Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem. Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences. Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems

Wave function engineering in quantum dot-ring nanostructures

Modern nanotechnology allows producing, depending on application, various quantum nanostructures with the desired properties. These properties are strongly influenced by the confinement potential which can be modified, e.g., by electrical gating. In this paper we analyze a nanostructure composed of a quantum dot surrounded by a quantum ring. We show that depending on the details of the confining potential the electron wave functions can be located in different parts of the structure. Since the properties of such a nanostructure strongly depend on the distribution of the wave functions, varying the applied gate voltage one can easily control them. In particular, we illustrate the high controllability of the nanostructure by demonstrating how its coherent, optical, and conducting properties can be drastically changed by a small modification of the confining potential.Comment: 8 pages, 10 figures, 2 tables, revte

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

The functional consequences of alternative splicing on altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimize the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the non-ribosomal protein transcripts

Notas para un ensayo sobre el ostracismo

Un eupátrida, Clístenes, de la familia alcmeónida, caudillo del patriciado durante la emigración, ganó finalmente la Acrópolis y se propuso contrarrestar la reacción pisistrátida capitaneando a los paralianos, a la clase media y a muchos nobles transigentes. Sus primeros actos fueron de una audacia desconcertante. Sus reformas constitucionales quitaron a los aristócratas toda esperanza de reconquistar privilegios y, contra la Montaña, dictó la ley de ostracismo, cuya severidad impediría en adelante la repetición del caso Pisistrato. "Si se quiere fundar la democracia - dice Aristóteles - se hará lo que Clístenes hizo entre los atenienses: se establecerán nuevas tribus y nuevas fratrias; a los sacrificios hereditarios de las familias se substituirán sacrificios en que todos los hombres serán admitidos, se confundirán cuanto sea posible las relaciones de los hombres entre sí, teniendo cuidado de destruir todas las asociaciones anteriores." (Párrafo extraído del texto a modo de resumen)Facultad de Humanidades y Ciencias de la Educació

CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress

The glutathione/cysteine exporter CydDC maintains redox balance in Escherichia coli. A cydD mutant strain was used to probe the influence of CydDC upon reduced thiol export, gene expression, metabolic perturbations, intracellular pH homeostasis, and tolerance to nitric oxide (NO). Loss of CydDC was found to decrease extracytoplasmic thiol levels, whereas overexpression diminished the cytoplasmic thiol content. Transcriptomic analysis revealed a dramatic up-regulation of protein chaperones, protein degradation (via phenylpropionate/phenylacetate catabolism), ?-oxidation of fatty acids, and genes involved in nitrate/nitrite reduction. 1H NMR metabolomics revealed elevated methionine and betaine and diminished acetate and NAD+ in cydD cells, which was consistent with the transcriptomics-based metabolic model. The growth rate and ?pH, however, were unaffected, although the cydD strain did exhibit sensitivity to the NO-releasing compound NOC-12. These observations are consistent with the hypothesis that the loss of CydDC-mediated reductant export promotes protein misfolding, adaptations to energy metabolism, and sensitivity to NO. The addition of both glutathione and cysteine to the medium was found to complement the loss of bd -type cytochrome synthesis in a cydD strain (a key component of the pleiotropic cydDC phenotype), providing the first direct evidence that CydDC substrates are able to restore the correct assembly of this respiratory oxidase. These data provide an insight into the metabolic flexibility of E. coli , highlight the importance of bacterial redox homeostasis during nitrosative stress, and report for the first time the ability of periplasmic low molecular weight thiols to restore haem incorporation into a cytochrome complex

Creating and observing N-partite entanglement with atoms

The Mermin inequality provides a criterion for experimentally ruling out local-realistic descriptions of multiparticle systems. A violation of this inequality means that the particles must be entangled, but does not, in general, indicate whether N-partite entanglement is present. For this, a stricter bound is required. Here we discuss this bound and use it to propose two different schemes for demonstrating N-partite entanglement with atoms. The first scheme involves Bose-Einstein condensates trapped in an optical lattice and the second uses Rydberg atoms in microwave cavities.Comment: 12 pages, 4 figure

Detecting Happiness in Italian Tweets: Towards an Evaluation Dataset for Sentiment Analysis in Felicittà

This paper focuses on the development of a gold standard corpus for the validation of Felicitta, an online platform which uses Twitter as data source in order to estimate and interactively display the degree of happiness in the Italian cities. The ultimate goal is the creation of an Italian reference Twitter dataset for sentiment analysis that can be used in several frameworks aimed at detecting sentiment from big data sources. We will provide an overview of the reference corpus created for evaluating Felicitta, with a special focus on the issues ` raised from its development, on the inter-annotator agreement discussion and on implications for the further development of the corpus, considering that the assumption that a single right answer exists for each annotated instance cannot be done in several cases in the particular kind of data at issue

Natural language generation in dialogue systems for customer care

In this paper we discuss the role of natural language generation (NLG) in modern dialogue systems (DSs). In particular, we will study the role that a linguistically sound NLG architecture can have in a DS. Using real examples from a new corpus of dialogue in customer-care domain, we will study how the non-linguistic contextual data can be exploited by using NLG

Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses

Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide an in-silico survey of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, structural epitope mapping by homology modelling revealed a potential immunogenic value also for specific sequences scoring a lower identity with SARS-CoV-2 nucleocapsid proteins. These evidence provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies

Effect of drying temperature on polyphenolic content and antioxidant activity of apricots

This study was carried out in order to check for the influence of drying parameters on the phenolic compounds and antioxidant activity on two apricot cultivars (Pelese and Cafona) using two sets of air drying temperatures: (1) air temperature at 55 °C; (2) air temperature at 75 °C. Whole fresh and dried fruits were assessed for: phenolics, ascorbic acid, antioxidant activity and redox potential (all parameters were calculated on a dry matter basis). Analysis of data shows that the decrease in chlorogenic and neochlorogenic acid in Cafona cultivar is higher at the lower drying temperature. Catechin showed the same behaviour of hydroxycinnamic acids in both cultivars, while the decrease in the other compounds was significantly more marked in the sample dried at 75 °C. The antioxidant activity increased significantly in Cafona fruits and this increase was confirmed by a diminution of the redox potential