372 results on '"Noé F"'
Search Results
2. DeepQMC: An open-source software suite for variational optimization of deep-learning molecular wave functions.
- Author
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Schätzle, Z., Szabó, P. B., Mezera, M., Hermann, J., and Noé, F.
- Subjects
WAVE functions ,SCHRODINGER equation ,LIBRARY software ,COMPUTATIONAL chemistry ,QUANTUM chemistry ,PARALLEL algorithms ,LEARNING communities - Abstract
Computing accurate yet efficient approximations to the solutions of the electronic Schrödinger equation has been a paramount challenge of computational chemistry for decades. Quantum Monte Carlo methods are a promising avenue of development as their core algorithm exhibits a number of favorable properties: it is highly parallel and scales favorably with the considered system size, with an accuracy that is limited only by the choice of the wave function Ansatz. The recently introduced machine-learned parametrizations of quantum Monte Carlo Ansätze rely on the efficiency of neural networks as universal function approximators to achieve state of the art accuracy on a variety of molecular systems. With interest in the field growing rapidly, there is a clear need for easy to use, modular, and extendable software libraries facilitating the development and adoption of this new class of methods. In this contribution, the DeepQMC program package is introduced, in an attempt to provide a common framework for future investigations by unifying many of the currently available deep-learning quantum Monte Carlo architectures. Furthermore, the manuscript provides a brief introduction to the methodology of variational quantum Monte Carlo in real space, highlights some technical challenges of optimizing neural network wave functions, and presents example black-box applications of the program package. We thereby intend to make this novel field accessible to a broader class of practitioners from both the quantum chemistry and the machine learning communities. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Genetische Varianten in Genen der Kreatin-Biosynthese bei Patient*innen mit extremer Adipositas oder Anorexia nervosa
- Author
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Rajcsanyi, L. S., additional, Hoffmann, A., additional, Ghosh, A., additional, Matrisch-Dinkler, B., additional, Zheng, Y., additional, Peters, T., additional, Sun, W., additional, Dong, H., additional, Noé, F., additional, Wolfrum, C., additional, Herpertz-Dahlmann, B., additional, Seitz, J., additional, de Zwaan, M., additional, Herzog, W., additional, Ehrlich, S., additional, Zipfel, S., additional, Giel, K., additional, Egberts, K., additional, Burghardt, R., additional, Föcker, M., additional, Tsai, L., additional, Müller, T. D., additional, Blüher, M., additional, Hebebrand, J., additional, Hirtz, R., additional, and Hinney, A., additional
- Published
- 2023
- Full Text
- View/download PDF
4. Convergence to the fixed-node limit in deep variational Monte Carlo.
- Author
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Schätzle, Z., Hermann, J., and Noé, F.
- Subjects
MONTE Carlo method ,ELECTRON configuration ,SCHRODINGER equation ,MAGNITUDE (Mathematics) - Abstract
Variational quantum Monte Carlo (QMC) is an ab initio method for solving the electronic Schrödinger equation that is exact in principle, but limited by the flexibility of the available Ansätze in practice. The recently introduced deep QMC approach, specifically two deep-neural-network Ansätze PauliNet and FermiNet, allows variational QMC to reach the accuracy of diffusion QMC, but little is understood about the convergence behavior of such Ansätze. Here, we analyze how deep variational QMC approaches the fixed-node limit with increasing network size. First, we demonstrate that a deep neural network can overcome the limitations of a small basis set and reach the mean-field (MF) complete-basis-set limit. Moving to electron correlation, we then perform an extensive hyperparameter scan of a deep Jastrow factor for LiH and H
4 and find that variational energies at the fixed-node limit can be obtained with a sufficiently large network. Finally, we benchmark MF and many-body Ansätze on H2 O, increasing the fraction of recovered fixed-node correlation energy of single-determinant Slater–Jastrow-type Ansätze by half an order of magnitude compared to previous variational QMC results, and demonstrate that a single-determinant Slater–Jastrow-backflow version of the Ansatz overcomes the fixed-node limitations. This analysis helps understand the superb accuracy of deep variational Ansätze in comparison to the traditional trial wavefunctions at the respective level of theory and will guide future improvements of the neural-network architectures in deep QMC. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
5. A transversal study on antibodies against selected pathogens in dromedary camels in the Canary Islands, Spain
- Author
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Mentaberre, Gregorio, Gutiérrez, Carlos, Rodríguez, Noé F., Joseph, Sunitha, González-Barrio, David, Cabezón, Oscar, de la Fuente, José, Gortazar, Christian, and Boadella, Mariana
- Published
- 2013
- Full Text
- View/download PDF
6. Roadmap on Machine learning in electronic structure
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Kulik, H J, primary, Hammerschmidt, T, additional, Schmidt, J, additional, Botti, S, additional, Marques, M A L, additional, Boley, M, additional, Scheffler, M, additional, Todorović, M, additional, Rinke, P, additional, Oses, C, additional, Smolyanyuk, A, additional, Curtarolo, S, additional, Tkatchenko, A, additional, Bartók, A P, additional, Manzhos, S, additional, Ihara, M, additional, Carrington, T, additional, Behler, J, additional, Isayev, O, additional, Veit, M, additional, Grisafi, A, additional, Nigam, J, additional, Ceriotti, M, additional, Schütt, K T, additional, Westermayr, J, additional, Gastegger, M, additional, Maurer, R J, additional, Kalita, B, additional, Burke, K, additional, Nagai, R, additional, Akashi, R, additional, Sugino, O, additional, Hermann, J, additional, Noé, F, additional, Pilati, S, additional, Draxl, C, additional, Kuban, M, additional, Rigamonti, S, additional, Scheidgen, M, additional, Esters, M, additional, Hicks, D, additional, Toher, C, additional, Balachandran, P V, additional, Tamblyn, I, additional, Whitelam, S, additional, Bellinger, C, additional, and Ghiringhelli, L M, additional
- Published
- 2022
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7. Roadmap on Machine learning in electronic structure
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Kulik, H J, Hammerschmidt, T, Schmidt, J, Botti, S, Marques, M A L, Boley, M, Scheffler, M, Todorović, M, Rinke, P, Oses, C, Smolyanyuk, A, Curtarolo, S, Tkatchenko, A, Bartók, A P, Manzhos, S, Ihara, M, Carrington, T, Behler, J, Isayev, O, Veit, M, Grisafi, A, Nigam, J, Ceriotti, M, Schütt, K T, Westermayr, J, Gastegger, M, Maurer, R J, Kalita, B, Burke, K, Nagai, R, Akashi, R, Sugino, O, Hermann, J, Noé, F, Pilati, S, Draxl, C, Kuban, Martin, Rigamonti, Santiago, Scheidgen, Markus, Esters, M, Hicks, D, Toher, C, Balachandran, P V, Tamblyn, I, Whitelam, S, Bellinger, C, Ghiringhelli, Luca M., Kulik, H J, Hammerschmidt, T, Schmidt, J, Botti, S, Marques, M A L, Boley, M, Scheffler, M, Todorović, M, Rinke, P, Oses, C, Smolyanyuk, A, Curtarolo, S, Tkatchenko, A, Bartók, A P, Manzhos, S, Ihara, M, Carrington, T, Behler, J, Isayev, O, Veit, M, Grisafi, A, Nigam, J, Ceriotti, M, Schütt, K T, Westermayr, J, Gastegger, M, Maurer, R J, Kalita, B, Burke, K, Nagai, R, Akashi, R, Sugino, O, Hermann, J, Noé, F, Pilati, S, Draxl, C, Kuban, Martin, Rigamonti, Santiago, Scheidgen, Markus, Esters, M, Hicks, D, Toher, C, Balachandran, P V, Tamblyn, I, Whitelam, S, Bellinger, C, and Ghiringhelli, Luca M.
