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2. Numerical modeling of the dynamic strain aging in steels at high strain rates and high temperatures

Author

Rubio R. A. and Hokka M.

Subjects
Physics, QC1-999
Abstract

Carbon steels can be heat treated to produce different microstructural variations and mechanical properties. At high temperatures the material plasticity and strength can be influenced by diffusional effects like the Portevin-Le Chatelier effect, leading to a commonly observed increased strength at elevated temperatures. The diffusional effects are influenced by the chemical composition, but also the heat treatment history that affects the local composition and especially the concentrations of free solute atoms. In this work, a numerical approach was implemented to reproduce the thermomechanical behaviour of two different microstructural variants of steel grade C45. The experimental data used to calibrate the model includes information of the plastic behaviour of material subjected to dynamic compression loading at a wide range of temperatures. Special emphasis was focused to describe the effects of the dynamic strain aging (DSA) on the flow stress. A strategy based on machine learning was implemented to obtain a model that reproduces the strengthening of the material due to diffusional effects. Cubic Support Vector Machine models were trained for both microstructure variants of the steel and different surfaces were obtained to describe the topology of the flow stress as function of temperature and strain rate. The model predictions were compared to the behaviour described by the Johnson-Cook model to estimate the influence of the DSA effect on the strength of the material at high strain rates and temperatures. Furthermore, the model quantifies how the microstructure affects the strength of the material and the strength of the DSA-hardening.

Published
2021
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5. Modified TruSeq Small RNA Library Prep using Randomized 4N Adapters: In house 4N Protocol D

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2023

6. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol C

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2023

7. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol B

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2023

8. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol A

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2023

9. Rotating Micro-Spheres for Adsorption Monitoring at a Fluid Interface

Author

Martín-Roca, J., Jiménez, M., Ortega, F., Calero, C., Valeriani, Ch., Rubio, R. G., and Martínez-Pedrero, F.

Subjects
Condensed Matter - Soft Condensed Matter, Condensed Matter - Other Condensed Matter
Abstract

Hypothesis: A broad range of phenomena, such as emulsification and emulsion stability, foam formation or liquid evaporation, are closely related to the dynamics of adsorbing colloidal particles. Elucidation of the mechanisms implied is key to a correct design of many different types of materials. Experiments: Microspheres forced to rotate near a fluid interface exhibit a roto-translational hydrodynamic mechanism that is hindered by capillary torques as soon as the particles protrude the interface. Under these conditions, the time evolution in the ratio of moving spheres provides a direct description of the adsorption kinetics, while microscopy monitoring of particle acceleration\deceleration informs about the adsorption\desorption dynamics. In this work, the proposed strategy is applied at an air/water interface loaded with spherical magnetic particles negatively charged, forced to rotate by the action of a rotating magnetic field. Findings: The proposed method enables the adsorption/desorption dynamics to be followed during the earliest phase of the process, when desorption of a small fraction of particles is detected, as well as to estimate approximated values of the adsorption/desorption constants. The results obtained show that the addition of a monovalent salt or a cationic (anionic) surfactant promotes (inhibits) both adsorption and formation of permanent bonds between particles.

Published
2022
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10. Search for fast radio transients using Arecibo drift-scan observations at 1.4 GHz

Author

Perera, B. B. P., Smith, A. J., Vaddi, S., Carballo-Rubio, R., McGilvray, A., Venkataraman, A., Roshi, D. Anish, Manoharan, P. K., Perillat, P., Lieb, E., Lorimer, D. R., McLaughlin, M. A., Agarwal, D., Aggarwal, K., and Ransom, S. M.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

We conducted a drift-scan observation campaign using the 305-m Arecibo telescope in January and March 2020 when the observatory was temporarily closed during the intense earthquakes and the initial outbreak of the COVID-19 pandemic, respectively. The primary objective of the survey was to search for fast radio transients, including Fast Radio Bursts (FRBs) and Rotating Radio Transients (RRATs). We used the 7-beam ALFA receiver to observe different sections of the sky within the declination region $\sim$(10$-$20) deg on 23 nights and collected 160 hours of data in total. We searched our data for single-pulse transients, covering up to a maximum dispersion measure of 11 000 pc cm$^{-3}$ at which the dispersion delay across the entire bandwidth is equal to the 13 s transit length of our observations. The analysis produced more than 18 million candidates. Machine learning techniques sorted the radio frequency interference and possibly astrophysical candidates, allowing us to visually inspect and confirm the candidate transients. We found no evidence for new astrophysical transients in our data. We also searched for emission from repeated transient signals, but found no evidence for such sources. We detected single pulses from two known pulsars in our observations and their measured flux densities are consistent with the expected values. Based on our observations and sensitivity, we estimated the upper limit for the FRB rate to be $<$2.8$\times10^5$ sky$^{-1}$ day$^{-1}$ above a fluence of 0.16 Jy ms at 1.4 GHz, which is consistent with the rates from other telescopes and surveys., Comment: 11 pages, 8 figures. Accepted 2021 October 27 for publication in MNRAS

