Fano-Liouville Spectral Signatures in Open Quantum Systems

The scattering amplitude from a set of discrete states coupled to a continuum became known as the Fano profile, characteristic for its asymmetric lineshape and originally investigated in the context of photoionization. The generality of the model, and the proliferation of engineered nanostructures with confined states gives immense success to the Fano lineshape, which is invoked whenever an asymmetric lineshape is encountered. However, many of these systems do not conform to the initial model worked out by Fano in that i) they are subject to dissipative processes and ii) the observables are not entirely analogous to the ones measured in the original photoionization experiments. In this letter, we work out the full optical response of a Fano model with dissipation. We find that the exact result for absorption, Raman, Rayleigh and fluorescence emission is a modified Fano profile where the typical lineshape has an additional Lorentzian contribution. Expressions to extract model parameters from a set of relevant observables are given.Comment: corrected typo

Unravelling the enhanced reactivity of bulk CeO 2 doped with gallium: A periodic DFT study

Doping CeO2 with gallium leads to promising materials with application in hydrogen purification processes for fuel cells. The bulk ceria?gallia is investigated by ab initio calculations. The outstanding reactivity is explained by important relaxations induced by gallium in the ceria host, having a strong impact in the electronic structure. As a result, the mixed oxide is found to be more reducible than the pure oxides in agreement with experimental data. It is thus possible to correlate structure and reactivity of the doped system on the molecular level, representing a step forward to the rational design of materials with selected properties.Fil: Quaino, Paola Monica. Universidad Nacional del Litoral. Facultad de Ingeniería Química. Programa de Electroquímica Aplicada e Ingeniería Electroquímica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Syzgantseva, Olga. Université Pierre et Marie Curie; FranciaFil: Siffert, Luca. Université Pierre et Marie Curie; FranciaFil: Tielens, Frederik. Université Pierre et Marie Curie; FranciaFil: Minot, Christian. Université Pierre et Marie Curie; FranciaFil: Calatayud, Monica. Universite de Paris; Franci

Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large-scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetics described by the Smoluchowski theory. Ultimately, molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, enabling safe design strategies

Physiological and Biochemical Responses to Salt Stress in Cultivated Eggplant (Solanum melongena L.) and in S. insanum L., a Close Wild Relative

