5,404 results on '"Vicente, M."'
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2. Preparation of porcelain tile granulates by more environmentally sustainable processes
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García-Ten, J., Quereda, F., Gil, C., Silvestre, D., Vicente, M. J., and Piquer, J.
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Porcelain tile ,dry milling ,granulation ,Gres porcelánico ,molienda en seco ,granulación ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
This study examines the feasibility of manufacturing glazed porcelain tiles with a more environmentally friendly manufacturing process, by reducing water and thermal energy consumption. The process studied in this paper is dry milling in a pendulum mill, with subsequent granulation (in order to obtain a press powder with similar flowability to that of spraydried powders). The different morphology of the new granulate with respect to the standard spray-dried granulate modifies the microstructure of the green compacts and thus, their behaviour and fired tile properties. In order to obtain porcelain tiles with the required properties (water absorption, mechanical strength,…) changes have been made in the raw materials mixture and in the processing variables. Finally, porcelain tiles measuring 50x50 cm have been manufactured at industrial scale with the new granulate using a conventional firing cycle, obtaining quality levels identical to those provided by the spray-dried granulate. These results open the possibility of preparing porcelain tile body compositions through a manufacturing process alternative to the standard one, more environmentally friendly and with lower costs.En el presente trabajo se ha estudiado la viabilidad de fabricar gres porcelánico esmaltado utilizando un sistema de preparación de la composición del soporte más respetuoso con el medio ambiente, lo que implica una reducción importante de los consumos de agua y de energía térmica. El proceso que se estudia en el presente trabajo es el consistente en la molienda vía seca en molino pendular y en la posterior granulación (para obtener un polvo de prensas con fluidez similar a la de los polvos atomizados). La distinta morfología de los nuevos gránulos obtenidos respecto al polvo atomizado actual, modifica la microestuctura en crudo de las piezas y, con ello, el comportamiento y propiedades finales de las baldosas obtenidas. Por ello, ha sido necesario modificar la mezcla de materias primas y ajustar algunas variables de operación para obtener baldosas de gres porcelánico con las propiedades requeridas (absorción de agua, resistencia mecánica, etc.). Finalmente, se han fabricado industrialmente piezas de gres porcelánico (50x50 cm2) con el nuevo granulado, mediante un ciclo de cocción convencional, obteniendo unos niveles de calidad idénticos a los que proporciona el polvo atomizado. Estos resultados abren la posibilidad de preparar las composiciones de soporte de gres porcelánico mediante un sistema alternativo al actual, más respetuoso con el medio ambiente y con un menor coste.
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- 2012
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3. A Qualitative Approach to the Analysis of Digital Leisure of the University Student Population
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Sánchez-Gómez, María Cruz, Cabanillas-García, Juan Luis, Martín-Cilleros, María Victoria, del Brío-Alonso, Irene, Verdugo-Castro, Sonia, Sánchez-Vicente, M. Inmaculada, Lorenzo-Sánchez, Oscar, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Ribeiro, Jaime, editor, Brandão, Catarina, editor, Ntsobi, Mfanelo, editor, Kasperiuniene, Judita, editor, and Costa, António Pedro, editor
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- 2024
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4. New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages
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Vicente M. Cabrera
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Medicine ,Science - Abstract
Abstract Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.
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- 2024
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5. Materiales con propiedades tecnológicas obtenidos por modificación química de un caolín natural
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Belver, C., Bañares, M. A., and Vicente, M. A.
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Kaolin ,acid treatment ,alkaline treatment ,Caolín ,activación ácida ,activación básica ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
The synthesis of materials of high added value from a natural kaolin has been studied. The kaolin was pre-activated by means of calcination to obtain the metakaolins, which are amorphous solids capable of being modified by simple and non expensive chemical treatments. These solids were then submitted to acid and basic treatments to modify their structure and properties. The acid activation under specific conditions gave place to the synthesis of solids mainly constituted by silica with good textural properties, developing so much their external and internal surface, these solids may be used like adsorbentes and catalytic supports. On the other hand, the basic activation produced the modification of the metakaolins and it gave place to the crystallisation of the zeolite K-F (Z), appearing as a simple and effective method for the synthesis of this material.En este trabajo se ha estudiado la síntesis de materiales de alto valor añadido a partir de un caolín natural. Para ello el caolín fue pre-activado mediante calcinación para dar lugar a la formación de metacaolines, sólidos amorfos susceptibles de ser modificados por tratamientos químicos de una manera sencilla y poco costosa. Estos sólidos fueron posteriormente sometidos a tratamientos ácidos y básicos para modificar su estructura y propiedades. La activación ácida bajo unas condiciones específicas dio lugar a la síntesis de sólidos constituidos mayoritariamente por sílice con buenas propiedades superficiales, desarrollándose tanto su superficie externa como interna, revelándose como sólidos que pueden ser empleados como adsorbentes y soportes catalíticos. Por su parte, la modificación causada por la activación básica dio lugar a la cristalización de la zeolita K-F (Z), presentándose como un método sencillo y eficaz para la síntesis de este material.
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- 2004
6. Caracterización cerámica de los sedimentos de la Albufera de Valencia
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Vicente, M., Llusar, M., and Monrós, G.
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Albufera of Valencia ,recycling ,sediment ,ceramic stoneware ,Albufera de Valencia ,reciclado ,sedimentos ,pasta cerámica ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
The Albufera is recognised as Natural Park by Generalitat Valenciana decree of 8´th July 1989 and is listed on the wet areas of international importance of the Ramsar Conference since 8´th May 1990. Batimetry studies show the gradual full up of the lake. If the stuffing and pollution process persist, lamentably, in order to preserve the lake identity it will be necessary to extract the sediments which must be environmental adequately managed. In this study the ceramic characteristics of the Albufera of Valencia sediments have been analysed in order to know the possibility of their use as ceramic raw material or as additive to ceramic stoneware of the valencian tile industry.El lago de la Albufera es Parque Natural por decreto de 8 de Julio de 1989 de la Generalitat Valenciana y está desde el 8 de Mayo de 1990 en el listado de Zonas Húmedas de importancia internacional de la Conferencia de Ramsar. Los estudios de batimetría del lago indican que el lago continúa su proceso lento de colmatación, Si el proceso de colmatación y contaminación persevera o se inducen severas contaminaciones locales por vertidos, es posible que lamentablemente, para preservar la identidad del sistema, sea necesario dragar el lago de forma selectiva y cuidadosa siendo necesario dar un fin último a los fangos obtenidos. En este estudio se analizan las características de los sedimentos de la Albufera de Valencia desde el punto de vista cerámico, con el fin de Conocer las posibles utilizaciones de los mismos para la producción de algún tipo de cerámica o como componentes de adición a pastas cerámicas de la industria azulejera Valenciana.
