Yield prediction by machine learning from UAS‑based mulit‑sensor data fusion in soybean

16 p.Nowadays, automated phenotyping of plants is essential for precise and cost-effective improvement in the efficiency of crop genetics. In recent years, machine learning (ML) techniques have shown great success in the classification and modelling of crop parameters. In this research, we consider the capability of ML to perform grain yield prediction in soybeans by combining data from different optical sensors via RF (Random Forest) and XGBoost (eXtreme Gradient Boosting). During the 2018 growing season, a panel of 382 soybean recombinant inbred lines were evaluated in a yield trial at the Agronomy Center for Research and Education (ACRE) in West Lafayette (Indiana, USA). Images were acquired by the Parrot Sequoia Multispectral Sensor and the S.O.D.A. compact digital camera on board a senseFly eBee UAS (Unnamed Aircraft System) solution at R4 and early R5 growth stages. Next, a standard photogrammetric pipeline was carried out by SfM (Structure from Motion). Multispectral imagery serves to analyse the spectral response of the soybean end-member in 2D. In addition, RGB images were used to reconstruct the study area in 3D, evaluating the physiological growth dynamics per plot via height variations and crop volume estimations. As ground truth, destructive grain yield measurements were taken at the end of the growing season.SI"Development of Analytical Tools for Drone-based Canopy Phenotyping in Crop Breeding" (American Institute of Food and Agriculture

Next station in microarray data analysis: GEPAS

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at

Mejoras en la estimación de la frecuencia y magnitud de avenidas torrenciales mediante técnicas dendrogeomorfológicas

Para prevenir el riesgo de inundación, en el análisis científico de la peligrosidad asociada a las avenidas fluviales, clásicamente se han empleado métodos hidrológico-hidráulicos y, en menor medida, histórico-paleohidrológicos y geológico-geomorfológicos. Sin embargo, estas técnicas plantean enormes incertidumbres científicas por la disponibilidad de los datos de partida, su validez espacio-temporal, y su representatividad estadística. La Dendrogeomorfología es un conjunto de técnicas que, aprovechando fuentes de información registradas en las raíces, troncos y ramas de los árboles y arbustos ubicados en determinadas posiciones geomorfológicas (bancos de orilla, barras longitudinales, llanura de inundación, etc.), permite completar (e incluso suplir) el registro sistemático y paleohidrológico de avenidas torrenciales que han acontecido en esa corriente. En este artículo se propone investigar, se muestran los resultados-tipo y se discute sobre la aplicación y limitaciones de las fuentes de datos y los métodos científicos derivados del análisis dendrogeomorfológico. Para llevarlo a cabo, se sugiere una combinación de métodos de adquisición de datos en campo, estudios de laboratorio y análisis de datos en gabinete, con un plan de trabajo que contempla doce tareas o actividades: 1, caracterización geomorfológica; 2, caracterización florística; 3, muestreo de ejemplares: 4, adquisición de datos topográficos detallados; 5, preparación de las muestras; 6, conteo y medida de los anillos de crecimiento; 7, estudio anatómico e histológico; 8, sincronización de las series; 9, detección y datación de eventos; 10, modelación hidráulica de tramos; 11, análisis estadístico de caudales de avenida; y 12, cartografía de las áreas de peligrosidad por avenidas torrenciales y mapas de riesgo. - In order to prevent flood risks, scientific fluvial flood hazard analysis has been carried out traditionally with hydrologic and hydraulic methods, and secondarily, using palaeohydrological-historical and geological-geomorphological methods. Nonetheless, these techniques pose countless uncertainties due to the availability of the data, their spatio-temporal validity and their statistical representativeness. Dendrogeomorphology is a set of techniques that takes advantage of sources of information registered in roots, trunks and branches of trees or treelike bushes placed in certain geomorphological locations (such as banks, longitudinal bars, flood prone areas, etc.), that may be useful to complete the systematic registry or paleohydrologic data of torrential floods that have occurred in a certain stream. The aim of this paper is to research the usefulness and limitations of the data sources and methodologies derived from the dendrogeomorphological analysis. For accomplishing this objective a combination of methods is proposed, from data acquisition methods in field, laboratory studies, to data analysis. The schedule comprises twelve tasks: 1, geomorphologic characterization; 2, floristic characterization; 3, species sampling: 4, acquisition of detailed topographic data; 5, sample arrangement; 6, growth ring count and measurement; 7, hystologic and anatomic study; 8, series synchronization; 9, event detection and dating; 10, hydraulic reach modelling; 11, flow data statistical analysis; y 12, hazard and flood prone areas cartography and risk mapping