- Abstract
In recent years, we have been witnessing a paradigm shift in computational materials science. In fact, traditional methods, mostly developed in the second half of the XXth century, are being complemented, extended, and sometimes even completely replaced by faster, simpler, and often more accurate approaches. The new approaches, that we collectively label by machine learning, have their origins in the fields of informatics and artificial intelligence, but are making rapid inroads in all other branches of science. With this in mind, this Roadmap article, consisting of multiple contributions from experts across the field, discusses the use of machine learning in materials science, and share perspectives on current and future challenges in problems as diverse as the prediction of materials properties, the construction of force-fields, the development of exchange correlation functionals for density-functional theory, the solution of the many-body problem, and more. In spite of the already numerous and exciting success stories, we are just at the beginning of a long path that will reshape materials science for the many challenges of the XXIth century., Peer Reviewed
- Published
- 2022
8. Collective hydrogen-bond rearrangement dynamics in liquid water.
- Author
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Schulz, R., von Hansen, Y., Daldrop, J. O., Kappler, J., Noé, F., and Netz, R. R.
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HYDROGEN bonding ,REARRANGEMENTS (Chemistry) ,WATER clusters ,MOLECULAR dynamics ,SPECTRUM analysis - Abstract
We investigate barrier-crossing processes corresponding to collective hydrogen-bond rearrangements in liquid water using Markov state modeling techniques. The analysis is based on trajectories from classical molecular dynamics simulations and accounts for the full dynamics of relative angular and separation coordinates of water clusters and requires no predefined hydrogen bond criterium. We account for the complete 12-dimensional conformational subspace of three water molecules and distinguish five well-separated slow dynamic processes with relaxation times in the picosecond range, followed by a quasi-continuum spectrum of faster modes. By analysis of the Markov eigenstates, these processes are shown to correspond to different collective interchanges of hydrogen-bond donors and acceptors. Using a projection onto hydrogen-bond states, we also analyze the switching of one hydrogen bond between two acceptor water molecules and derive the complete transition network. The most probable pathway corresponds to a direct switch without an intermediate, in agreement with previous studies. However, a considerable fraction of paths proceeds along alternative routes that involve different intermediate states with short-lived alternative hydrogen bonds or weakly bound states. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
9. A flat Dirichlet process switching model for Bayesian estimation of hybrid systems
- Author
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Wu, H. and Noé, F.
- Published
- 2011
- Full Text
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10. Maximum a posteriori estimation for Markov chains based on Gaussian Markov random fields
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Wu, H. and Noé, F.
- Published
- 2010
- Full Text
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11. Pathogens and Immunity
- Author
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Azouz, N. P., Klingler, A. M., Callahan, Victoria, Akhrymuk, Ivan V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noé, F., Kehn-Hall, Kylene, Rothenberg, M. E., and Biomedical Sciences and Pathobiology
- Subjects
viruses ,camostat mesylate ,alpha 1 antitrypsin ,coronavirus ,protease ,TMPRSS2 ,COVID - Abstract
Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein priming, an important step for binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) receptor before cell entry. Methods: We developed a cell-based assay to identify TMPRSS2 inhibitors. Inhibitory activity was established in SARS-CoV-2 viral load systems. Results: We identified the human extracellular serine protease inhibitor (serpin) alpha 1 anti-trypsin (A1AT) as a novel TMPRSS2 inhibitor. Structural modeling revealed that A1AT docked to an extracellular domain of TMPRSS2 in a conformation that is suitable for catalysis, resembling similar serine protease inhibitor complexes. Inhibitory activity of A1AT was established in a SARS-CoV-2 viral load system. Notably, plasma A1AT levels were associated with COVID-19 disease severity. Conclusions: Our data support the key role of extracellular serine proteases in SARS CoV-2 infections and indicate that treatment with serpins, particularly the FDA-approved drug A1AT, may be effective in limiting SARS-CoV-2 dissemination by affecting the surface of the host cells. Published version
- Published
- 2021
12. Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2
- Author
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Azouz, N. P., Klingler, A. M., Callahan, Victoria, Akhrymuk, Ivan V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noé, F., Kehn-Hall, Kylene, Rothenberg, M. E., Azouz, N. P., Klingler, A. M., Callahan, Victoria, Akhrymuk, Ivan V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noé, F., Kehn-Hall, Kylene, and Rothenberg, M. E.
- Abstract
Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein priming, an important step for binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) receptor before cell entry. Methods: We developed a cell-based assay to identify TMPRSS2 inhibitors. Inhibitory activity was established in SARS-CoV-2 viral load systems. Results: We identified the human extracellular serine protease inhibitor (serpin) alpha 1 anti-trypsin (A1AT) as a novel TMPRSS2 inhibitor. Structural modeling revealed that A1AT docked to an extracellular domain of TMPRSS2 in a conformation that is suitable for catalysis, resembling similar serine protease inhibitor complexes. Inhibitory activity of A1AT was established in a SARS-CoV-2 viral load system. Notably, plasma A1AT levels were associated with COVID-19 disease severity. Conclusions: Our data support the key role of extracellular serine proteases in SARS CoV-2 infections and indicate that treatment with serpins, particularly the FDA-approved drug A1AT, may be effective in limiting SARS-CoV-2 dissemination by affecting the surface of the host cells.