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- 2003
7. Caracterización medioambiental de residuos de pigmentos cerámicos
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Calbo, J., Llusar, M., Tena, M. A., Vicente, M., and Monrós, G.
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Ceramic pigment ,wastes ,environment ,Pigmentos cerámico ,residuos ,medioambiente ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
Industrial wastes produced by the ceramic pigment industry have been characterized according to chemical and ecotoxicity overview and classified as “Dangerous or Not Dangerous” waste with regard to environmental Spanish Law. Analysis carried out on wastes comming from an industrial pecipitation-sedimentation process indicate that such wastes do not exceed any of the environmental limits checked, if only colorant ions are present; however the industrial practice often give rise to enamel wastes wich present Pb and B levels exceeding legal limits.En el presente trabajo se han caracterizado los residuos generados por la industria de pigmentos cerámicos, desde un punto de vista tanto químico como atendiendo a su ecotoxicidad, clasificándolos después como "Peligrosos o No peligrosos" de acuerdo a la legislación española. Así, los análisis realizados a residuos procedentes del proceso de depuración industrial de precipitación-decantación, indican que tales residuos no superan las concentraciones limite establecidas para ninguno de los contaminantes estudiados, si la componente de estos residuos es únicamente debida a residuos de colorantes. Sin embargo, la práctica habitual tiende a mezclar estos residuos con los de procedencia de esmaltes, que a menudo presentan concentraciones de Pb y B que superan los límites legales.
- Published
- 2002
8. Factores que controlan las propiedades texturales de arcillas intercaladas con disoluciones de circonio y aluminio
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Gil, A., Vicente, M. A., and Gandia, L. M.
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Pillared clays ,interlayer distance ,interpillar distance ,nitrogen adsorption ,Arcillas intercaladas ,distancia interlaminar ,distancia interpilar ,adsorción de nitrógeno ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
The texture development of a saponite and a montmorillonite, intercalated with zirconium and aluminium oligomers, after calcination at 500 ºC has been studied. Remarkable differences were observed among samples, depending on the source of the intercalating polycations and the parent material. On calcining, the alumina pillared clays suffered noticeable specific surface area and micropore volume losses, which have been related to the interlayer and interpillar distances of the samples. On the contrary, the zirconia pillared clays showed a slight surface area increase, which affected both micropores and mesopores and could be due to the combined effect of the thermal decomposition of the zirconium oligomers and the possible presence of mesoporous ZrO2 particles.En este trabajo se ha estudiado la evolución de las propiedades texturales de una saponita y una montmorillonita intercaladas con disoluciones de circonio y aluminio tras calcinación a 500 ºC. Los sólidos presentaron un diferente comportamiento en función de la naturaleza de la disolución de intercalación y de la arcilla empleada. Tras calcinación, la superficie específica y el volumen microporoso de las arcillas intercaladas con disoluciones de aluminio disminuyeron de manera importante, lo cual se ha relacionado con las distancias interlaminar e interpilar que presentaron los materiales intercalados. Por contra, las superficies específicas de las arcillas intercaladas con disoluciones de circonio aumentaron, probablemente gracias al efecto combinado de la descomposición térmica de los ligandos orgánicos unidos al circonio en los policationes y la posible presencia de partículas mesoporosas de ZrO2 sobre la superficie de los sólidos.
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- 2000
9. Occlusion of chromophore oxides by Sol-Gel methods: Application to the synthesis of hematite-silica red pigments
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Vicent, J. B., Llusar, M., Badenes, J., Tena, M. A., Vicente, M., and Monrós, G.
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Pigment ,Oclussion ,Sol-Gel ,Silica ,Pigmento ,Encapsulado ,Sílice ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
Heteromorphic pigments present the chromophore particle occluded in an encapsulating matrix which is thermally stable and insoluble in glazes. The occluded chromophore compound is also insoluble in the host matrix. In this work the mechanisms of formation of this type of pigments are analyzed and the occlusion of hematite into silica matrix is discussed. The formation of this hematite-silica red pigment follows a sintering-coarsening mechanism, and, consequently, the control of both hematite particles nucleation and their crystal growth results to be decisive to obtain a good coloring effectiveness.En los pigmentos heteromórficos la partícula de cromóforo es ocluida en una matriz encapsuladora estable tanto termicamente como frente a los vidriados. El compuesto cromóforo ocluido y la matriz no coloreada son insolubles. En este trabajo se analiza los diferentes mecanismos de formación de estos pigmentos heteromórficos y se estudia la oclusión de hematita en sílice mediante métodos sol-gel acuoso. El pigmento sigue un mecanismo de sinterización-crecimiento cristalino por lo que es muy importante controlar el momento de nucleación y la velocidad de crecimiento de las partículas de hematita en el seno de la matriz.
- Published
- 2000
10. Effect of the synthesis method and praseodymium on the electrical properties of Mg-Cubic Zirconia
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Badenes, J., Forés, A., Vicente, M., Llusar, M., Calbo, J., Tena, M. A., and Monrós, G.
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Cubic zirconia ,synthesis ,praseodymium ,Circona cúbica ,síntesis ,praseodimio ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
The synthesis of nanostructured Mg-FSZ fully stabized zirconia by chemical methods such as colloidal gel, polyester resin and hydrolisis of alkoxides has been studied. The addition of praseodymium ion facilitates cubic stabilization avoiding the Mg- FSZ partitioning with temperature. Praseodymium improve the ionic conductivity of the material probably by the entrance of Pr3+ on the host lattice substitting Zr4+ and subsequently introduction of additional oxygen vacancies trapped near the zirconium ion.En este trabajo se estudia la obtención de circona cúbica estabilizada con magnesio nanoestructurada por métodos químicos tales como el gel coloidal, resina poliester de citrato así como hidrólisis de alcóxidos. La adición de praseodimio mejora la reactividad del sistema y evita la transformación a monoclínica con la temperatura. Asimismo el praseodimio mejora la conductividad iónica del material por un mecanismo de disolución sólida de modo que el Pr3+ introduce nuevas vacantes de oxígeno que podrían quedar asociadas a iones circonio en la red.