Published
2021
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13. INFLUENCIAS DE UN RELLENO SANITARIO SOBRE LA COMPOSICIÓN, ABUNDANCIA Y DISPERSIÓN DIURNA DE LOS PECES EN LA QUEBRADA EL VENADO, CORREGIMIENTO DE CÓRDOBA, MUNICIPIO DE BUENAVENTURA (VALLE DEL CAUCA, COLOMBIA)

Author

Carlos E. Fernández M., Maicol Ramírez, and Efraín A. Rubio R.

Subjects
composición, abundancia, dispersión, peces continentales, quebrada El Venado, Valle del Cauca, Science (General), Q1-390
Abstract

En 2009, se estudió la composición, abundancia y dispersión diurna de los peces presentes en la quebrada El Venado, ubicada en el corregimiento de Córdoba, municipio de Buenaventura, Valle del Cauca, Colombia. La quebrada es uno de los afluentes del río Dagua que desemboca en la Bahía de Buenaventura, en la costa Pacífica de Colombia. Se realizaron 6 muestreos mensuales con la técnica de electropesca (Lagler, 1956), identificándose 37 especies de peces hasta el nivel de especie y 9 morfotipos hasta el nivel de género. Los órdenes Characiformes (Familia Characidae) y Siluriformes (Familia Loricariidae) dominaron entre los peces en la quebrada durante el estudio, especialmente en las estaciones cercanas al basurero. En la estación 3, el número de especies (n = 23), familias (n = 13) y órdenes (n = 4) fue relativamente bajo en comparación con las otras estaciones. Por lo general, los peces registraron comunidades más saludables aguas arriba del basurero. Debido a sus características adaptativas, algunos peces, especialmente de la Familia Loricariidae, toleraron mejor las condiciones de las aguas aguas abajo del basurero que otros (Familia Characidae).

Published
2023
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14. Grain boundary strengthening of FCC polycrystals

Author

Rubio, R. A., Haouala, S., and LLorca, J.

Subjects
Condensed Matter - Materials Science
Abstract

The effect of grain size on the flow strength of FCC polycrystals was analyzed by means of computational homogenization. The mechanical behavior of each grain was dictated by a dislocation-based crystal plasticity model in the context of finite strain plasticity and takes into the account the formation of pile-ups at grain boundaries. All the model parameters have a clear physical meaning and were identified for different FCC metals from dislocation dynamics simulations or experiments. It was found that the influence of the grain size on the flow strength of FCC polycrystals was mainly dictated by the similitude coefficient $K$ that establishes the relationship between the dislocation mean free path and the dislocation density in the bulk. Finally, the modelling approach was validated by comparison with experimental results of the effect of grain size on the flow strength of Ni, Al, Cu and Ag.

Published
2019
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16. Scale-dependent galaxy bias, CMB lensing-galaxy cross-correlation, and neutrino masses

Author

Giusarma, E, Vagnozzi, S, Ho, S, Ferraro, S, Freese, K, Kamen-Rubio, R, and Luk, KB

Subjects
astro-ph.CO, astro-ph.GA, astro-ph.HE, gr-qc, hep-ph
Abstract

One of the most powerful cosmological data sets when it comes to constraining neutrino masses is represented by galaxy power spectrum measurements, Pgg(k). The constraining power of Pgg(k) is however severely limited by uncertainties in the modeling of the scale-dependent galaxy bias b(k). In this work we present a new proof-of-principle for a method to constrain b(k) by using the cross-correlation between the cosmic microwave background (CMB) lensing signal and galaxy maps (C κg) using a simple but theoretically well-motivated parametrization for b(k). We apply the method using C κg measured by cross-correlating Planck lensing maps and the Baryon Oscillation Spectroscopic Survey (BOSS) Data Release 11 (DR11) CMASS galaxy sample, and Pgg(k) measured from the BOSS DR12 CMASS sample. We detect a nonzero scale-dependence at moderate significance, which suggests that a proper modeling of b(k) is necessary in order to reduce the impact of nonlinearities and minimize the corresponding systematics. The accomplished increase in constraining power of Pgg(k) is demonstrated by determining a 95% confidence level upper bound on the sum of the three active neutrino masses Mν of Mν