- Published
- 2021
- Full Text
- View/download PDF
13. Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2
- Author
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Biomedical Sciences and Pathobiology, Azouz, N. P., Klingler, A. M., Callahan, Victoria, Akhrymuk, Ivan V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noé, F., Kehn-Hall, Kylene, Rothenberg, M. E., Biomedical Sciences and Pathobiology, Azouz, N. P., Klingler, A. M., Callahan, Victoria, Akhrymuk, Ivan V., Elez, K., Raich, L., Henry, B. M., Benoit, J. L., Benoit, S. W., Noé, F., Kehn-Hall, Kylene, and Rothenberg, M. E.
- Abstract
Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein priming, an important step for binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) receptor before cell entry. Methods: We developed a cell-based assay to identify TMPRSS2 inhibitors. Inhibitory activity was established in SARS-CoV-2 viral load systems. Results: We identified the human extracellular serine protease inhibitor (serpin) alpha 1 anti-trypsin (A1AT) as a novel TMPRSS2 inhibitor. Structural modeling revealed that A1AT docked to an extracellular domain of TMPRSS2 in a conformation that is suitable for catalysis, resembling similar serine protease inhibitor complexes. Inhibitory activity of A1AT was established in a SARS-CoV-2 viral load system. Notably, plasma A1AT levels were associated with COVID-19 disease severity. Conclusions: Our data support the key role of extracellular serine proteases in SARS CoV-2 infections and indicate that treatment with serpins, particularly the FDA-approved drug A1AT, may be effective in limiting SARS-CoV-2 dissemination by affecting the surface of the host cells.
- Published
- 2021
14. Trypanosoma evansi Assessment in Equines: A Study in Conducted for One Decade in an Endemic Area of the Canary Islands, Spain
- Author
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Rodríguez, Noé F., Tejedor-Junco, Maria T., González-Martín, Margarita, Doreste, Francisco, and Gutierrez, Carlos
- Published
- 2013
- Full Text
- View/download PDF
15. Aethionema arabicum dimorphic seed trait resetting during transition to seedlings
- Author
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Waheed Arshad, Tina Steinbrecher, Per K.I. Wilhelmsson, Noe Fernandez-Pozo, Marta Pérez, Zsuzsanna Mérai, Stefan A. Rensing, Jake O. Chandler, and Gerhard Leubner-Metzger
- Subjects
fruit and seed heteromorphism ,bet-hedging strategy ,diaspore dimorphism ,seed seedling transition ,transcriptome resetting ,seedling stress resilience ,Plant culture ,SB1-1110 - Abstract
The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M− seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M− seeds, and IND fruits. The dimorphic seedlings derived from M+ and M− seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M− seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.
- Published
- 2024
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16. Effets neuromusculaires de l'électrostimulation transcutanée surimposée et combinée à l'activité volontaire : une revue
- Author
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Paillard, T., Noé, F., and Edeline, O.
- Published
- 2005
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17. Polymer-like model to study the dynamics of dynamin filaments on deformable membrane tubes
- Author
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Noel, J.K., Noé, F., Daumke, O., and Mikhailov, A.S.
- Subjects
Cancer Research ,macromolecular substances - Abstract
Peripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvatureand shape modulators of the underlying membranes. A well-studied example of such proteins is themechano-chemical GTPase dynamin that assembles into helical filaments around membrane tubes andcatalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, withoutGTP, can constrict membrane tubes to radii of about 10 nanometers, indicating that the intrinsic shape andelasticity of dynamin filaments should play an important role in membrane remodeling. However, molecularand dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain modelfor a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting forthermal fluctuations in the filament and lipid flows in the membrane. We obtained the elastic parametersof the dynamin filament by molecular dynamics simulations of its tetrameric building block and also fromcoarse-grained structure-based simulations of a 17-dimer filament. The results show that the stiffness ofdynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament andthe membrane, and find that mostly the pitch of the filament, not its radius, is sensitive to variations inmembrane tension and stiffness. The close correspondence between experimental estimates of the innertube radius and those predicted by the model suggests that dynamin’s “stalk” region is responsible for itsGTP-independent membrane-shaping ability. The model paves the way for future mesoscopic modeling ofdynamin with explicit motor function.
- Published
- 2019
18. Organometallic and coordination chemistry on phosphazenes. III. Synthesis, characterization, and electrochemical behavior of transition metal-cinnamonitrile cyclophosphazene derivatives
- Author
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Gleria, M., Bertani, R., Facchin, G., Noé, F., Michelin, R. A., Mozzon, M., Pombeiro, A. J. L., da Silva, M. F. C. G., and Machado, I. L. F.
- Published
- 1996
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- View/download PDF
19. Effect of expertise and visual contribution on postural control in soccer
- Author
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Paillard, Th. and Noé, F.
- Published
- 2006
20. Is postural control affected by expertise in alpine skiing?
- Author
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Noé, F and Paillard, T
- Published
- 2005
21. Dynamic Metamaterials for Structural Stopband Creation
- Author
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Claus Claeys, Noé F. Melo, Wim Desmet, Elke Deckers, and Bert Pluymers
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Engineering ,business.industry ,Acoustics ,Metamaterial ,02 engineering and technology ,General Medicine ,Stopband ,01 natural sciences ,Vibration ,Noise ,020303 mechanical engineering & transports ,0203 mechanical engineering ,0103 physical sciences ,Electronic engineering ,010306 general physics ,business - Published
- 2016
22. Dynamic properties of force fields.
- Author
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Vitalini, F., Mey, A. S. J. S., Noé, F., and Keller, B. G.
- Subjects
MOLECULAR dynamics ,BIOLOGICAL systems ,CONFORMATIONAL analysis ,PREDICTION models ,MARKOV processes - Abstract
Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A
10 ) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question. [ABSTRACT FROM AUTHOR]- Published
- 2015
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23. Estrategia energética y operativa en las PYMES del sector manufacturero de la ZMG
- Author
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Meza-Andrade, Rosenda, Vega-Campos, Alex P., Lucio-Contreras, Noé F., Cázarez-Duarte, Alejandra, and Flores-Martínez, Alberto C.
