radially-uniform box splines are constructed through the repeated convolution of a fixed number of box distributions, which have been suitably scaled and distributed radially in an uniform fashion. The attractive features of these box splines are their asymptotic behavior, their simple covariance structure, and their quasi-separability. They converge to Gaussians with the increase of their order, and are used to approximate anisotropic Gaussians of varying covariance simply by ...

  15. Variant attachments of the anterior horn of the medial meniscus.

    Science.gov (United States)

    Jakubowicz, Marian; Ratajczak, Wojciech; Pytel, Andrzej

    2003-01-01

    The purpose of this study was to analyse the occurrence of variants of anomalous insertions of the anterior horn of the medial meniscus in human knee joints. The study was carried out on 78 human lower limbs of both sexes (42 males and 36 females). Out of 78 knee joints, 10 knee joints (12.82%) presented atypical attachments of the anterior horn of the medial meniscus. In 9 cases we found that the anterior horn of the medial meniscus was attached to the transverse ligament of the knee and in 1 case it was attached to the coronary ligament. In the remaining cases the anterior horn of the medial meniscus was attached to the anterior intercondylar area of the tibia.

  16. Pedunculated Nodules as a Variant of Dermatofibrosarcoma Protuberans

    Science.gov (United States)

    Kim, Min Jung; Hur, Min Seok; Choi, Byung Gon; Kim, Soo Young; Lee, Yang Won; Choe, Yong Beom

    2016-01-01

    Dermatofibrosarcoma protuberans (DFSP) is a rare disease of dermal fibroblastic origin that accounts for less than 5% of all soft tissue sarcomas in adults. DFSP grows slowly and is an asymptomatic lesion at the initial diagnosis. Herein, we report a case of multiple pedunculated nodules as a variant of DFSP. A 47-year-old man presented with a 7-month history of multiple well-circumscribed, firm, pedunculated nodules on the inguinal area. Histopathologic examination results showed densely packed uniform spindle cells with a storiform and cartwheel pattern, and positivity for CD34. Wide excision and skin graft were performed and at the 6-month follow-up, there was no evidence of recurrence or metastasis. PMID:27746644

  17. Hyperostotic esthesioneuroblasma: Rare variant and fibrous dysplasia mimicker

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Manzoor [Neuroradiology Section, Imaging Institute, Cleveland Clinic Foundation, Cleveland (United States); Knott, Phillip Daniel [Director of Facial Plastic and Reconstructive Surgery, Associate Professor of Otolaryngology, UCSF School of Medicine, San Fransisco (United States)

    2014-02-15

    A 65-year-old male presented with a 3-year history of orbital symptoms. An imaging-based diagnosis of fibrous dysplasia involving the skull base was made at another institution. CT showed a diffuse sinonasal mass and ground-glass appearance of the bones of the anterior skull base with bony defects and mucocele formation. MRI demonstrated an accompanying intracranial and orbital rind of soft tissue mass along the hyperostotic bones. FDG-PET showed corresponding intense hypermetabolism. Small cysts were observed at the tumor-brain interface. Biopsy revealed esthesioneuroblastoma with bone infiltration that is compatible with the hyperostotic variant of esthesioneuroblastoma. There are a few cases of hyperostotic esthesioneuroblastoma reported in the literature.

  18. Desmoplastic variant of ameloblastoma of the maxilla: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Koh, Kwang Joon; Park, Ha Na; Kim, Kyoung A [Oral and Maxillofacial Radiology, School of Dentistry and Institute of Oral Bioscience, Chonbuk National University, Jeonju (Korea, Republic of)

    2015-12-15

    The desmoplastic variant of ameloblastoma is a rare form of ameloblastoma characterized by unique radiographic and histologic features. A 46-year-old female was referred to our hospital, complaining of swelling in the left upper lip area. Radiographic findings revealed an ill-defined multilocular lesion with a large cystic lesion and thick sclerotic trabeculae on the left anterior maxilla. After the patient underwent partial osteotomy, histologic analysis revealed a desmoplastic ameloblastoma with no evidence of a hybrid lesion or cyst formation. The radiographic findings in the present case were different from those described in previous case reports. These findings are of special importance due to the unfamiliar radiographic and histologic features of this lesion.

  19. Bilateral variant of sciatic nerve exhibiting intra-pelvic division

    Directory of Open Access Journals (Sweden)

    Rejeena P Raj, Kunjumon PC, More Anju B

    2014-04-01

    Full Text Available Context (background: In case of high division of the sciatic nerve in the pelvis its, common peroneal component may pierce the Piriformis muscle. This anatomical variant can explain many clinical findings. Aims: Its objective is to report a case of high division of the sciatic nerve in order to contribute towards better anatomical understanding of the gluteal region. Methods and Material: Routine undergraduate dissection of a male cadaver revealed bilateral variation in sciatic nerve. Results: Sciatic nerve is dividing into tibial and common peroneal components in the pelvis. Common peroneal component is piercing through the piriformis muscle. Tibial component is emerging between piriformis and superior gemelli muscle. Conclusions: Sciatic nerve variation can lead to a Piriformis muscle syndrome, inadvertent injury during operations in the gluteal region, failure of sciatic nerve block and/or sciatic neuropathy. The differences in routes of these two nerve components can explain them.

  20. Piriformis Syndrome With Variant Sciatic Nerve Anatomy: A Case Report.

    Science.gov (United States)

    Kraus, Emily; Tenforde, Adam S; Beaulieu, Christopher F; Ratliff, John; Fredericson, Michael

    2016-02-01

    A 68-year-old male long distance runner presented with low back and left buttock pain, which eventually progressed to severe and debilitating pain, intermittently radiating to the posterior thigh and foot. A comprehensive workup ruled out possible spine or hip causes of his symptoms. A pelvic magnetic resonance imaging neurogram with complex oblique planes through the piriformis demonstrated variant anatomy of the left sciatic nerve consistent with the clinical diagnosis of piriformis syndrome. The patient ultimately underwent neurolysis with release of the sciatic nerve and partial resection of the piriformis muscle. After surgery the patient reported significant pain reduction and resumed running 3 months later. Piriformis syndrome is uncommon but should be considered in the differential diagnosis for buttock pain. Advanced imaging was essential to guide management.