Published
2018

17. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol A

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2018

18. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol C

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2018

19. Modified TruSeq Small RNA Library Prep using Randomized 4N Adapters: In house 4N Protocol D

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2018

20. Library Preparation for small RNA sequencing using 4N adapters: In house 4N Protocol B

Author

Alexander, Roger P, Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Published
2018

23. Uniqueness and non-existence of minimal submanifolds

Author

Rubio, R. M. and Salamanca, J. J.

Subjects
Mathematics - Differential Geometry, 53C2, 53C40, 53C42
Abstract

We provide uniqueness results for compact minimal submanifolds in a large class of Riemannian manifolds of arbitrary dimension. In the case compact and Cartan-Hadamard manifolds we obtain general results for these submanifolds. Several applications to Geometric Analysis are also showed.

Published
2016

24. Jumping to conclusions and suicidal behavior in depression and psychosis

Author

Acevedo, A., Anglès, J., Argany, M.A., Barajas, A., Barrigón, M.L., Beltrán, M., Birulés, I., Bogas, J.L., Camprubí, N., Carbonero, M., Carmona Farrés, C., Carrasco, E., Casañas, R., Cid, J., Conesa, E., Corripio, I., Cortes, P., Crosas, J.M., de Apraiz, A., Delgado, M., Domínguez, L., Escartí, M.J., Escudero, A., Esteban Pinos, I., Figueras, M., Franco, C., García, C., Gil, V., Giménez-Díaz, D., Gonzalez-Casares, R., González Higueras, F., González- Montoro, MaL., González, E., Grasa Bello, E., Guasp, A., Huerta-Ramos, Ma E., Huertas, P., Jiménez-Díaz, A., Lalucat, L.L., LLacer, B., López-Alcayada, R., López- Carrilero, R., Lorente, E., Luengo, A., Mantecón, N., Mas-Expósito, L., Montes, M., Moritz, S., Murgui, E., Nuñez, M., Ochoa, S., Palomer, E., Paniego, E., Peláez, T., Pérez, V., Planell, K., Planellas, C., Pleguezuelo-Garrote, P., Pousa, E., Rabella, M., Renovell, M., Rubio, R., Ruiz- Delgado, I., San Emeterio, M., Sánchez, E., Sanjuán, J., Sans, B., Schilling, L., Sió, H., Teixidó, M., Torres, P., Vila, M.A., Vila-Badia, R., Villegas, F., Villellas, R., Sastre-Buades, Aina, Ochoa, Susana, Lorente-Rovira, Esther, Barajas, Ana, Grasa, Eva, López-Carrilero, Raquel, Luengo, Ana, Ruiz-Delgado, Isabel, Cid, Jordi, González-Higueras, Fermín, Sánchez-Alonso, Sergio, Baca-García, Enrique, and Barrigón, Maria L.

Published
2021
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25. Systematic assessment of next generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

Author

Giraldez, MD, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Nolte-‘t Hoen, ENM, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Subjects
Genetics, Human Genome, Generic health relevance
Abstract

Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.

Published
2017

26. Systematic assessment of next generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories

Author

Giraldez, Spengler, RM, Etheridge, A, Godoy, PM, Barczak, AJ, Srinivasan, S, De Hoff, PL, Tanriverdi, K, Courtright, A, Lu, S, Khoory, J, Rubio, R, Baxter, D, Driedonks, TAP, Buermans, HPJ, Hoen, ENM Nolte-t, Jiang, H, Wang, K, Ghiran, I, Wang, Y, Van Keuren-Jensen, K, Freedman, JE, Woodruff, PG, Laurent, LC, Erle, DJ, Galas, DJ, and Tewari, M

Subjects
Genetics, Human Genome, Generic health relevance
Abstract

Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.