- Subjects
Eficiencia Operativa ,Pequeña y Mediana Empresa PyME ,Industria Manufacturera ,Administración Energética - Abstract
Este proyecto muestra la exploración y validación de la problemática en el ámbito energético y operativo identificada en empresas del sector manufactura de Jalisco. Como parte del contexto, se consideraron algunas tendencias respecto a la generación de energía eléctrica a través de fuentes renovables y la implementación de sistemas de gestión de energía. El modelo de negocio aplicado fue mediante la oferta de servicios. La exploración en el mercado se realizó a través de entrevistas presenciales, conferencias y llamadas telefónicas. La validación de las hipótesis de solución se llevó a cabo mediante prototipos que representaron la solución propuesta a través de un producto mínimo viable. La retroalimentación fue clave para enriquecer el modelo de negocio y llegar a la propuesta de solución final.
- Published
- 2018
24. Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (Annona cherimola)
- Author
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Alicia Talavera, Noe Fernandez‐Pozo, Antonio J. Matas, Jose I. Hormaza, and Aureliano Bombarely
- Subjects
Annona cherimola ,Annonaceae ,cherimoya ,genome ,neglected and underutilized crops ,Environmental sciences ,GE1-350 ,Botany ,QK1-989 - Abstract
Societal Impact Statement Cherimoya has been an important food source since Pre‐Columbian times in the Americas. Although it is currently considered an underutilized fruit crop, it is still important at the local level in several regions of Central and South America, and has a clear niche for expansion in regions with subtropical climates. However, the availability of genomic resources to facilitate breeding programs and improve the understanding of Annonaceae genetic diversity is limited. In this work, we provide an important resource to fill this knowledge gap, with the hope that it will ultimately increase this crop's resilience under different climate change scenarios, which will increase food security in regions with subtropical climates. Summary Cherimoya (Annona cherimola Mill.) is a perennial fruit tree crop native to the Neotropics valued since pre‐Columbian times by different native American civilizations. It belongs to the Annonaceae, the largest family of the Magnoliid clade, sister to the eudicot and monocot clades of angiosperms. Despite its excellent organoleptic and nutritive qualities, this crop remains underutilized, although it has a clear niche for expansion in regions with subtropical climates. To date, no previous significant genomic information is available for this species, which would be a key tool to optimize breeding programs and advance in the study and conservation of its extant genetic diversity. A combination of different sequencing technologies (Illumina, Pacific Biosciences) has been implemented in order to assemble a chromosome‐level reference genome of A. cherimola. The final reference genome resulted in an assembly of 1.13 Gb and N50 of 170.86 Mb, anchored into seven pseudomolecules and with a completeness of 95.6%. A total of 41,413 protein‐coding genes were identified, many of which were related to secondary metabolism, defense mechanisms, stress response, and development. The results of this study provide novel significant genomic resources not only for cherimoya and other species of the Annonaceae but also for understanding the evolution of the earlier divergent angiosperms.
- Published
- 2023
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25. Food & You: A digital cohort on personalized nutrition
- Author
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Harris Héritier, Chloé Allémann, Oleksandr Balakiriev, Victor Boulanger, Sean F. Carroll, Noé Froidevaux, Germain Hugon, Yannis Jaquet, Djilani Kebaili, Sandra Riccardi, Geneviève Rousseau-Leupin, Rahel M. Salathé, Talia Salzmann, Rohan Singh, Laura Symul, Elif Ugurlu-Baud, Peter de Verteuil, and Marcel Salathé
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 - Published
- 2023
26. Sixty years of species diversity and population density decline of freshwater mussels in a global biodiversity hotspot
- Author
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Xiongjun Liu, Noé Ferreira-Rodríguez, Ruiwen Wu, Shan Ouyang, and Xiaoping Wu
- Subjects
Unionoida ,Biodiversity loss ,Regional homogenization ,Habitat degradation ,Asia ,Ecology ,QH540-549.5 - Abstract
The worldwide decline in freshwater biodiversity due to rising anthropogenic pressures is of growing concern. Much evidence reveals that biodiversity loss and taxonomic homogenization results in loss of ecosystem functions. Understanding temporal and spatial patterns of biodiversity is, a major challenge in ecological conservation. Of all groups of threatened aquatic animals, freshwater mussels are responsible for critical trophic and non-trophic functions. Based on published inventories and field surveys, here we aim to evaluate whether freshwater mussel diversity, density and biomass has changed in the last 60 years, as well as the factors driving these patterns in different areas within the Poyang Lake basin, a global biodiversity hotspot in the middle reach of the Yangtze River. Results showed that alpha diversity has declined in the current period (2016–2020) as compared to diversity in the historical (1960–2003) and intermediate periods (2003–2014). Overall species richness declined by 28 % over 60 years. Density and biomass also declined by 79 % and 42 %, respectively. Population declines led to homogenization of freshwater mussel faunas. Additionally, there was a significant association between pH and alpha and beta diversity, suggesting that acidification related to intensive agriculture development may be one major factor behind mussel declines. In summary, this study provides new insights into the patterns and drivers of freshwater mussel population dynamics in the Poyang Lake basin. The results have implications for the design of freshwater protected areas to slow, and even reverse, current declines.