- Published
- 1999
11. Meloidogyne enterolobii-induced Changes in Guava Root Exudates Are Associated With Root Rotting Caused by Neocosmospora falciformis
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Souza Ricardo M., Oliveira Denilson F., Gomes Vicente M., Viana Abraão J. S., Silva Geraldo H., and Machado Alan R. T.
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1,5-dinitrobiuret ,disease complex ,guava ,guava decline ,meloidogyne enterolobii ,nematode-fungus interaction ,neocosmospora falciformis ,psidium guajava ,root exudate ,root-knot nematode ,Biology (General) ,QH301-705.5 - Abstract
Despite the worldwide importance of disease complexes involving root-feeding nematodes and soilborne fungi, there have been few in-depth studies on how these organisms interact at the molecular level. Previous studies of guava decline have shown that root exudates from Meloidogyne enterolobii-parasitized guava plants (NP plants), but not from nematode-free plants (NF plants), enable the fungus Neocosmospora falciformis to rot guava roots, leading to plant death. To further characterize this interaction, NP and NF root exudates were lyophilized; extracted with distinct solvents; quantified regarding amino acids, soluble carbohydrates, sucrose, phenols, and alkaloids; and submitted to a bioassay to determine their ability to enable N. falciformis to rot the guava seedlings’ roots. NP root exudates were richer than NF root exudates in amino acids, carbohydrates, and sucrose. Only the fractions NP-03 and NP-04 enabled fungal root rotting. NP-03 was then sequentially fractionated through chromatographic silica columns. At each step, the main fractions were reassessed in bioassay. The final fraction that enabled fungal root rotting was submitted to analysis using high performance liquid chromatography, nuclear magnetic resonance, mass spectrometry, energy-dispersive X-ray fluorescence, and computational calculations, leading to the identification of 1,5-dinitrobiuret as the predominant substance. In conclusion, parasitism by M. enterolobii causes an enrichment of guava root exudates that likely favors microorganisms capable of producing 1,5-dinitrobiuret in the rhizosphere. The accumulation of biuret, a known phytotoxic substance, possibly hampers root physiology and the innate immunity of guava to N. falciformis.
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- 2023
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12. Sexual dimorphism of Dyschiriini (Coleoptera, Carabidae): Comparative morphological SEM study of palpi sensilla and its possible role in intraspecific chemical communication
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Muñoz-Santiago, José and Ortuño, Vicente M.
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- 2024
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13. Consumer attitudes and perceptions towards chilled ready-to-eat foods: a multi-national study
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Smigic, Nada, Ozilgen, Sibel, Gómez-López, Vicente M., Osés, Sandra María, Miloradovic, Zorana, Aleksic, Biljana, Miocinovic, Jelena, Smole Možina, Sonja, Kunčič, Ajda, Guiné, Raquel, Gonçalves, João Carlos, Trafialek, Joanna, Czarniecka-Skubina, Ewa, Goel, Gunjan, Blazic, Marijana, Herljevic, Dora, Nikolić, Aleksandra, Mujčinović, Alen, and Djekic, Ilija
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- 2023
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14. Test-beam characterisation of the CLICTD technology demonstrator - a small collection electrode High-Resistivity CMOS pixel sensor with simultaneous time and energy measurement
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Ballabriga, R., Buschmann, E., Campbell, M., Dannheim, D., Dort, K., Egidos, N., Huth, L., Kremastiotis, I., Kröger, J., Linssen, L., Llopart, X., Munker, M., Nürnberg, A., Snoeys, W., Spannagel, S., Vanat, T., Vicente, M., and Williams, M.
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Physics - Instrumentation and Detectors ,High Energy Physics - Experiment - Abstract
The CLIC Tracker Detector (CLICTD) is a monolithic pixel sensor. It is fabricated in a 180 nm CMOS imaging process, modified with an additional deep low-dose n-type implant to obtain full lateral depletion. The sensor features a small collection diode, which is essential for achieving a low input capacitance. The CLICTD sensor was designed as a technology demonstrator in the context of the tracking detector studies for the Compact Linear Collider (CLIC). Its design characteristics are of broad interest beyond CLIC, for HL-LHC tracking detector upgrades. It is produced in two different pixel flavours: one with a continuous deep n-type implant, and one with a segmented n-type implant to ensure fast charge collection. The pixel matrix consists of $16\times128$ detection channels measuring $300 \times 30$ microns. Each detection channel is segmented into eight sub-pixels to reduce the amount of digital circuity while maintaining a small collection electrode pitch. This paper presents the characterisation results of the CLICTD sendor in a particle beam. The different pixel flavours are compared in detail by using the simultaneous time-over-threshold and time-of-arrival measurement functionalities. Most notably, a time resolution down to $(5.8 \pm 0.1)$ ns and a spatial resolution down to $(4.6 \pm 0.2)$ microns are measured. The hit detection efficiency is found to be well above 99.7% for thresholds of the order of several hundred electrons.
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- 2021
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15. It's more complicated than it seems: understanding nonverbal indicators of sexual consent among college students
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Harrell, Kristen, Lechuga, Vicente M., and Hudock, Marigold M.
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- 2023
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16. Use of YOLOv4 and Yolov4Tiny for Intelligent Vehicle Detection in Smart City Environments
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de la Iglesia, Daniel H., Blas, Héctor Sánchez San, López, Vivian F., Moreno-García, María N., Vicente, M. Dolores Muñoz, Ovejero, Raul Garcia, Villarrubia, Gabriel, de Paz Santana, Juan F., Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, de la Iglesia, Daniel H., editor, de Paz Santana, Juan F., editor, and López Rivero, Alfonso J., editor
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- 2023
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17. Instalaciones rurales del Hierro Antiguo en el Valle del Tajo, en su contexto europeo. El yacimiento de Soto del Henares (Torrejón de Ardoz, Madrid)/Rural installations of Early Iron Age in the Tagus Valley, in its European context. The Soto del Henares deposit (Torrejón de Ardoz, Madrid)
- Author
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Blasco, Concepción, Galindo, Lorenzo, Sánchez, Vicente M., and RÃos, Patricia
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- 2023
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18. A session-based song recommendation approach involving user characterization along the play power-law distribution
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Sánchez-Moreno, Diego, Batista, Vivian F. López, Vicente, M. Dolores Muñoz, González, Ana B. Gil, and Moreno-García, María N.