Published
2017

27. Grupos de apoyo de pares para sobrevivientes de intento de suicidio (SOSA): Revisión sistemática.

Author

Inostroza R.,Carolina, Fernández V.,Dany, Quijada I.,Yanet, Rubio R.,Francisca, Bühring S.,Vasily, Vargas G.,Belén, Riquelme B.,Alejandro, Paz Araya Á.,María, Inostroza R.,Carolina, Fernández V.,Dany, Quijada I.,Yanet, Rubio R.,Francisca, Bühring S.,Vasily, Vargas G.,Belén, Riquelme B.,Alejandro, and Paz Araya Á.,María

Abstract

RESUMEN Antecedentes: el intento de suicidio es el principal factor de riesgo de muerte por suicidio. La Organización Mundial de la Salud sugiere grupos de apoyo como intervención para esta población. Objetivo: Este estudio tuvo como objetivo determinar la eficacia de los grupos de apoyo de pares para sobrevivientes de intento de suicidio (SOSA). Método: Revisión sistemática (PROSPERO ID: CRD42022307581). Resultados: En total se identificaron 946 artículos potenciales, se revisaron 81 textos completos y se incluyó un artículo. El artículo informa sobre un estudio piloto abierto con evaluaciones pre y post intervención, sin grupo de control y con alto riesgo de sesgo. Esta es una intervención prometedora, porque los resultados mostraron una disminución de la ideación suicida (d=0,33), y del intento de suicidio (d=0,31). El pequeño número de investigaciones empíricas limita las generalizaciones. Conclusión: El nivel de certeza de la evidencia es bajo (baja certeza), por lo tanto, el grado de recomendación corresponde a evidencia insuficiente (I), para recomendar esta estrategia para las políticas públicas. En este artículo se analizan las razones de estos resultados y los posibles caminos para avanzar en este campo.

Published
2024

33. Syndrome of transient headache and neurological deficits with cerebrospinal fluid lymphocytosis (HaNDL) in a patient with confusional symptoms, diffuse EEG abnormalities, and bilateral vasospasm in transcranial Doppler ultrasound: A case report and literature review

Author

Hidalgo de la Cruz, M., Domínguez Rubio, R., Luque Buzo, E., Díaz Otero, F., Vázquez Alén, P., Orcajo Rincón, J., Prieto Montalvo, J., Contreras Chicote, A., and Grandas Pérez, F.

Published
2019
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34. Síndrome de cefalea transitoria con déficits neurológicos asociados y pleocitosis en líquido cefalorraquídeo (HaNDL) con cuadro confusional, EEG compatible con afectación difusa y datos de vasoespasmo bilateral en estudio Doppler transcraneal: presentación de un caso y revisión de la literatura

Author

Hidalgo de la Cruz, M., Domínguez Rubio, R., Luque Buzo, E., Díaz Otero, F., Vázquez Alén, P., Orcajo Rincón, J., Prieto Montalvo, J., Contreras Chicote, A., and Grandas Pérez, F.

Published
2019
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37. Propagation of Avalanches in Mn$_{12}$-acetate: Magnetic Deflagration

Author

Suzuki, Yoko, Sarachik, M. P., Chudnovsky, E. M., McHugh, S., Gonzalez-Rubio, R., Avraham, Nurit, Myasoedov, Y., Zeldov, E., Shtrikman, H., Chakov, N. E., and Christou, G.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

Local time-resolved measurements of fast reversal of the magnetization of single crystals of Mn12-acetate indicate that the magnetization avalanche spreads as a narrow interface that propagates through the crystal at a constant velocity that is roughly two orders of magnitude smaller than the speed of sound. We argue that this phenomenon is closely analogous to the propagation of a flame front (deflagration) through a flammable chemical substance., Comment: 5 pages, 5 figures

Published
2005
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39. First record of Archanara neurica (Hübner, 1808) from the Iberian Peninsula (Lepidoptera: Noctuidae) according to DNA barcoding and internal male genitalia

Author

Ortiz, A. S., Rubio, R. M., Ranki, T., Guerrero, J. J., and Yela, J. L.

Subjects
Animal Science and Zoology, Biodiversity, Ecology, Evolution, Behavior and Systematics, Taxonomy
Abstract

Archanara neurica (Hübner, 1808) is recorded for the first time from the Iberian Peninsula. The Iberian population represent a link between central European, including French, and Moroccan populations. Male internal genitalia are comparatively described. DNA barcode is presented and compared with those of the other European Archanara, Lenisa and Globia species, formerly considered congeneric. An analysis based on the COI mitochondrial gene provisionally supports the morphologically proposed statement that recognize the three mentioned taxa at the generic level.