- Published
- 2023
- Full Text
- View/download PDF
27. Detection of Coxiella burnetii DNA in Peridomestic and Wild Animals and Ticks in an Endemic Region (Canary Islands, Spain)
- Author
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Cristina Carranza-Rodríguez, Noé F. Rodríguez, Margarita Bolaños-Rivero, José Luis Pérez-Arellano, and Carlos Gutierrez
- Subjects
0301 basic medicine ,DNA, Bacterial ,Veterinary medicine ,Livestock ,Endemic Diseases ,Rhipicephalus sanguineus ,030106 microbiology ,030231 tropical medicine ,Q fever ,Animals, Wild ,Tick ,Microbiology ,Hyalomma lusitanicum ,03 medical and health sciences ,0302 clinical medicine ,Virology ,Zoonoses ,parasitic diseases ,medicine ,Animals ,Coxiella burnetii DNA ,biology ,business.industry ,fungi ,Rhipicephalus pusillus ,bacterial infections and mycoses ,biology.organism_classification ,Coxiella burnetii ,medicine.disease ,Infectious Diseases ,Spain ,business ,Q Fever - Abstract
Coxiella burnetii, the etiological agent of human Q fever, can infect mammals, birds, and arthropods. The Canary Islands (Spain) are considered an endemic territory, with a high prevalence in both humans and livestock. Nonetheless, there is no epidemiological information about the wild and peridomestic cycles of C. burnetii. Tissue samples from rodents on farms (100) and wild rabbits (129) were collected and assessed by PCR to detect C. burnetii DNA. In parallel, ticks were also collected from vegetation (1169), livestock (335), domestic dogs (169), and wild animals (65). Globally, eight rodents (8%) and two rabbits (1.5%) were found to be positive, with the spleen being the most affected organ. Tick species identified were Hyalomma lusitanicum, Rhipicephalus turanicus, Rhipicephalus sanguineus, and Rhipicephalus pusillus. Hyalomma lusitanicum (80%) was the main species identified in vegetation, livestock, and wild animals, whereas Rhipicephalus sanguineus was the most prevalent in domestic dogs. Overall, C. burnetii DNA was detected in 6.1% of the processed ticks, distributed between those removed from livestock (11.3%), domestic dogs (6.9%), and from wild animals (6%). Ticks from vegetation were all negative. Results suggest that, in the Canary Islands, C. burnetii develops in a peridomestic rather than a wild cycle.
- Published
- 2017
28. Physical activity limits the effects of age and Alzheimer's disease on postural control [L'activité physique limite les effets de l’âge et de la maladie d'Alzheimer sur le contrôle postural]
- Author
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Debove, L., Bru, Noëlle, Couderc, M., Noé, F., Paillard, Thierry, Mouvement, Équilibre, Performance, Santé (MEPS), Université de Pau et des Pays de l'Adour (UPPA), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), and Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
surgical procedures, operative ,[SDV]Life Sciences [q-bio] ,education ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,musculoskeletal system ,human activities ,health care economics and organizations - Abstract
ACL; International audience
- Published
- 2017
29. Bird conservation status and cultural values in Indigenous Mexican communities: towards a bioculturally informed conservation policy
- Author
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Graciela Alcántara-Salinas, Eugene S. Hunn, María Elena Ibáñez-Bravo, Elda Miriam Aldasoro-Maya, Noé Flores-Hernández, Juan Antonio Pérez-Sato, Natalia Real-Luna, Rafael Arturo Muñoz-Márquez Trujillo, Diana Lope-Alzina, and Jaime Ernesto Rivera-Hernández
- Subjects
Ethnoornithology ,Mexican Indigenous communities ,Nomenclatural recognition ,Cultural values of birds ,Biocultural conservation policies ,Other systems of medicine ,RZ201-999 ,Botany ,QK1-989 - Abstract
Abstract Background We summarize comparative ethnoornithological data for ten Mexican Indigenous communities, an initial step towards a comprehensive archive of the avian diversity conserved within Mexico’s Indigenous territories. We do so by counting highlighted species listed for bird conservation status on widely recognized “red lists” and their cultural value to build biocultural policies in Mexico for their conservation. Methods Indigenous bird names for each study site were determined to allow calculation of the “Scientific Species Recognition Ratio” (SSRR) for high cultural value birds obtained across communities. This demonstrated patterns of cultural prominence. A matrix of 1275 bird versus seven biocultural values was analysed using a correspondence analysis (InfoStat/L-v2020) to illustrate patterns of concordance between bird conservation status and cultural values. Results This paper contributes to quantitative and qualitative data on the role of ethnoornithology and ethnobiology in biocultural conservation. The areas studied provide refugia for almost 70% of the Mexican avifauna within a fraction of 1% of the national territory, that is 769 bird species recorded for all communities. The global correspondence of regions of biological and linguistic megadiversity is well established, while linguistic diversity is widely accepted as a good proxy for general cultural diversity. Our correspondence analysis explained 81.55% of the variation, indicating a strong relation between cultural importance and bird conservation status. We propose three main categories to establish a bioculturally informed public policy in Mexico for the conservation of what we described as high, medium, and bioculturally prominent bird species all include cultural value in any material or symbolic aspect. High are those species appearing on any threatened list, but also considered in any endemic status, while medium include threatened listed species. The last category included species not necessarily listed on any threat list, but with a wide range of social and cultural uses. We suggest that the concept might be extended to other species of biocultural importance. Conclusions We argue that bird conservation policies should be biocultural, that is they should recognize birds of cultural value on a par with bird species “of special interest” because they are most critical for biodiversity conservation. The desire of local people to protect their traditional community lands and livelihoods can be an effective biodiversity conservation strategy, which should be recognized in national biocultural policies.
- Published
- 2022
- Full Text
- View/download PDF
30. A transversal study on antibodies against selected pathogens in dromedary camels in the Canary Islands, Spain
- Author
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José de la Fuente, Mariana Boadella, Sunitha Joseph, Carlos Gutierrez, Oscar Cabezón, Gregorio Mentaberre, Christian Gortázar, David González-Barrio, Noé F. Rodríguez, and European Commission
- Subjects
Male ,viruses ,Antibodies, Protozoan ,Paratuberculosis ,Antibodies, Viral ,0403 veterinary science ,0302 clinical medicine ,Seroepidemiologic Studies ,Serosurvey ,Protozoan Infections, Animal ,media_common ,education.field_of_study ,biology ,Bacterial Infections ,04 agricultural and veterinary sciences ,General Medicine ,Antibodies, Bacterial ,Neospora caninum ,Virus ,3. Good health ,Parasite ,Virus Diseases ,Female ,Camelus ,Camelpox virus ,040301 veterinary sciences ,030231 tropical medicine ,Population ,Enzyme-Linked Immunosorbent Assay ,Microbiology ,03 medical and health sciences ,Dromedary camel ,parasitic diseases ,medicine ,Animals ,media_common.cataloged_instance ,European union ,education ,Bacteria ,General Veterinary ,bacterial infections and mycoses ,biology.organism_classification ,medicine.disease ,Coxiella burnetii ,Virology ,Rickettsia ,Spain ,Peste-des-petits-ruminants virus ,bacteria - Abstract
The Canary Islands contain the most important dromedary camel ( Camelus dromedarius) population in the European Union and are the main export point of dromedaries to continental Europe and Latin America. We investigated the presence of antibodies against relevant disease agents in 100 Canarian camel sera. Selected blood samples of the same animals were also tested by PCR. Sera were tested for antibodies against Bluetongue virus (BTV; 0%), Bovine Viral Diarrhoea virus (BVDV; 0%), Camelpox virus (CPV; 8% by serum neutralization, 16% by ELISA), Peste des Petits Ruminants virus (PPRV, 0%), Rift Valley Fever virus (RVFV; 0%) and West Nile Fever virus (WNV; 3%), the bacterial pathogens Anaplasma sp. (3%), Brucella sp. (1%), Coxiella burnetii (19%), Mycobacterium avium paratuberculosis (MAP; 22%), Mycobacterium tuberculosis complex (MTC; 10%) and Rickettsia sp. (83%), and the parasites Toxoplasma gondii (36%) and Neospora caninum (86%). The most remarkable findings were the detection of antibodies against CPV and the high antibody prevalence against C. burnetii, Rickettsia sp., T. gondii and N. caninum. By PCR, we found no C. burnetii, N. caninum and Anaplasma sp. DNA in the tested samples. However, Rickettsia sp. DNA was detected in six antibody positive tested samples. These results should be taken into consideration in order to implement adequate control measures and avoid a potential dissemination of infections to other territories., This is a contribution to EU grants ANTIGONE (278976) and APHAEA (EMIDA ERA-NET).