[EN] Eggplant (Solanum melongena) has been described as moderately sensitive to salinity. We characterised the responses to salt stress of eggplant andS. insanum, its putative wild ancestor. Young plants of two accessions of both species were watered for 25 days with an irrigation solution containing NaCl at concentrations of 0 (control), 50, 100, 200, and 300 mM. Plant growth, photosynthetic activity, concentrations of photosynthetic pigments, K+, Na+, and Cl(-)ions, proline, total soluble sugars, malondialdehyde, total phenolics, and total flavonoids, as well as superoxide dismutase, catalase, and glutathione reductase specific activities, were quantified. Salt stress-induced reduction of growth was greater inS. melongenathan inS. insanum.The photosynthetic activity decreased in both species, except for substomatal CO2 concentration (Ci) inS. insanum, although the photosynthetic pigments were not degraded in the presence of NaCl. The levels of Na+ and Cl(-)increased in roots and leaves with increasing NaCl doses, but leaf K(+)concentrations were maintained, indicating a relative stress tolerance in the two accessions, which also did not seem to suffer a remarkable degree of salt-induced oxidative stress. Our results suggest that the higher salt tolerance ofS. insanummostly lies in its ability to accumulate higher concentrations of proline and, to a lesser extent, Na(+)and Cl-. The results obtained indicate thatS. insanumis a good candidate for improving salt tolerance in eggplant through breeding and introgression programmes.This work was undertaken as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing CropWild Relatives", which is supported by the Government of Norway and managed by the Global Crop Diversity Trust. For further information, see the project website: http://cwrdiversity.org/. Funding was also received from Ministerio de Ciencia, Innovacion y Universidades, Agencia Estatal de Investigacion and Fondo Europeo de Desarrollo Regional (grant RTI-2018-094592-B-100 from MCIU/AEI/FEDER, UE), European Union's Horizon 2020 Research and Innovation Programme under grant agreement No. 677379 (Linking genetic resources, genomes, and phenotypes of Solanaceous crops; G2P-SOL) and Vicerrectorado de Investigacion, Innovacion y Transferencia de la Universitat Politecnica de Valencia (Ayuda a Primeros Proyectos de Investigacion; PAID-06-18). Mariola Plazas is grateful to Generalitat Valenciana and Fondo Social Europeo for a post-doctoral grant (APOSTD/2018/014). Marco Brenes is indebted to the Faculty of Biology of the Costa Rica Institute of Technology for partially supporting his stay in Valencia ("Fondo Solidario y Desarrollo Estudiantil").Brenes, M.; Solana, A.; Boscaiu, M.; Fita, A.; Vicente, O.; Calatayud, Á.; Prohens Tomás, J.... (2020). 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Journal of Agricultural and Food Chemistry, 60(47), 11821-11831. doi:10.1021/jf3037424Plazas, M., López-Gresa, M. P., Vilanova, S., Torres, C., Hurtado, M., Gramazio, P., … Prohens, J. (2013). Diversity and Relationships in Key Traits for Functional and Apparent Quality in a Collection of Eggplant: Fruit Phenolics Content, Antioxidant Activity, Polyphenol Oxidase Activity, and Browning. Journal of Agricultural and Food Chemistry, 61(37), 8871-8879. doi:10.1021/jf402429kPlazas, M., Vilanova, S., Gramazio, P., Rodríguez-Burruezo, A., Fita, A., Herraiz, F. J., … Prohens, J. (2016). Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools. Journal of the American Society for Horticultural Science, 141(1), 34-44. doi:10.21273/jashs.141.1.34Gramazio, P., Prohens, J., Plazas, M., Mangino, G., Herraiz, F. J., & Vilanova, S. (2017). Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.01477García-Fortea, E., Gramazio, P., Vilanova, S., Fita, A., Mangino, G., Villanueva, G., … Plazas, M. (2019). First successful backcrossing towards eggplant (Solanum melongena) of a New World species, the silverleaf nightshade (S. elaeagnifolium), and characterization of interspecific hybrids and backcrosses. Scientia Horticulturae, 246, 563-573. doi:10.1016/j.scienta.2018.11.018Knapp, S., & Vorontsova, M. (2016). A revision of the «African Non-Spiny» Clade of Solanum L. (Solanum sections Afrosolanum Bitter, Benderianum Bitter, Lemurisolanum Bitter, Lyciosolanum Bitter, Macronesiotes Bitter, and Quadrangulare Bitter: Solanaceae). PhytoKeys, 66, 1-142. doi:10.3897/phytokeys.66.8457Ranil, R. H. G., Prohens, J., Aubriot, X., Niran, H. M. L., Plazas, M., Fonseka, R. 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Effects of cytokinin on photosynthetic gas exchange, chlorophyll fluorescence parameters and antioxidative system in seedlings of eggplant (Solanum melongena L.) under salinity stress. Acta Physiologiae Plantarum, 34(6), 2105-2114. doi:10.1007/s11738-012-1010-2Shaheen, S., Naseer, S., Ashraf, M., & Akram, N. A. (2013). Salt stress affects water relations, photosynthesis, and oxidative defense mechanisms inSolanum melongenaL. Journal of Plant Interactions, 8(1), 85-96. doi:10.1080/17429145.2012.718376Shahbaz, M., Mushtaq, Z., Andaz, F., & Masood, A. (2013). Does proline application ameliorate adverse effects of salt stress on growth, ions and photosynthetic ability of eggplant (Solanum melongena L.)? Scientia Horticulturae, 164, 507-511. doi:10.1016/j.scienta.2013.10.001Volkov, V. (2015). Salinity tolerance in plants. Quantitative approach to ion transport starting from halophytes and stepping to genetic and protein engineering for manipulating ion fluxes. 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Oxygen Vacancies in Oxide Nanoclusters: When Silica Is More Reducible Than Titania

Oxygen vacancies are related to specific optical, conductivity and magnetic properties in macroscopic SiO2 and TiO2 compounds. As such, the ease with which oxygen vacancies form often determines the application potential of these materials in many technological fields. However, little is known about the role of oxygen vacancies in nanosized materials. In this work we compute the energies to create oxygen vacancies in highly stable nanoclusters of (TiO2)N, (SiO2)N, and mixed (TixSi1−xO2)N for sizes between N = 2 and N = 24 units. Contrary to the results for bulk and surfaces, we predict that removing an oxygen atom from global minima silica clusters is energetically more favorable than from the respective titania species. This unexpected chemical behavior is clearly linked to the inherent presence of terminal unsaturated oxygens at these nanoscale systems. In order to fully characterize our findings, we provide an extensive set of descriptors (oxygen vacancy formation energy, electron localization, density of states, relaxation energy, and geometry) that can be used to compare our results with those for other compositions and sizes. Our results will help in the search of novel nanomaterials for technological and scientific applications such as heterogeneous catalysis, electronics, and cluster chemistry