Published
2023

40. Molecular characterization of congenital myasthenic syndromes in Spain

Author

Natera-de Benito, D., Töpf, A., Vilchez, J.J., González-Quereda, L., Domínguez-Carral, J., Díaz-Manera, J., Ortez, C., Bestué, M., Gallano, P., Dusl, M., Abicht, A., Müller, J.S., Senderek, J., García-Ribes, A., Muelas, N., Evangelista, T., Azuma, Y., McMacken, G., Paipa Merchan, A., Rodríguez Cruz, P.M., Camacho, A., Jiménez, E., Miranda-Herrero, M.C., Santana-Artiles, A., García-Campos, O., Dominguez-Rubio, R., Olivé, M., Colomer, J., Beeson, D., Lochmüller, H., and Nascimento, A.

Published
2017
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41. A Novel Multiplex Assay Combining Autoantibodies Plus PSA Has Potential Implications for Classification of Prostate Cancer from Non-malignant Cases

Author

Xie, Chong, Kim, Hyun J, Haw, Jonathan G, Kalbasi, Anusha, Gardner, Brian K, Li, Gang, Rao, Jianyu, Chia, David, Liong, Monty, Punzalan, Rubio R, Marks, Leonard S, Pantuck, Allan J, de la Taille, Alexandre, Wang, Guomin, Mukouyama, Hideki, and Zeng, Gang

Abstract

Abstract Background The lack of sufficient specificity and sensitivity among conventional cancer biomarkers, such as prostate specific antigen (PSA) for prostate cancer has been widely recognized after several decades of clinical implications. Autoantibodies (autoAb) among others are being extensively investigated as potential substitute markers, but remain elusive. One major obstacle is the lack of a sensitive and multiplex approach for quantifying autoAb against a large panel of clinically relevant tumor-associated antigens (TAA). Methods To circumvent preparation of phage lysates and purification of recombinant proteins, we identified B cell epitopes from a number of previously defined prostate cancer-associated antigens (PCAA). Peptide epitopes from cancer/testis antigen NY-ESO-1, XAGE-1b, SSX-2,4, as well as prostate cancer overexpressed antigen AMACR, p90 autoantigen, and LEDGF were then conjugated with seroMAP microspheres to allow multiplex measurement of autoAb present in serum samples. Moreover, simultaneous quantification of autoAb plus total PSA was achieved in one reaction, and termed the "A+PSA" assay. Results Peptide epitopes from the above 6 PCAA were identified and confirmed that autoAb against these peptide epitopes reacted specifically with the full-length protein. A pilot study was conducted with the A+PSA assay using pre-surgery sera from 131 biopsy-confirmed prostate cancer patients and 121 benign prostatic hyperplasia and/or prostatitis patients. A logistic regression-based A+PSA index was found to enhance sensitivities and specificities over PSA alone in distinguishing prostate cancer from nonmalignant cases. The A+PSA index also reduced false positive rate and improved the area under a receiver operating characteristic curve. Conclusions The A+PSA assay represents a novel platform that integrates autoAb signatures with a conventional cancer biomarker, which may aid in the diagnosis and prognosis of prostate cancer and others.