Towards a classificatión of dendrogeomorphological evidences and their utility in flood hazard analysis

Se analizan los diferentes parámetros dendrogeomorfológicos válidos para la estimación de riesgo

Wood anatomy of debris-flood scars in broadleaved tree species of central Spain

Valor de las características de la anatomía de la madera en la cordillera central ibérica en relación con las avalanchas de alta montañ

On the relevance of thrombomodulin variants in atypical hemolytic uremic syndrome

5 p.-1 fig.-1 tab.This project was funded by the Instituto de Salud Carlos III: REDinREN (RD016/009/009) and Instituto de Investigacion Puerta de Hierro-Segovia Arana (IDIPHISA) to AH and by grants from the Spanish Ministerio de Economía y Competitividad–FEDER (European Regional Development Fund) (PID2019-104912RB-I00) and the Autonomous Region of Madrid (S2017/BMD-3673 and S2022/BMD-7278) to SRdC. TC was supported by grant from National Health Institute Carlos III (RETIC ISCIII RD21/0005. RICORS),Peer reviewe

Radio Frequency and DC High Voltage Breakdown of High Pressure Helium, Argon, and Xenon

[EN] Motivated by the possibility of guiding daughter ions from double beta decay events to single-ion sensors for barium tagging, the NEXT collaboration is developing a program of R&D to test radio frequency (RF) carpets for ion transport in high pressure xenon gas. This would require carpet functionality in regimes at higher pressures than have been previously reported, implying correspondingly larger electrode voltages than in existing systems. This mode of operation appears plausible for contemporary RF-carpet geometries due to the higher predicted breakdown strength of high pressure xenon relative to low pressure helium, the working medium in most existing RF carpet devices. In this paper we present the first measurements of the high voltage dielectric strength of xenon gas at high pressure and at the relevant RF frequencies for ion transport (in the 10MHz range), as well as new DC and RF measurements of the dielectric strengths of high pressure argon and helium gases at small gap sizes. We find breakdown voltages that are compatible with stable RF carpet operation given the gas, pressure, voltage, materials and geometry of interest.Woodruff, K.; Baeza-Rubio, J.; Huerta, D.; Jones, BJP.; Mcdonald, AD.; Norman, L.; Nygren, DR.... (2020). Radio Frequency and DC High Voltage Breakdown of High Pressure Helium, Argon, and Xenon. Journal of Instrumentation. 15(4):1-15. https://doi.org/10.1088/1748-0221/15/04/P04022S115154Dehmelt, H. G., & Major, F. G. (1962). Orientation of(He4)+Ions by Exchange Collisions with Cesium Atoms. Physical Review Letters, 8(5), 213-214. doi:10.1103/physrevlett.8.213Wada, M., Ishida, Y., Nakamura, T., Yamazaki, Y., Kambara, T., Ohyama, H., … Katayama, I. (2003). Slow RI-beams from projectile fragment separators. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 204, 570-581. doi:10.1016/s0168-583x(02)02151-1Gehring, A. E., Brodeur, M., Bollen, G., Morrissey, D. J., & Schwarz, S. (2016). Research and development of ion surfing RF carpets for the cyclotron gas stopper at the NSCL. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 376, 221-224. doi:10.1016/j.nimb.2016.02.012Ranjan, M., Purushothaman, S., Dickel, T., Geissel, H., Plass, W. R., Schäfer, D., … Dendooven, P. (2011). New stopping cell capabilities: RF carpet performance at high gas density and cryogenic operation. EPL (Europhysics Letters), 96(5), 52001. doi:10.1209/0295-5075/96/52001Arai, F., Ito, Y., Katayama, I., Schury, P., Sonoda, T., Wada, M., & Wollnik, H. (2015). Performance of Ion Surfing Rf-carpets for High-Energy RI Beam Gas Catcher. Proceedings of the Conference on Advances in Radioactive Isotope Science (ARIS2014). doi:10.7566/jpscp.6.030110Schwarz, S. (2011). RF ion carpets: The electric field, the effective potential, operational parameters and an analysis of stability. International