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Computer Science - Information Retrieval ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning ,Computer Science - Sound ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
In recent years, streaming music platforms have become very popular mainly due to the huge number of songs these systems make available to users. This enormous availability means that recommendation mechanisms that help users to select the music they like need to be incorporated. However, developing reliable recommender systems in the music field involves dealing with many problems, some of which are generic and widely studied in the literature, while others are specific to this application domain and are therefore less well-known. This work is focused on two important issues that have not received much attention: managing gray-sheep users and obtaining implicit ratings. The first one is usually addressed by resorting to content information that is often difficult to obtain. The other drawback is related to the sparsity problem that arises when there are obstacles to gather explicit ratings. In this work, the referred shortcomings are addressed by means of a recommendation approach based on the users' streaming sessions. The method is aimed at managing the well-known power-law probability distribution representing the listening behavior of users. This proposal improves the recommendation reliability of collaborative filtering methods while reducing the complexity of the procedures used so far to deal with the gray-sheep problem., Comment: Accepted in Complexity (ISSN: 1099-0526)
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- 2020
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19. Correction for Castaño-Rodriguez et al., 'Role of Severe Acute Respiratory Syndrome Coronavirus Viroporins E, 3a, and 8a in Replication and Pathogenesis'
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Carlos Castaño-Rodríguez, Jose M. Honrubia, Javier Gutierrez-Álvarez, Marta L. DeDiego, Jose L. Nieto-Torres, Jose M. Jimenez-Guardeño, Jose A. Regla-Nava, Raul Fernandez-Delgado, Carmina Verdia-Báguena, Maria Queralt-Martín, Grazyna Kochan, Stanley Perlman, Vicente M. Aguilella, Isabel Sola, and Luis Enjuanes
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Microbiology ,QR1-502 - Published
- 2023
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20. Cross preferences and genetic diversity of Psidium interspecific hybrids through morphoagronomic traits and resistance to Meloidogyne enterolobii
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ODIMAR F. DE ALMEIDA, ALEXANDRE P. VIANA, VICENTE M. GOMES, RICARDO M. DE SOUZA, PAULO RICARDO DOS SANTOS, ANTÔNIO T. DO AMARAL JÚNIOR, and DANIELE L. RODRIGUES
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Genetic diversity ,guava decline ,interspecific hybridization ,root-knot nematode ,ward-MLM ,Science - Abstract
Abstract The introgression of M. enterolobii resistance-related genes in guava breeding programs can be compromised by incompatibility among Psidium species. This study aimed to evaluate the female parent preference and genetic diversity of Psidium interspecific hybrids using morphoagronomic traits and resistance to M. enterolobii. There were evaluated cross successes and germination from crosses between accesses of P. cattleyanum, P. guineense and P. guajava and the genetic diversity by Ward-MLM method of hybrids according to descriptors developed for the genus. Crosses were more successful when P. cattleyanum was the female parent. Germination was more successful in crosses involving P. cattleyanum and P. guajava. Four groups were formed. The group IV clustered the most resistant genotypes, composed by genotypes of P. cattleyanum x P. guineense, while the group II was the most susceptible. The groups I and III grouped some genotypes of P. cattleyanum x P. guajava with low levels of susceptibility. There are preferences of female parent species among crosses. Some individuals of groups I and III can be used as source of resistance genes for the breeding program, due the presence of favorable alleles inherited from guava parent. The high susceptibility leads to reduction in root development.
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- 2023
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21. Tracking performance and simulation of capacitively coupled pixel detectors for the CLIC vertex detector
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Alipour~Tehrani, N., Benoit, M., Buckland, M., Dannheim, D., Fiergolski, A., Green, S., Hynds, D., Kremastiotis, I., Kulis, S., Munker, M., Nürnberg, A., Peric, I., Petric, M., Sicking, E., and Vicente, M.
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Physics - Instrumentation and Detectors ,High Energy Physics - Experiment - Abstract
In order to achieve the challenging requirements on the CLIC vertex detector, a range of technology options have been considered in recent years. One prominent idea is the use of active sensors implemented in a commercial high-voltage CMOS process, capacitively coupled to hybrid pixel readout chips. Recent results have shown the approach to be feasible, though more detailed studies of the performance of such devices, including simulation, are required. The CLICdp collaboration has developed a number of ASICs as part of its vertex detector R&D programme, and here we present results on the performance of a CCPDv3 active sensor glued to a CLICpix readout chip. Charge collection characteristics and tracking performance have been measured over the full expected angular range of incident particles using 120 GeV/c secondary hadron beams from the CERN SPS. Single hit efficiencies have been observed above 99% in the full range of track incidence angles, down to shallow angles. The single hit resolution has also been observed to be stable over this range, with a resolution around 6 $\mu$m. The measured charge collection characterstics have been compared to simulations carried out using the Sentaurus TCAD finite-element simulation package combined with circuit simulations and parametrisations of the readout chip response. The simulations have also been successfully used to reproduce electric fields, depletion depths and the current-voltage characteristics of the device, and have been further used to make predictions about future device designs.