Published
2011

46. Dung removal increases under higher dung beetle functional diversity regardless of grazing intensification

Author

Noriega, J.A., Hortal, J., deCastro-Arrazola, I., Alves-Martins, F., Ortega, J.C.G, Bini, L.M., Andrew, N.R., Arellano, L., Beynon, S., Davis, A.L.V., Favila, M.E., Floate, K.D., Horgan, F.G., Menéndez, R., Milotic, T., Nervo, B., Palestrini, C., Rolando, A., Scholtz, C.H., Senyüz, Y., Wassmer, T., Ádam, R., de O. Araújo, C., Barragan-Ramírez, J.L., Boros, G., Camero-Rubio, R., Cruz, M., Cuesta, E., Pieri Damborsky, M., Deschodt, C.M., Dharma Rajan, P., D’hondt, B., Díaz Rojas, A., Dindar, K., Escobar, F., Espinoza, V.R., Ferrer-Paris, J.R., Gutiérrez Rojas, P.E., Hemmings, Z., Hernández, B., Hill, S.J., Hoffmann, M., Jay-Robert, P., Lewis, K., Lewis, M., Lozano, C., Marín-Armijos, D., Menegaz de Farias, P., Murcia-Ordoñez, B., Narayanan Karimbumkara, S., Navarrete-Heredia, J.L., Ortega-Echeverría, C., Pablo-Cea, J.D., Perrin, W., Pessoa, M.B., Radhakrishnan, A., Rahimi, I., Raimundo, A.T., Ramos, D.C., Rebolledo, R.E., Roggero, A., Sánchez-Mercado, A., Somay, L., Stadler, Jutta, Tahmasebi, P., Triana Céspedes, J.D., Santos, A.M.C., Noriega, J.A., Hortal, J., deCastro-Arrazola, I., Alves-Martins, F., Ortega, J.C.G, Bini, L.M., Andrew, N.R., Arellano, L., Beynon, S., Davis, A.L.V., Favila, M.E., Floate, K.D., Horgan, F.G., Menéndez, R., Milotic, T., Nervo, B., Palestrini, C., Rolando, A., Scholtz, C.H., Senyüz, Y., Wassmer, T., Ádam, R., de O. Araújo, C., Barragan-Ramírez, J.L., Boros, G., Camero-Rubio, R., Cruz, M., Cuesta, E., Pieri Damborsky, M., Deschodt, C.M., Dharma Rajan, P., D’hondt, B., Díaz Rojas, A., Dindar, K., Escobar, F., Espinoza, V.R., Ferrer-Paris, J.R., Gutiérrez Rojas, P.E., Hemmings, Z., Hernández, B., Hill, S.J., Hoffmann, M., Jay-Robert, P., Lewis, K., Lewis, M., Lozano, C., Marín-Armijos, D., Menegaz de Farias, P., Murcia-Ordoñez, B., Narayanan Karimbumkara, S., Navarrete-Heredia, J.L., Ortega-Echeverría, C., Pablo-Cea, J.D., Perrin, W., Pessoa, M.B., Radhakrishnan, A., Rahimi, I., Raimundo, A.T., Ramos, D.C., Rebolledo, R.E., Roggero, A., Sánchez-Mercado, A., Somay, L., Stadler, Jutta, Tahmasebi, P., Triana Céspedes, J.D., and Santos, A.M.C.

Abstract

Dung removal by macrofauna such as dung beetles is an important process for nutrient cycling in pasturelands. Intensification of farming practices generally reduces species and functional diversity of terrestrial invertebrates, which may negatively affect ecosystem services. Here, we investigate the effects of cattle-grazing intensification on dung removal by dung beetles in field experiments replicated in 38 pastures around the world. Within each study site, we measured dung removal in pastures managed with low- and high-intensity regimes to assess between-regime differences in dung beetle diversity and dung removal, whilst also considering climate and regional variations. The impacts of intensification were heterogeneous, either diminishing or increasing dung beetle species richness, functional diversity, and dung removal rates. The effects of beetle diversity on dung removal were more variable across sites than within sites. Dung removal increased with species richness across sites, while functional diversity consistently enhanced dung removal within sites, independently of cattle grazing intensity or climate. Our findings indicate that, despite intensified cattle stocking rates, ecosystem services related to decomposition and nutrient cycling can be maintained when a functionally diverse dung beetle community inhabits the human-modified landscape.

Published
2023

49. Resistance to downy mildew in wildly growing Eurasian Vitis viniferaL. grapevines

Author

Bitsadze, N., Kikilashvili, Sh., Chipashvili, R., Mamasakhlisashvili, L., Maghradze, T., Kikvadze, M., Toffolatti, S. L., De Lorenzis, G., Failla, O., Ocete Rubio, R., and Maghradze, D.

Abstract

Plasmopara viticola(Berk. & M. A. Curtis) Berl. & De Toni, the causal agent of downy mildew, affects both cultivated and wild grapevine. Wild species of the genus VitisL. are reliable sources of resistance to many of the diseases that affect cultivated grapevines. For this reason, it is important to study wildly growing (typical wild and feral) accessions belonging to V. viniferaL. The aim of this research was to study the levels of resistance to P. viticolaof 57 Georgian wildly growing grapevine accessions by leaf disc method. The data were collected over eight years, from 2014 to 2021. Different degrees of resistance have been detected, ranging from susceptible (8.8% of accessions), low resistance (8.8% of accessions) moderate resistance (22.8%), and resistance (12.3% of accessions). Resistance of the 33,3% of the tested accessions was unstable and varied from susceptible to resistance across the years. Among resistant wildly growing grapevine genotypes, there are several accessions with a high density of the trichomes, although the data showed that the density of prostrate and erect hairs of the leaves is not correlated with the resistance trait. A large number of resistant genotypes among wildly growing grapevines suggests that in its natural habitat more resistant forms to downy mildew survives in the process of natural selection. Further studies are needed to characterize the plant-pathogen interaction and the mechanism of resistance of the wild accessions, although the resistant accessions, such as Tedotsminda 07, Tedotsminda 09, Tedotsimda 10 can be interesting for the breeding purposes in the future.

Published
2024
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