- Published
- 2013
31. Trypanosoma evansi Assessment in Equines: A Study in One Decade in an Endemic Area of the Canary Islands, Spain
- Author
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Carlos Gutierrez, Margarita González-Martín, Noé F. Rodríguez, María Teresa Tejedor-Junco, and F. Doreste
- Subjects
medicine.medical_specialty ,geography ,Veterinary medicine ,education.field_of_study ,geography.geographical_feature_category ,Equine ,Population ,Biology ,Trypanosoma evansi ,Surra ,biology.organism_classification ,Vector (epidemiology) ,Epidemiology ,Archipelago ,medicine ,Herd ,Parasite hosting ,education - Abstract
Trypanosoma evansi was diagnosed in a camel in the Canary Islands for the first time in 1997, and the parasite is still present in a little area of the Archipelago. Since then, the disease has exclusively affected camel herds, and clinical evidence of the infection has not been demonstrated in any other animal hosts. In the frame of a control plan of the disease in the Archipelago, 864 equines located in the infected area were examined during one decade (2001-2010), of which a total of 26 (3%) were serologically positive but showed negative results at parasitological and molecular examinations. FreeCalc, an epidemiological tool to detect presence/absence of disease, showed that the population would be diseased at a confidence level of 99.916%. These results must suppose to implement the control plan against the disease including the equine population present in the surrounding area of the infected camel farms.
- Published
- 2013
32. Stomoxys calcitrans as possible vector of Trypanosoma evansi among camels in an affected area of the Canary Islands, Spain
- Author
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Margarita González-Martín, María Teresa Tejedor-Junco, Noé F. Rodríguez, and Carlos Gutierrez
- Subjects
Microbiology (medical) ,Trypanosoma ,endocrine system ,Veterinary medicine ,Trypanosoma evansi ,lcsh:Arctic medicine. Tropical medicine ,Camelus ,biology ,Stable flies ,lcsh:RC955-962 ,Muscidae ,Stomoxys ,biology.organism_classification ,Stomoxys calcitrans ,Insect Vectors ,Infectious Diseases ,Spain ,Vector (epidemiology) ,parasitic diseases ,Herd ,Animals ,Parasitology ,Seasons - Abstract
Introduction Trypanosoma evansi was first identified in the Canary Islands in 1997, and is still present in a small area of the Archipelago. To date, the disease has exclusively affected camel herds, and has not been detected in any other animal hosts. However potential vectors of Trypanosoma evansi must be identified. Methods One Nzi trap was placed on a camel farm located in the infected area for a period of one year. Results Two thousand five hundred and five insects were trapped, of which Stomoxys calcitrans was the sole hematophagous vector captured. Conclusions Stomoxys calcitrans could be exclusively responsible for the transmission of Trypanosoma evansi among camels in the surveyed area, as other species do not seem to be infected by S. calcitrans in the presence of camels.
- Published
- 2014
33. The role of wild rodents in the transmission of Trypanosoma evansi infection in an endemic area of the Canary Islands (Spain)
- Author
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María Teresa Tejedor-Junco, Noé F. Rodríguez, Y. Hernández-Trujillo, Carlos Gutierrez, and Margarita González
- Subjects
Trypanosoma ,Veterinary medicine ,Diagnostic methods ,Endemic Diseases ,General Veterinary ,biology ,Rodent ,Transmission (medicine) ,Endemic area ,Animals, Wild ,General Medicine ,Trypanosoma evansi ,biology.organism_classification ,Virology ,Rats ,Serology ,Mice ,Spain ,Trypanosomiasis ,biology.animal ,Animals ,Parasitology - Abstract
Trypanosoma evansi was diagnosed for the first time in camels in the Canary Islands in 1997. Several sanitary measures including treatment of infected animals were taken; however, nowadays a little area is still infected. In order to determine possible reservoirs 138 wild rodents were trapped, 64 of them in the infected farms and the remaining 74 in other areas. The captured species were Rattus rattus (24), Rattus norvegicus (69) and Mus musculus domesticus (45). Serological (CATT/T. evansi), parasitological (micro-Hematocrit Centrifugation technique and stained smears) and molecular (PCR) methods for T. evansi and T. lewisi were used as diagnostic methods. None of the examined rodents was positive for T. evansi; 18, however, showed motile trypanosomes at micro-Hematocrit Centrifugation technique and resulted positive for T. lewisi by PCR. The results would suggest that the studied rodent species would not play a relevant role in the epidemiology of T. evansi infection in Canaries.
- Published
- 2010
34. Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)
- Author
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Lydia Gramzow, Katharina Klupsch, Noé Fernández-Pozo, Martin Hölzer, Manja Marz, Stefan A. Rensing, and Günter Theißen
- Subjects
Transcriptome ,Fruit development ,Dehiscence ,Differentially expressed genes ,Lepidium appelianum ,Lepidium campestre ,Botany ,QK1-989 - Abstract
Abstract Background Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system. Results We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs. Conclusions Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.
- Published
- 2022
- Full Text
- View/download PDF
35. Crystal structure of the dynamin tetramer
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Reubold, T.F., Faelber, K., Plattner, N., Posor, Y., Ketel, K., Curth, U., Schlegel, J., Anand, R., Manstein, D.J., Noé, F., Haucke, V., Daumke, O., and Eschenburg, S.