Journal of Mass Spectrometry, 299(2-3), 71-77. doi:10.1016/j.ijms.2010.09.021Paschen, F. (1889). Ueber die zum Funkenübergang in Luft, Wasserstoff und Kohlensäure bei verschiedenen Drucken erforderliche Potentialdifferenz. Annalen der Physik, 273(5), 69-96. doi:10.1002/andp.18892730505Jones, F. L., & Morgan, G. D. (1951). High-Frequency Discharges: I Breakdown Mechanism and Similarity Relationship. Proceedings of the Physical Society. Section B, 64(7), 560-573. doi:10.1088/0370-1301/64/7/303Townsend, W. G., & Williams, G. C. (1958). The Electrical Breakdown of Gases in Uniform High Frequency Fields at Low Pressure. Proceedings of the Physical Society, 72(5), 823-832. doi:10.1088/0370-1328/72/5/318Sato, M., & Shoji, M. (1997). Breakdown Characteristics of RF Argon Capacitive Discharge. Japanese Journal of Applied Physics, 36(Part 1, No. 9A), 5729-5730. doi:10.1143/jjap.36.5729Lisovskiy, V. A., & Yegorenkov, V. D. (1998). Rf breakdown of low-pressure gas and a novel method for determination of electron-drift velocities in gases. Journal of Physics D: Applied Physics, 31(23), 3349-3357. doi:10.1088/0022-3727/31/23/008Fukugita, M., & Yanagida, T. (1986). Barygenesis without grand unification. Physics Letters B, 174(1), 45-47. doi:10.1016/0370-2693(86)91126-3Moe, M. K. (1991). Detection of neutrinoless double-beta decay. Physical Review C, 44(3), R931-R934. doi:10.1103/physrevc.44.r931Sinclair, D., Rollin, E., Smith, J., Mommers, A., Ackeran, N., Aharmin, B., … Breidenbach, M. (2011). Prospects for Barium Tagging in Gaseous Xenon. Journal of Physics: Conference Series, 309, 012005. doi:10.1088/1742-6596/309/1/012005Brunner, T., Fudenberg, D., Sabourov, A., Varentsov, V. L., Gratta, G., & Sinclair, D. (2013). A setup for Ba-ion extraction from high pressure Xe gas for double-beta decay studies with EXO. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 317, 473-475. doi:10.1016/j.nimb.2013.05.086Twelker, K., Kravitz, S., Díez, M. M., Gratta, G., Fairbank, W., Albert, J. B., … Benitez-Medina, C. (2014). An apparatus to manipulate and identify individual Ba ions from bulk liquid Xe. Review of Scientific Instruments, 85(9), 095114. doi:10.1063/1.4895646Mong, B., Cook, S., Walton, T., Chambers, C., Craycraft, A., Benitez-Medina, C., … Auty, D. J. (2015). Spectroscopy of Ba andBa+deposits in solid xenon for barium tagging in nEXO. Physical Review A, 91(2). doi:10.1103/physreva.91.022505Brunner, T., Fudenberg, D., Varentsov, V., Sabourov, A., Gratta, G., Dilling, J., … Albert, J. B. (2015). An RF-only ion-funnel for extraction from high-pressure gases. International Journal of Mass Spectrometry, 379, 110-120. doi:10.1016/j.ijms.2015.01.003Nygren, D. R. (2016). Detection of the barium daughter in 136Xe →136Ba+2e− by in situ single-molecule fluorescence imaging. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 824, 2-5. doi:10.1016/j.nima.2015.11.038Jones, B. J. P., McDonald, A. D., & Nygren, D. R. (2016). Single molecule fluorescence imaging as a technique for barium tagging in neutrinoless double beta decay. Journal of Instrumentation, 11(12), P12011-P12011. doi:10.1088/1748-0221/11/12/p12011Byrnes, N., Foss, F. W., Jones, B. J. ., McDonald, A. D., Nygren, D. R., … Thapa, P. (2019). Progress toward Barium Tagging in High Pressure Xenon Gas with Single Molecule Fluorescence Imaging. Journal of Physics: Conference Series, 1312, 012001. doi:10.1088/1742-6596/1312/1/012001McDonald, A. D., Jones, B. J. P., Nygren, D. R., Adams, C., Álvarez, V., Azevedo, C. D. R., … Cárcel, S. (2018). Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging. Physical Review Letters, 120(13). doi:10.1103/physrevlett.120.132504(2019). Imaging individual barium atoms in solid xenon for barium tagging in nEXO. Nature, 569(7755), 203-207. doi:10.1038/s41586-019-1169-4Thapa, P., Arnquist, I., Byrnes, N., Denisenko, A. A., Foss, F. W., Jones, B. J. P., … Woodruff, K. (2019). Barium Chemosensors with Dry-Phase Fluorescence for Neutrinoless Double Beta Decay. Scientific Reports, 9(1). doi:10.1038/s41598-019-49283-xMartín-Albo, J., Muñoz Vidal, J., Ferrario, P., Nebot-Guinot, M., Gómez-Cadenas, J. J., … Cárcel, S. (2016). Sensitivity of NEXT-100 to neutrinoless double beta decay. Journal of High Energy Physics, 2016(5). doi:10.1007/jhep05(2016)159Bainglass, E., Jones, B. J. P., Foss, F. W., Huda, M. N., & Nygren, D. R. (2018). Mobility and clustering of barium ions and dications in high-pressure xenon gas. Physical Review A, 97(6). doi:10.1103/physreva.97.062509Postel, O. B., & Cappelli, M. A. (2000). Vacuum emission and breakdown characteristics of a planar He–Xe microdischarge. Applied Physics Letters, 76(5), 544-546. doi:10.1063/1.125813Sosov, Y., & Theodosiou, C. E. (2004). Determination of electric field-dependent effective secondary emission coefficients for He/Xe ions on brass. Journal of Applied Physics, 95(8), 4385-4388. doi:10.1063/1.1655677Lieberman, M. A., & Lichtenberg, A. J. (2005). Principles of Plasma Discharges and Materials Processing. doi:10.1002/0471724254Lisovskiy, V. A., Yakovin, S. D., & Yegorenkov, V. D. (2000). Low-pressure gas breakdown in uniform dc electric field. Journal of Physics D: Applied Physics, 33(21), 2722-2730. doi:10.1088/0022-3727/33/21/310Smith, H. B., Charles, C., & Boswell, R. W. (2003). Breakdown behavior in radio-frequency argon discharges. Physics of Plasmas, 10(3), 875-881. doi:10.1063/1.1531615Bhattacharya, A. K. (1976). Measurement of breakdown potentials and Townsend ionization coefficients for the Penning mixtures of neon and xenon. Physical Review A, 13(3), 1219-1225. doi:10.1103/physreva.13.1219Jacques, L., Bruynooghe, W., Boucique, R., & Wieme, W. (1986). Experimental determination of the primary and secondary ionisation coefficients in krypton and xenon. Journal of Physics D: Applied Physics, 19(9), 1731-1739. doi:10.1088/0022-3727/19/9/017Bradford, H. M., Fraser, D. M., Langstroth, G. F. O., & MacDonald, A. D. (1959). ELECTRICAL BREAKDOWN IN XENON AND KRYPTON AT ULTRAHIGH FREQUENCIES. Canadian Journal of Physics, 37(10), 1166-1170. doi:10.1139/p59-133Park, J., Henins, I., Herrmann, H. W., & Selwyn, G. S. (2001). Gas breakdown in an atmospheric pressure radio-frequency capacitive plasma source. Journal of Applied Physics, 89(1), 15-19. doi:10.1063/1.1323754Moravej, M., Yang, X., Nowling, G. R., Chang, J. P., Hicks, R. F., & Babayan, S. E. (2004). Physics of high-pressure helium and argon radio-frequency plasmas. Journal of Applied Physics, 96(12), 7011-7017. doi:10.1063/1.1815047Borg Dezani, V., & Ginoux, J. L. (1994). Investigation of breakdown voltage curves for pure helium and silane–helium mixtures. Physics of Plasmas, 1(4), 1060-1063. doi:10.1063/1.870786McDonald, A. D., Woodruff, K., Atoum, B. A., González-Díaz, D., Jones, B. J. P., Adams, C., … Azevedo, C. D. . (2019). Electron drift and longitudinal diffusion in high pressure xenon-helium gas mixtures. Journal of Instrumentation, 14(08), P08009-P08009. doi:10.1088/1748-0221/14/08/p08009Rogers, L., Clark, R. A., Jones, B. J. P., McDonald, A. D., Nygren, D. R., Psihas, F., … Azevedo, C. D. . (2018). High voltage insulation and gas absorption of polymers in high pressure argon and xenon gases. Journal of Instrumentation, 13(10), P10002-P10002. doi:10.1088/1748-0221/13/10/p10002Okawa, M., Shioiri, T., Okubo, H., & Yanabu, S. (1988). Area effect on electric breakdown of copper and stainless steel electrodes in vacuum. IEEE Transactions on Electrical Insulation, 23(1), 77-81. doi:10.1109/14.2336Kihara, T. (1952). The Mathematical Theory of Electrical Discharges in Gases. Reviews of Modern Physics, 24(1), 45-61. doi:10.1103/revmodphys.24.45Hamaker, A., Brodeur, M., Kelly, J. M., Long, J., Nicoloff, C., Ryan, S., … Wada, M. (2016). Experimental investigation of the repelling force from RF carpets. International Journal of Mass Spectrometry, 404, 14-19. doi:10.1016/j.ijms.2016.04.00