- Published
- 2019
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22. Chlorine dioxide
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Gómez-López, Vicente M., primary
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- 2023
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23. Digging into the admixture strata of current-day Canary Islanders based on mitogenomes
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García-Olivares, Víctor, Rubio-Rodríguez, Luis A., Muñoz-Barrera, Adrián, Díaz-de Usera, Ana, Jáspez, David, Iñigo-Campos, Antonio, Rodríguez Pérez, María Del Cristo, Cabrera de León, Antonio, Lorenzo-Salazar, José M., González-Montelongo, Rafaela, Cabrera, Vicente M., and Flores, Carlos
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- 2023
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24. POS0908 THE IMPACT OF ANTI-RO52 ANTIBODIES ON MICROCIRCULATION AND ORGAN INVOLVEMENT IN AUTOIMMUNE CONNECTIVE TISSUE DISEASES
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Bernardino, V., primary, Rodrigues, A., additional, Fernandes, M., additional, Llado, A., additional, Vicente, M., additional, Botelho de Sousa, M., additional, Vieira, R., additional, Martinho, R., additional, Dias, S., additional, Gomes, A. R., additional, Taulaigo, A., additional, Guerreiro Castro, S., additional, Patarata, E., additional, and Gruner, H., additional
- Published
- 2024
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25. Top-Quark Physics at the CLIC Electron-Positron Linear Collider
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Abramowicz, H., Tehrani, N. Alipour, Arominski, D., Benhammou, Y., Benoit, M., Blaising, J. -J., Boronat, M., Borysov, O., Bosley, R. R., Jelisavčić, I. Božović, Boyko, I., Brass, S., Brondolin, E., de Renstrom, P. Bruckman, Buckland, M., Burrows, P. N., Chefdeville, M., Chekanov, S., Coates, T., Dannheim, D., Demarteau, M., Denizli, H., Durieux, G., Eigen, G., Elsener, K., Fullana, E., Fuster, J., Gabriel, M., Gaede, F., García, I., Goldstein, J., Lopez, P. Gomis, Graf, C., Green, S., Grefe, C., Grojean, C., Hoang, A., Hynds, D., Joffe, A., Kalinowski, J., Kačarević, G., Kilian, W., van der Kolk, N., Krawczyk, M., Kucharczyk, M., Leogrande, E., Lesiak, T., Levy, A., Levy, I., Linssen, L., Maier, A. A., Makarenko, V., Marshall, J. S., Martin, V., Mateu, V., Matsedonskyi, O., Metcalfe, J., Dumbelović, G. Milutinović, Münker, R. M., Nefedov, Yu., Nowak, K., Nürnberg, A., Pandurović, M., Perelló, M., Codina, E. Perez, Petric, M., Pitters, F., Price, T., Quast, T., Redford, S., Repond, J., Robson, A., Roloff, P., Ros, E., Rozwadowska, K., Ruiz-Jimeno, A., Sailer, A., Salvatore, F., Schnoor, U., Schulte, D., Senol, A., Shelkov, G., Sicking, E., Simon, F., Simoniello, R., Sopicki, P., Spannagel, S., Stapnes, S., Ström, R., Szalay, M., Thomson, M. A., Turbiarz, B., Viazlo, O., Vicente, M., Vila, I., Vos, M., Vossebeld, J., Watson, M. F., Watson, N. K., Weber, M. A., Weerts, H., Wells, J. D., Widl, A., Williams, M., Winter, A. G., Wojtoń, T., Wulzer, A., Xu, B., Xia, L., You, T., Żarnecki, A. F., Zawiejski, L., Zhang, C., Zhang, J., Zhang, Y., Zhang, Z., and Zhemchugov, A.
- Subjects
High Energy Physics - Experiment ,High Energy Physics - Phenomenology - Abstract
The Compact Linear Collider (CLIC) is a proposed future high-luminosity linear electron-positron collider operating at three energy stages, with nominal centre-of-mass energies: 380 GeV, 1.5 TeV, and 3 TeV. Its aim is to explore the energy frontier, providing sensitivity to physics beyond the Standard Model (BSM) and precision measurements of Standard Model processes with an emphasis on Higgs boson and top-quark physics. The opportunities for top-quark physics at CLIC are discussed in this paper. The initial stage of operation focuses on top-quark pair production measurements, as well as the search for rare flavour-changing neutral current (FCNC) top-quark decays. It also includes a top-quark pair production threshold scan around 350 GeV which provides a precise measurement of the top-quark mass in a well-defined theoretical framework. At the higher-energy stages, studies are made of top-quark pairs produced in association with other particles. A study of ttH production including the extraction of the top Yukawa coupling is presented as well as a study of vector boson fusion (VBF) production, which gives direct access to high-energy electroweak interactions. Operation above 1 TeV leads to more highly collimated jet environments where dedicated methods are used to analyse the jet constituents. These techniques enable studies of the top-quark pair production, and hence the sensitivity to BSM physics, to be extended to higher energies. This paper also includes phenomenological interpretations that may be performed using the results from the extensive top-quark physics programme at CLIC., Comment: 86 pages, accepted for publication in JHEP
- Published
- 2018
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26. Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands.
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Fregel, Rosa, Ordóñez, Alejandra C, Santana-Cabrera, Jonathan, Cabrera, Vicente M, Velasco-Vázquez, Javier, Alberto, Verónica, Moreno-Benítez, Marco A, Delgado-Darias, Teresa, Rodríguez-Rodríguez, Amelia, Hernández, Juan C, Pais, Jorge, González-Montelongo, Rafaela, Lorenzo-Salazar, José M, Flores, Carlos, Cruz-de-Mercadal, M Carmen, Álvarez-Rodríguez, Nuria, Shapiro, Beth, Arnay, Matilde, and Bustamante, Carlos D
- Subjects
Mitochondria ,Humans ,Sequence Analysis ,DNA ,Genetics ,Population ,Genetic Drift ,Ethnic Groups ,Transients and Migrants ,Africa ,Northern ,Middle East ,Europe ,Spain ,Genome ,Mitochondrial ,Phylogeography ,High-Throughput Nucleotide Sequencing ,MD Multidisciplinary ,General Science & Technology - Abstract
The Canary Islands' indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.
- Published
- 2019
27. Using TD-NMR relaxometry to assess the effects of diet type and stocking rate on the incidence and degree of severity of myopathies in broilers
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Cônsolo, Nara R.B., Barbosa, Luis C.G.S., Moraes, Tiago B., Buraque, Vicente M., Colnago, Luiz A., Queiroz Júnior, Luiz H.K., Oliveira, Vitor M., Hannaford, Rina, Araújo, Cristiane S.S., Roque, Fabrícia de A., Granghelli, Carlos A., Fonseca, André C., and Araújo, Lucio F.