- Subjects
Cancer Research ,macromolecular substances ,biological phenomena, cell phenomena, and immunity - Abstract
The mechanochemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes. Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane. Previous studies have described the architecture of dynamin dimers, but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here we present the crystal structure of the human dynamin tetramer in the nucleotide-free state. Combining structural data with mutational studies, oligomerization measurements and Markov state models of molecular dynamics simulations, we suggest a mechanism by which oligomerization of dynamin is linked to the release of intramolecular autoinhibitory interactions. We elucidate how mutations that interfere with tetramer formation and autoinhibition can lead to the congenital muscle disorders Charcot-Marie-Tooth neuropathy and centronuclear myopathy, respectively. Notably, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.
- Published
- 2015
36. Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in Hsp90- and Sgt1-Silenced Plants: Insights from Gene Expression Dynamics
- Author
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Irene Ontiveros, Noé Fernández-Pozo, Anna Esteve-Codina, Juan José López-Moya, and Juan Antonio Díaz-Pendón
- Subjects
basal resistance ,Hsp90 ,Sgt1 ,ToCV ,Bemisia tabaci ,tomato ,Microbiology ,QR1-502 - Abstract
The emerging whitefly-transmitted crinivirus tomato chlorosis virus (ToCV) causes substantial economic losses by inducing yellow leaf disorder in tomato crops. This study explores potential resistance mechanisms by examining early-stage molecular responses to ToCV. A time-course transcriptome analysis compared naïve, mock, and ToCV-infected plants at 2, 7, and 14 days post-infection (dpi). Gene expression changes were most notable at 2 and 14 dpi, likely corresponding to whitefly feeding and viral infection. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed key genes and pathways associated with ToCV infection, including those related to plant immunity, flavonoid and steroid biosynthesis, photosynthesis, and hormone signaling. Additionally, virus-derived small interfering RNAs (vsRNAs) originating from ToCV predominantly came from RNA2 and were 22 nucleotides in length. Furthermore, two genes involved in plant immunity, Hsp90 (heat shock protein 90) and its co-chaperone Sgt1 (suppressor of the G2 allele of Skp1) were targeted through viral-induced gene silencing (VIGS), showing a potential contribution to basal resistance against viral infections since their reduction correlated with increased ToCV accumulation. This study provides insights into tomato plant responses to ToCV, with potential implications for developing effective disease control strategies.
- Published
- 2023
- Full Text
- View/download PDF
37. Comparison between micro-hematocrit centrifugation technique and polymerase chain reaction (PCR) to detect Trypanosoma evansi in experimentally inoculated goats
- Author
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Margarita González, Juan Alberto Corbera, Noé F. Rodríguez, María Teresa Tejedor-Junco, and Carlos Gutierrez
- Subjects
education.field_of_study ,medicine.diagnostic_test ,Population ,Parasitemia ,Hematocrit ,Biology ,Trypanosoma evansi ,medicine.disease ,biology.organism_classification ,Virology ,law.invention ,genomic DNA ,Food Animals ,law ,medicine ,Animal Science and Zoology ,Centrifugation ,Primer (molecular biology) ,education ,Polymerase chain reaction - Abstract
Natural Trypanosoma evansi infection in the Canary Islands has only been diagnosed in the camel population, but dissemination of the disease in other hosts has not been excluded. To evaluate the role of the goats in the dissemination of the disease, 8 goats were inoculated and examined during 6 months using a polymerase chain reaction (PCR) with a primer targeting a repetitive region specific for Trypanozoon subgenus used to amplify a 227 bp fragment from the genomic DNA. PCR was able to detect parasitemia in all tested samples; therefore it was considered as gold standard test in this study. The results were compared with those obtained using the micro-hematocrit centrifugation technique showing a sensitivity of 92.7%, specificity of 100%, positive predictive value of 1 and negative predictive value of 0.87. Both techniques seem to be adequate to detect T. evansi from infected goats.
- Published
- 2011
38. Dynamic Metamaterials for Structural Stopband Creation
- Author
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Melo, Noé F., primary, Claeys, Claus, additional, Deckers, Elke, additional, Pluymers, Bert, additional, and Desmet, Wim, additional
- Published
- 2016
- Full Text
- View/download PDF
39. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields
- Author
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Vitalini, F., primary, Noé, F., additional, and Keller, B.G., additional
- Published
- 2016
- Full Text
- View/download PDF
40. Influence des chaussures de ski-alpin sur le contrôle postural de skieurs de haut niveau
- Author
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Noé, F., Paillard, Thierry, Mouvement, Équilibre, Performance, Santé (MEPS), and Université de Pau et des Pays de l'Adour (UPPA)
- Subjects
[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2013
41. Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors
- Author
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Amanda Bullones, Antonio Jesús Castro, Elena Lima-Cabello, Noe Fernandez-Pozo, Rocío Bautista, Juan de Dios Alché, and Manuel Gonzalo Claros
- Subjects
germination ,olive ,pollen ,pollen tube ,RNA-seq ,transcriptomics ,Botany ,QK1-989 - Abstract
The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide events underlying pollen hydration and growth in this species. To fill this gap, triplicate mRNA samples at 0, 1, 3, and 6 h of in vitro germination of olive cultivar Picual pollen were analysed by RNA-seq. A bioinformatics R workflow called RSeqFlow was developed contemplating the best practices described in the literature, covering from expression data filtering to differential expression and clustering, to finally propose hub genes. The resulting olive pollen transcriptome consisted of 22,418 reliable transcripts, where 5364 were differentially expressed, out of which 173 have no orthologue in plants and up to 3 of them might be pollen-specific transcription factors. Functional enrichment revealed a deep transcriptional reprogramming in mature olive pollen that is also dependent on protein stability and turnover to allow pollen tube emergence, with many hub genes related to heat shock proteins and F-box-containing proteins. Reprogramming extends to the first 3 h of growth, including processes consistent with studies performed in other plant species, such as global down-regulation of biosynthetic processes, vesicle/organelle trafficking and cytoskeleton remodelling. In the last stages, growth should be maintained from persistent transcripts. Mature pollen is equipped with transcripts to successfully cope with adverse environments, even though the in vitro growth seems to induce several stress responses. Finally, pollen-specific transcription factors were proposed as probable drivers of pollen germination in olive trees, which also shows an overall increased number of pollen-specific gene isoforms relative to other plants.