FungalBraid: A GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology

[EN] Current challenges in the study and biotechnological exploitation of filamentous fungi are the optimization of DNA cloning and fungal genetic transformation beyond model fungi, the open exchange of ready-to-use and standardized genetic elements among the research community, and the availability of universal synthetic biology tools and rules. The GoldenBraid (GB) cloning framework is a Golden Gate-based DNA cloning system developed for plant synthetic biology through Agrobacterium tumefaciens-mediated genetic transformation (ATMT). In this study, we develop reagents for the adaptation of GB version 3.0 from plants to filamentous fungi through: (i) the expansion of the GB toolbox with the domestication of fungal-specific genetic elements; (ii) the design of fungal-specific GB structures; and (iii) the ATMT and gene disruption of the plant pathogen Penicillium digitatum as a proof of concept. Genetic elements domesticated into the GB entry vector pUPD2 include promoters, positive and negative selection markers and terminators. Interestingly, some GB elements can be directly exchanged between plants and fungi, as demonstrated with the marker hph for Hyg(R) or the fluorescent protein reporter YFP. The iterative modular assembly of elements generates an endless number of diverse transcriptional units and other higher order combinations in the pDGB3 alpha/pDGB3 Omega destination vectors. Furthermore, the original plant GB syntax was adapted here to incorporate specific GB structures for gene disruption through homologous recombination and dual selection. We therefore have successfully adapted the GB technology for the ATMT of fungi. We propose the name of FungalBraid (FB) for this new branch of the GB technology that provides open, exchangeable and collaborative resources to the fungal research community.This work was funded by grants BIO2015-68790-C2-1-R and BIO2016-78601-R from the "Ministerio de Economia y Competitividad" (MINECO, Spain). SG was recipient of a predoctoral scholarship (FPU13/04584) within the FPU program from "Ministerio de Educacion, Cultura y Deporte" (MECD, Spain). We acknowledge the excellent technical assistance of Tania Campos and the help in the microscopy experiments of Jose M. Coll-Marques (IATA, Valencia, Spain). We also thank Dr. Pilar Moya (Universitat Politecnica de Valencia, Spain) for helpful discussions during the initial stages of this project.Hernanz-Koers, M.; Gandía-Gómez, M.; Garrigues-Cubells, SM.; Manzanares-Mir, PM.; Yenush, L.; Orzáez Calatayud, DV.; Marcos -Lopez, JF. (2018). FungalBraid: A GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology. Fungal Genetics and Biology. 116:51-61. https://doi.org/10.1016/j.fgb.2018.04.010S516111

Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials.

Funder: laura and john arnold foundationBACKGROUND: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, https://doi.org/10.17605/OSF.IO/GEHFX ). METHODS: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. RESULTS: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. CONCLUSIONS: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Estudis teòrics de clusters, superfícies i cristalls d'òxids metàl.lics. Propietats estructurals, electròniques i catalítiques

La present tesi doctoral tracta la modelitzacio de diferents estats de la materia: clusters o agregats, superficies i cristalls d'oxids metal.lics. Els metodes disponibles per abordar cada sistema han estat breument descrits, per justificar la seua utilitzacio en diverses aplicacions a materials. Primer, s'han proposat geometries per als agregats de V2O5 cations i neutres en fase gas, i s'han caracteritzat els estats electronics, estructura, espectre de vibracio i enllac quimic. Segon, s'han simulat superficies d'oxids metal.lics i processos d'adsorcio de molecules o atoms metal.lics: CH3OH i O2 sobre SnO2, Cu sobre ZnO. La interaccio adsorbat-superficie te lloc per un mecanisme acid/base, i s'ha caracteritzat la geometria i energia de cada supersistema (mode d'adsorcio, paper dels defectes de superficie). Finalment, s'ha estudiat el cristall de TiO2 en fase anatasa des de multiples punts de vista: descripcio de l'estructura en poliedres, estructura electronica (bandes i densitat d'estats), termodinamic (equacio d'estat) i d'enllac quimic ("Atoms In Molecules"). Les superficies mes estables han estat construides i els efectes de relaxacio avaluats