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- 2022
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28. Los Carabidae (Insecta: Coleoptera) del valle de Salientes (León, norte de España): fauna, corología y notas taxonómicas
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Vicente M. Ortuño, Óscar Arribas, and Elena Andrés
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Carábidos ,Trechus suturalis ,Trechus gallaecus ,Trechus teverganus ,Oreophilus ,abundancia ,Zoology ,QL1-991 - Abstract
El valle de Salientes (norte de León, España) es un área situada inmediatamente al sur del eje principal de la Cordillera Cantábrica, de la que se halla relativamente aislada debido a los procesos erosivos producidos entre las cabeceras de los ríos Sil y Luna. Este hecho histórico/geológico convierte a este valle en un enclave muy singular y a su biota en un interesante objetivo de estudio. Este trabajo, con un enfoque faunístico, aporta información sobre Carabidae (Insecta, Coleoptera) que habitan en esta área. Se realizaron cuatro campañas entomológicas en tres años consecutivos, donde se recogieron 1255 especímenes, pertenecientes a 101 especies, en 61 puntos de muestreo, mediante captura activa e instalación de trampas pitfall. Los resultados revelan que, en términos de diversidad específica y abundancia, la mayoría de los ejemplares pertenecen a la subfamilia Harpalinae, teniendo especial relevancia Harpalini (18 spp, 167 exx), Zabrini (11 spp, 55 exx), Pterostichini (10 spp, 200 exx), Sphodrini (9 spp, 150 exx) y Platynini (6 spp, 83 exx). Además, se realizó un análisis biogeográfico que puso de manifiesto la elevada contribución que hacen los endemismos ibéricos en la composición faunística de los Carabidae de este enclave geográfico. Finalmente, se discuten aspectos taxonómicos de algunas especies colectadas: 1) el caso de Trechus (Trechus) suturalis Putzeys, 1870 y Trechus (Trechus) gallaecus Jeannel, 1921, cuya morfologíadel edeago, ilustrada en este trabajo, es clave para la distinción inequívoca de ambas especies; 2) también se pone de manifiesto la gran variabilidad observada respecto a los caracteres externos de dos especies ibéricas de Oreophilus Chaudoir, 1838, Pterostichus (O.) cantaber (Chaudoir, 1868) y Pterostichus (O.) franzi Nègre, 1955, concluyendo que no son lo suficientemente consistentes, teniendo que recurrir a la morfología del edeago como único carácter totalmente fiable para identificar ambas especies. Además, se aportan comentarios en relación con la autoecología y preferencia de hábitat (áreas forestales, riparias/palustres, ruderales y subterráneas) de las especies más representativas. Por último, se amplía el rango de distribución del microendemismo Trechus teverganus Toribio, 2015, a pesar de las aparentes barreras geográficas y geológicas que podrían existir para esta especie de vida subterránea.
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- 2023
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29. Post-fire management effects on hillslope-stream sediment connectivity in a Mediterranean forest ecosystem
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González-Romero, J., López-Vicente, M., Gómez-Sánchez, E., Peña-Molina, E., Galletero, P., Plaza-Álvarez, P., Fajardo-Cantos, A., Moya, D., De las Heras, J., and Lucas-Borja, M.E.
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- 2022
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30. Strengthening global institutional philanthropy: insights from an organisational capacity index in Latin America1
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Bird, Matthew D. and León, Vicente M.
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- 2024
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31. Influencing variables on total and free 25(OH)D levels in healthy population
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Fernández-Vicente, M., Miján-de-la-Torre, A., Vella-Ramírez, J.C., Martí-Bonmatí, E., Benito-Ibáñez, V.V., and Martínez-de-Arriba, R.
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- 2022
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32. Variables influyentes en los niveles de 25(OH)D total y libre en población sana
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Fernández-Vicente, M., Miján-de-la-Torre, A., Vella-Ramírez, J.C., Martí-Bonmatí, E., Benito-Ibáñez, V.V., and Martínez-de-Arriba, R.
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- 2022
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33. SARS-CoV-2 accessory protein 7b forms homotetramers in detergent
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Surya, Wahyu, Queralt-Martin, Maria, Mu, Yuguang, Aguilella, Vicente M., and Torres, Jaume
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- 2022
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34. Use of YOLOv4 and Yolov4Tiny for Intelligent Vehicle Detection in Smart City Environments
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de la Iglesia, Daniel H., primary, Blas, Héctor Sánchez San, additional, López, Vivian F., additional, Moreno-García, María N., additional, Vicente, M. Dolores Muñoz, additional, Ovejero, Raul Garcia, additional, Villarrubia, Gabriel, additional, and de Paz Santana, Juan F., additional
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- 2022
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35. DA EVIDÊNCIA SOCIAL À CULTURA BRASILEIRA: o jeitinho brasileiro em Lima Barreto, Tarsila do Amaral e Ariano Suassuna
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Nunes de Jesus, Sérgio, primary, VICENTE, M. F., additional, ALGAYER, A. C., additional, and MOREIRA, F. G., additional
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- 2022
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36. METAMORFOSES: leituras da poesia contemporânea brasileira
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VICENTE, M. F., primary, Nunes de Jesus, Sérgio, additional, and DAMASCENO, A. C. S., additional
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- 2022
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37. O PROCESSO DE EVOLUÇÃO DA LÍNGUA: por uma questão histórica e linguística
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Bindaco, Ronilse Bonfá, primary, Nunes de Jesus, Sérgio, additional, BERTÓCHI, C. A., additional, VICENTE, M. F., additional, and MORAIS, Elizângela Ataíde de Souza, additional
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- 2022
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38. Digging into the admixture strata of current-day Canary Islanders based on mitogenomes
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Víctor García-Olivares, Luis A. Rubio-Rodríguez, Adrián Muñoz-Barrera, Ana Díaz-de Usera, David Jáspez, Antonio Iñigo-Campos, María Del Cristo Rodríguez Pérez, Antonio Cabrera de León, José M. Lorenzo-Salazar, Rafaela González-Montelongo, Vicente M. Cabrera, and Carlos Flores
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Molecular biology ,Genomics ,Anthropology ,Human Geography ,Science - Abstract
Summary: The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.