Unraveling the effect of silent, intronic and missense mutations on VWF splicing: contribution of next generation sequencing in the study of mRNA

Large studies in von Willebrand disease patients, including Spanish and Portuguese registries, led to identification of >250 different mutations. It is a challenge to determine the pathogenic effect of potential splice site mutations on VWF mRNA. This study aimed to elucidate the true effects of 18 mutations on VWF mRNA processing, investigate the contribution of next-generation sequencing to in vivo mRNA study in von Willebrand disease, and compare the findings with in silico prediction. RNA extracted from patient platelets and leukocytes was amplified by RT-PCR and sequenced using Sanger and next generation sequencing techniques. Eight mutations affected VWF splicing: c.1533+1G>A, c.5664+2T>C and c.546G>A (p.=) prompted exon skipping; c.3223-7_3236dup and c.7082-2A>G resulted in activation of cryptic sites; c.3379+1G>A and c.7473G>A (p.=) demonstrated both molecular pathogenic mechanisms simultaneously; and the p.Cys370Tyr missense mutation generated two aberrant transcripts. Of note, the complete effect of 3 mutations was provided by next generation sequencing alone because of low expression of the aberrant transcripts. In the remaining 10 mutations, no effect was elucidated in the experiments. However, the differential findings obtained in platelets and leukocytes provided substantial evidence that 4 of these would have an effect on VWF levels. In this first report using next generation sequencing technology to unravel the effects of VWF mutations on splicing, the technique yielded valuable information. Our data bring to light the importance of studying the effect of synonymous and missense mutations on VWF splicing to improve the current knowledge of the molecular mechanisms behind von Willebrand disease.info:eu-repo/semantics/publishedVersio

Radio frequency and DC high voltage breakdown of high pressure helium, argon, and xenon

Motivated by the possibility of guiding daughter ions from double beta decay events to single-ion sensors for barium tagging, the NEXT collaboration is developing a program of R&D to test radio frequency (RF) carpets for ion transport in high pressure xenon gas. This would require carpet functionality in regimes at higher pressures than have been previously reported, implying correspondingly larger electrode voltages than in existing systems. This mode of operation appears plausible for contemporary RF-carpet geometries due to the higher predicted breakdown strength of high pressure xenon relative to low pressure helium, the working medium in most existing RF carpet devices. In this paper we present the first measurements of the high voltage dielectric strength of xenon gas at high pressure and at the relevant RF frequencies for ion transport (in the 10 MHz range), as well as new DC and RF measurements of the dielectric strengths of high pressure argon and helium gases at small gap sizes. We find breakdown voltages that are compatible with stable RF carpet operation given the gas, pressure, voltage, materials and geometry of interest

Unraveling the effect of silent, intronic and missense mutations on VWF splicing: contribution of next generation sequencing in the study of mRNA

Large studies in von Willebrand disease patients, including Spanish and Portuguese registries, led to the identification of >250 different mutations. It is a challenge to determine the pathogenic effect of potential splice site mutations on VWF mRNA. This study aimed to elucidate the true effects of 18 mutations on VWF mRNA processing, investigate the contribution of next-generation sequencing to in vivo mRNA study in von Willebrand disease, and compare the findings with in silico prediction. RNA extracted from patient platelets and leukocytes was amplified by RT-PCR and sequenced using Sanger and next generation sequencing techniques. Eight mutations affected VWF splicing: c.1533+1G>A, c.5664+2T>C and c.546G>A (p.=) prompted exon skipping; c.3223-7_3236dup and c.7082-2A>G resulted in activation of cryptic sites; c.3379+1G>A and c.7437G>A) demonstrated both molecular pathogenic mechanisms simultaneously; and the p.Cys370Tyr missense mutation generated two aberrant transcripts. Of note, the complete effect of three mutations was provided by next generation sequencing alone because of low expression of the aberrant transcripts. In the remaining 10 mutations, no effect was elucidated in the experiments. However, the differential findings obtained in platelets and leukocytes provided substantial evidence that four of these would have an effect on VWF levels. In this first report using next generation sequencing technology to unravel the effects of VWF mutations on splicing, the technique yielded valuable information. Our data bring to light the importance of studying the effect of synonymous and missense mutations on VWF splicing to improve the current knowledge of the molecular mechanisms behind von Willebrand disease. clinicaltrials.gov identifier:02869074