- Published
- 2023
- Full Text
- View/download PDF
42. Cross-sectional study on prevalence of Trypanosoma evansi infection in domestic ruminants in an endemic area of the Canary Islands (Spain)
- Author
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Margarita González-Martín, Carlos Gutierrez, María Teresa Tejedor-Junco, Noé F. Rodríguez, and A. Santana del Pino
- Subjects
Veterinary medicine ,Trypanosoma ,Population ,Cattle Diseases ,Sheep Diseases ,Polymerase Chain Reaction ,Serology ,Food Animals ,Trypanosomiasis ,Agglutination Tests ,medicine ,Prevalence ,Animals ,African trypanosomiasis ,education ,Disease Reservoirs ,education.field_of_study ,Goat Diseases ,Sheep ,biology ,business.industry ,Incidence (epidemiology) ,Goats ,Trypanosoma evansi ,Surra ,medicine.disease ,biology.organism_classification ,Cross-Sectional Studies ,Parasitology ,Spain ,Animal Science and Zoology ,Livestock ,Cattle ,business - Abstract
Trypanosoma evansi is the most widely spread of the pathogenic African trypanosomes of animals. The disease (surra) was first diagnosed in the Canary Islands in a dromedary camel in 1997; thus, a control plan was implemented achieving the eventual eradication of T. evansi from most of the infected areas in the Archipelago. However, a little area remains still infected despite the use of the same control measures. To evaluate possible reservoirs in the area a representative sample of domestic ruminants was examined by serological, parasitological and molecular tests. Of a total of 1228 ruminants assessed, 61 (5%) were serologically positive (7 cattle, 21 goats, 33 sheep), but T. evansi could be demonstrated in none of them. According to FreeCalc assessment, cattle and goat populations would be free from disease; however, the results from sheep are not adequate to conclude that the population would be free from disease. As a conclusion, surveillance must be exercised on ruminant farms in the surroundings of the infected area in order to evaluate the possible extension of the disease and their potential role as reservoirs of T. evansi.
- Published
- 2011
43. Epidemiología clínica y molecular de la tripanosomosis animal por Trypanosoma evansi en Canarias
- Author
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Rodríguez González, Noé F., Gutiérrez Cabrera, Carlos, Tejedor Junco, María Teresa, González Martín, Margarita Rosa, and Departamento de Patología Animal, Producción Animal, Bromatología y Tecnología de los Alimentos
- Subjects
3109 Ciencias veterinarias ,240112 Parasitología animal - Abstract
Premio Extraordinario de Doctorado. Rama de Ciencias de la Salud, [ES] Los objetivos de este trabajo son: 1. Comparar las técnicas diagnósticas de concentración del hematocrito (MHCT) y de la reacción en cadena de la polimerasa (PCR) para detectar T.evansi en cabras inoculadas experimentalmente, de cara a su utilidad en el posterior estudio de campo sobre rumiantes. 2. Determinar el papel de los rumiantes domésticos en la epidemiología de T.evansi en la isla de Gran Canaria. 3. Determinar el papel de los équidos residentes o próximos a la zona afectada en la epidemiología de la enfermedad en Gran Canaria. 4. Determinar los vectores responsables de la transmisión de la enfermedad en Canarias. 5. Determinar el papel de los roedores silvestres en la epidemiología de T. evansi en la isla de Gran Canaria.
- Published
- 2011
44. Implication des articulations du genou et de la hanche dans le contrôle postural sur un plateau mobile
- Author
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Noé, F., primary, Garcà-A-Massà, X., additional, and Paillard, T., additional
- Published
- 2015
- Full Text
- View/download PDF
45. Évolution de la locomotion au cours de la journée chez des patients atteints de la maladie d’Alzheimer
- Author
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Paillard, T., primary, Noé, F., additional, Bru, N., additional, Couderc, M., additional, and Debove, L., additional
- Published
- 2015
- Full Text
- View/download PDF
46. Les performances posturale et cognitive divergent et varient selon l’état physiologique
- Author
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Paillard, T., primary, Garcà-A-Massà, X., additional, Huertas Olmedo, F., additional, Pablos Abella, C., additional, Noé, F., additional, and Bermejo, J.-L., additional
- Published
- 2015
- Full Text
- View/download PDF
47. A Basis Set for Peptides for the Variational Approach to Conformational Kinetics
- Author
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Vitalini, F., primary, Noé, F., additional, and Keller, B. G., additional
- Published
- 2015
- Full Text
- View/download PDF
48. OliveAtlas: A Gene Expression Atlas Tool for Olea europaea
- Author
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Amanda Bullones, Antonio Jesús Castro, Elena Lima-Cabello, Juan de Dios Alché, Francisco Luque, Manuel Gonzalo Claros, and Noe Fernandez-Pozo
- Subjects
Olea europaea ,RNA-seq ,bioinformatics ,gene expression ,abiotic stress ,Verticillium ,Botany ,QK1-989 - Abstract
The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the ‘Picual’ genome reference and gene annotation.
- Published
- 2023
- Full Text
- View/download PDF
49. MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica
- Author
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Aynhoa Gómez-Ollé, Amanda Bullones, Jose I. Hormaza, Lukas A. Mueller, and Noe Fernandez-Pozo
- Subjects
mango ,Mangifera indica ,bioinformatics ,genomics ,gene expression ,RNA-seq ,Botany ,QK1-989 - Abstract
Mango (Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated in more than 100 countries, with a production of more than 40 million tons. Recently the genome sequences of several mango varieties have been released, but there are no bioinformatics platforms dedicated to mango genomics and breeding to host mango omics data. Here, we present MangoBase, a web portal dedicated to mango genomics, which provides multiple interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. Additionally, MangoBase includes a gene expression atlas with 12 datasets and 80 experiments representing some of the most significant mango RNA-seq experiments published to this date. These experiments study mango fruit ripening in several cultivars with different pulp firmness and sweetness or peel coloration, and other experiments also study hot water postharvest treatment, infection with C. gloeosporioides, and the main mango tree organ tissues.
- Published
- 2023
- Full Text
- View/download PDF
50. A Network-Based Approach to Biomolecular Dynamics
- Author
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Noé, F., Smith, J. C., and Schütte, Ch.
- Subjects
ddc:004 - Published
- 2007
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