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- 2023
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39. Coexistence of immune-mediated diseases in sarcoidosis. Frequency and clinical significance in 1737 patients
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De-Escalante, B., Chara-Cervantes, J., Pérez-Conesa, M., Rascón, J., Pallarés, L., Perez-Guerrero, P., De-la-Red, G., Calvo, E., Soler, C., Peral-Gutiérrez, E., Gómez-Cerezo, J.F., Rodríguez-Fernández, S., Pinilla, B., Toledo-Samaniego, N., Gato, A., Chamorro, A.J., Morcillo, C., Ojeda, I., Vives, M.J., de-Miguel, B., Penadés, M., De-Vicente, M., Brito-Zerón, Pilar, Pérez-Alvarez, Roberto, Feijoo-Massó, Carles, Gracia-Tello, Borja, González-García, Andres, Gómez-de-la-Torre, Ricardo, Alguacil, Ana, López-Dupla, Miguel, Robles, Angel, Garcia-Morillo, Salvador, Bonet, Mariona, Cruz-Caparrós, Gracia, Fonseca-Aizpuru, Eva, Akasbi, Miriam, Callejas, Jose Luis, de Miguel-Campo, Borja, Pérez-de-Lis, Marta, and Ramos-Casals, Manuel
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- 2021
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40. Loss of pitx2c causes early alterations in atrial calcium handling in zebrafish
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Vicente, M, primary, Cevallos-Salvador, M P, additional, Martinez-Sielva, A, additional, Collins, M M, additional, Salgado-Almario, J, additional, Domingo, B, additional, and Llopis, J, additional
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- 2024
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41. The RGK protein rrad regulates cardiac calcium levels in zebrafish
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Salgado-Almario, J, primary, Martinez-Sielva, A, additional, Mercedes, P, additional, Vicente, M, additional, Domingo, B, additional, and Llopis, J, additional
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- 2024
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42. The role of cover crops in the loss of protected and non-protected soil organic carbon fractions due to water erosion in a Mediterranean olive grove
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López-Vicente, M., Gómez, J.A., Guzmán, G., Calero, J., and García-Ruiz, R.
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- 2021
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43. Electromagnetic Technologies in Food Science
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Vicente M. Gómez-López, Rajeev Bhat, Vicente M. Gómez-López, Rajeev Bhat
- Published
- 2021
44. Spherical Distance Metrics Applied to Protein Structure Classification
- Author
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DeFelice, James and Reyes, Vicente M.
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Quantitative Biology - Biomolecules - Abstract
Structural relationships among proteins are important in the study of their evolution as well as in drug design and development. The protein 3D structure has been shown to be effective with respect to classifying proteins. Prior work has shown that the Double Centroid Reduced Representation (DCRR) model is a useful geometric representation for protein structure with respect to visual models, reducing the quantity of modeled information for each amino acid, yet retaining the most important geometrical and chemical features of each: the centroids of the backbone and of the side-chain. DCRR has not yet been applied in the calculation of geometric structural similarity. Meanwhile, multi-dimensional indexing (MDI) of protein structure combines protein structural analysis with distance metrics to facilitate structural similarity queries and is also used for clustering protein structures into related groups. In this respect, the combination of geometric models with MDI has been shown to be effective. Prior work, notably Distance and Density based Protein Indexing (DDPIn), applies MDI to protein models based on the geometry of the CA backbone. DDPIn distance metrics are based on radial and density functions that incorporate spherical-based metrics, and the indices are built from metric tree (M-tree) structures. This work combines DCRR with DDPIn for the development of new DCRR centroid-based metrics: spherical binning distance and inter-centroid spherical distance. The use of DCRR models will provide additional significant structural information via the inclusion of side-chain centroids. Additionally, the newly developed distance metric functions combined with DCRR and M-tree indexing attempt to improve upon the performance of prior work (DDPIn), given the same data set, with respect to both individual k-nearest neighbor (kNN) search queries as well as clustering all proteins in the index., Comment: 48 pages, 8 figures, 6 tables
- Published
- 2015
45. A Cancer Biotherapy Resource
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Priya, Preety and Reyes, Vicente M.
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Quantitative Biology - Biomolecules ,Quantitative Biology - Tissues and Organs - Abstract
Cancer Biotherapy (CB), as opposed to cancer chemotherapy, is the use of macromolecular, biological agents instead of organic chemicals or drugs to treat cancer. Biological agents usually have higher selectivity and have less toxic side effects than chemical agents. The I.S.B.T.C., being the only major information database for CB, seems lacking in some crucial information on various cancer biotherapy regimens. It is thus necessary to have a comprehensive curated CB database. The database accessible to cancer patients and also should be a sounding board for scientific ideas by cancer researchers. The database/web server has information about main families of cancer biotherapy regimens to date, namely, Protein Kinase Inhibitors, Ras Pathway Inhibitors, Cell-Cycle Active Agents, MAbs (monoclonal antibodies), ADEPT (Antibody-Directed Enzyme Pro-Drug Therapy), Cytokines, Anti-Angiogenesis Agents, Cancer Vaccines, Cell-based Immunotherapeutics, Gene Therapy, Hematopoietic Growth Factors, Retinoids, and CAAT. For each biotherapy regimen, we will extract the following attributes in populating the database: Cancer type, Gene/s and gene product/s involved, Gene sequence, Organs affected, Reference papers, Clinical phase/stage, Survival rate, Clinical test center locations, Cost, Patient blogs, Researcher blogs, and Future work. The database will be accessible to public through a website and had FAQs for making it understandable to the laymen and discussion page for researchers to express their views and ideas. In addition to information about the biotherapy regimens, the website will link to other biologically significant databases like structural proteomics, metabolomics, glycomics, and lipidomics databases, as well as to news around the world regarding cancer therapy results. The database attributes would be regularly updated for novel attributes as discoveries are made., Comment: 65 pages, 30 figures, 1 table
- Published
- 2015
46. Representing Rod-Shaped Protein 3D Structures in Cylindrical Coordinates
- Author
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Cheguri, Srujana and Reyes, Vicente M.
- Subjects
Quantitative Biology - Biomolecules - Abstract
Based on overall 3D structure, proteins may be grouped into two broad categories, namely, globular proteins (spheroproteins), and elongated or rod-shaped proteins (RSP). The former comprises a significant majority of proteins. This work concerns the second category. Unlike a spheroprotein, an RSP possesses a conspicuous axis along its longest dimension. To take advantage of this symmetry element, we decided to represent RSPs using cylindrical coordinates, (rho, theta, z), with the z-axis as the main axis, and one tip of the protein at the origin. A "tip" is one of two extreme points in the protein lying along the protein axis along its longest dimension. We first identify the two tips, T1 and T2, of the RSP using a protein graphics software, then determine their (Cartesian) coordinates, (h, k, l) and (m, n, o), respectively. Arbitrarily selecting T1 as the tip at the origin, we translate the protein by subtracting (h, k, l) from all structural coordinates. We then find the angle alpha between vector T1-T2 and the positive z-axis by computing the scalar product of vectors T1- T2 and OP where P is an arbitrary point along the positive z-axis. We typically use (0, 0, p) where p is a suitable positive number. Then we compute the cross product of the two vectors to determine the axis about which we should rotate vector T1-T2 to make it coincide with the positive z-axis. We use a matrix form of Rodrigues' formula to do the rotation. We then apply the Cartesian to cylindrical coordinate transformation equations to the system. We have applied the above transformation to 15 RSPs: 1QCE, 2JJ7, 2KPE, 3K2A, 3LHP, 2LOE, 2L3H, 2L1P, 1KSG, 1KSJ, 1KSH, 2KOL, 2KZG, 2KPF and 3MQC. We have also created a web server that can take the PDB coordinate file of an RSP and output its cylindrical coordinates. The URL of our web server will be announced publicly in due course., Comment: 40 pages, 14 figures, 1 table
- Published
- 2015
47. Prediction of Flavin Mononucleotide (FMN) Binding Sites in Proteins Using the 3D Search Motif Method and Double-Centroid Reduced Representation of Protein 3D Structures
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Banerjee, Arkanjan and Reyes, Vicente M.
- Subjects
Quantitative Biology - Biomolecules - Abstract
A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express the biological and pharmacological effects of the ligand. It is usually a substructure of the entire structure of the ligand. Small organic molecules called ligands or metabolites in the cell form complexes with biomolecules (usually proteins) to serve different purposes. The sites at which the ligands bind are known as ligand binding sites, which are essentially "pockets" which have complementary shapes and patterns of charge distribution with the ligands. Sometimes a pocket is induced by the ligand itself. If we study different bound conformations of ligands it is found that they share a specific three- dimensional pattern that is more or less common and is responsible for its binding and which is complementary in three-dimensional geometry and charge distribution pattern with its cognate binding site in the protein. This work studies the three dimensional structure of the consensus ligand binding site for the ligand FMN. A training set for the ligand binding sites was made and a 3D consensus binding site motif was determined for FMN. The FMN system was studied and its binding sites in its respective regulator proteins. The ability to identify ligand binding site by scanning the 3D binding site consensus motif in protein 3D structures is an important step in drug target discovery. Once a pharmacophore template is found it can also be used to design other potential molecules that can bind to it and thus serve as novel drugs., Comment: 72 pages, 19 figures, 6 tables
- Published
- 2015
48. Visualization of Protein 3D Structures in Reduced Representation with Simultaneous Display of Intra- and Inter-Molecular Interactions
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Sheth, Vrunda and Reyes, Vicente M.
- Subjects
Quantitative Biology - Biomolecules - Abstract
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require. Currently there is no available method of protein 3D structure representation which captures enough chemical information from the protein sequence and clearly shows the intra-molecular and the inter-molecular H-bonds and VDW interactions at the same time. This project aims to reduce the 3D structure of a protein and display the reduced representation along with intermolecular and the intra- molecular H-bonds and van der Waals interactions. A reduced protein representation has a significantly lower atomicity (i.e., number of atom coordinates) than one which is in all- atom representation. In this work, we transform the protein structure from all-atom representation" (AAR) to double-centroid reduced representation (DCRR), which contains amino acid backbone (N, CA, C', O) and side chain (CB and beyond) centroid coordinates instead of atomic coordinates. Another aim of this project is to develop a visualization interface for the reduced representation. This interface is implemented in MATLAB and displays the protein in DCRR along with its inter-molecular, as well as intra-molecular, interaction. Visually, DCRR is easier to comprehend than AAR. We also developed a Web Server called the Protein DCRR Web Server wherein users can enter the PDB id or upload a modeled protein and get the DCRR of that protein. The back end to the Web Server is a database which has the reduced representation for all the x-ray crystallographic structure in the PDB., Comment: 72 pages, 24 figures, 2 tables
- Published
- 2015
49. Size-Independent Quantification of Ligand Binding Site Depth in Receptor Proteins
- Author
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Cheguri, Srujana and Reyes, Vicente M.
- Subjects
Quantitative Biology - Biomolecules - Abstract
We have developed a web server that implements two complementary methods to quantify the depth of ligand binding site (LBS) in protein-ligand complexes: the "secant plane" (SP) and "tangent sphere" (TS) methods. The protein molecular centroid (global centroid, GC), and the LBS centroid (local centroid, LC) are first determined. The SP is the plane passing through the LC and normal to the line passing through the LC and the GC. The "exterior side" of the SP is the side opposite GC. The TS is the sphere with center at GC and tangent to the SP at LC. The percentage of protein atoms inside the TS (TS index) and on the exterior side of the SP (SP index), are complementary measures of LBS depth. The SPi is directly proportional to LBS depth while the TSi is inversely proportional. We tested the two methods using a test set of 67 well-characterized protein-ligand structures (Laskowski, et al. 1996), as well as that of an artificial protein in the form of a grid of points in the overall shape of a sphere and in which LBS of any depth can be specified. Results from both the SP and TS methods agree well with reported data (ibid.), and results from the artificial case confirm that both methods are suitable measures of LBS depth. The web server may be used in two modes. In the "ligand mode", user inputs the protein PDB coordinates as well as those of the ligand. The "LBS mode" is the same as the former, except that the ligand coordinates are assumed to be unavailable; hence the user inputs what s/he believes to be the coordinates of the LBS amino acid residues. In both cases, the web server outputs the SP and TS indices. LBS depth is usually directly related to the amount of conformational change a protein undergoes upon ligand binding - ability to quantify it could allows meaningful comparison of protein flexibility and dynamics. The URL of our web server will be announced publicly in due course., Comment: 51 pages, 9 figures, 1 table
- Published
- 2015
50. Effect of pH on pulsed light inactivation of polyphenol oxidase
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Pellicer, José A., Gabaldón, José A., and Gómez-López, Vicente M.
- Published
- 2021
- Full Text
- View/download PDF
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