Stability threshold approach for complex dynamical systems

Acknowledgments This paper was developed within the scope of the IRTG 1740/TRP 2011/50151-0, funded by the DFG/FAPESP, and supported by the Government of the Russian Federation (Agreement No. 14.Z50.31.0033 with the Institute of Applied Physics RAS). The first author thanks Dr Roman Ovsyannikov for valuable discussions regarding estimation of the mistake probability.

A trait-based approach for predicting species responses to environmental change from sparse data : how well might terrestrial mammals track climate change?

Funded by COST (European Cooperation in Science and Technology) CEH projects. Grant Numbers: NEC05264, NEC05100 Natural Environment Research Council UK. Grant Number: NE/J008001/1 © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Phenotypic knockout of HIV type 1 chemokine coreceptor CCR-5 by intrakines as potential therapeutic approach for HIV-1 infection

A genetic defect in a CC-chemokine receptor (CCR)-5, the principal coreceptor for the macrophage-tropic HIV type 1 (HIV-1), recently was found to naturally protect CCR-5-defective, but healthy, individuals from HIV-1 infection. In this study, we mimic the natural resistance of the CCR-5-defective individuals by designing a strategy to phenotypically knock out CCR-5. The inactivation of the CCR-5 coreceptor is accomplished by targeting a modified CC-chemokine to the endoplasmic reticulum to block the surface expression of newly synthesized CCR-5. The lymphocytes transduced to express the intracellular chemokine, termed “intrakine,” were found to be viable and resistant to macrophage-tropic HIV-1 infection. Thus, this gene-based intrakine strategy targeted at the conserved cellular receptor for the prevention of HIV-1 entry should have significant advantages over currently described approaches for HIV-1 therapy.

A novel approach for the identification of protein–protein interaction with integral membrane proteins

Protein–protein interaction plays a major role in all biological processes. The currently available genetic methods such as the two-hybrid system and the protein recruitment system are relatively limited in their ability to identify interactions with integral membrane proteins. Here we describe the development of a reverse Ras recruitment system (reverse RRS), in which the bait used encodes a membrane protein. The bait is expressed in its natural environment, the membrane, whereas the protein partner (the prey) is fused to a cytoplasmic Ras mutant. Protein–protein interaction between the proteins encoded by the prey and the bait results in Ras membrane translocation and activation of a viability pathway in yeast. We devised the expression of the bait and prey proteins under the control of dual distinct inducible promoters, thus enabling a rapid selection of transformants in which growth is attributed solely to specific protein–protein interaction. The reverse RRS approach greatly extends the usefulness of the protein recruitment systems and the use of integral membrane proteins as baits. The system serves as an attractive approach to explore novel protein–protein interactions with high specificity and selectivity, where other methods fail.

A demographic approach to selection

The concepts of demography provide a means of combining the ecological approach to population growth with the genetical approach to natural selection. We have utilized the demographic theory of natural selection developed by Norton and Charlesworth to analyze life history schedules of births and deaths for populations of genotypes in Drosophila pseudoobscura. Our populations illustrate a stable genetic equilibrium, an unstable genetic equilibrium, and a case of no equilibrium. We have estimated population growth rates and Darwinian fitnesses of the genotypes and have explored the role of population growth in determining natural selection. The age-specific rates of births and deaths provide insights into components of selection. Both viability and fertility are important components in our populations.

A total system approach to sustainable pest management

A fundamental shift to a total system approach for crop protection is urgently needed to resolve escalating economic and environmental consequences of combating agricultural pests. Pest management strategies have long been dominated by quests for “silver bullet” products to control pest outbreaks. However, managing undesired variables in ecosystems is similar to that for other systems, including the human body and social orders. Experience in these fields substantiates the fact that therapeutic interventions into any system are effective only for short term relief because these externalities are soon “neutralized” by countermoves within the system. Long term resolutions can be achieved only by restructuring and managing these systems in ways that maximize the array of “built-in” preventive strengths, with therapeutic tactics serving strictly as backups to these natural regulators. To date, we have failed to incorporate this basic principle into the mainstream of pest management science and continue to regress into a foot race with nature. In this report, we establish why a total system approach is essential as the guiding premise of pest management and provide arguments as to how earlier attempts for change and current mainstream initiatives generally fail to follow this principle. We then draw on emerging knowledge about multitrophic level interactions and other specific findings about management of ecosystems to propose a pivotal redirection of pest management strategies that would honor this principle and, thus, be sustainable. Finally, we discuss the potential immense benefits of such a central shift in pest management philosophy.

Human immunodeficiency virus (HIV) type 2-mediated inhibition of HIV type 1: a new approach to gene therapy of HIV-infection.

Human immunodeficiency virus (HIV) type 2, the second AIDS-associated human retrovirus, differs from HIV-1 in its natural history, infectivity, and pathogenicity, as well as in details of its genomic structure and molecular behavior. We report here that HIV-2 inhibits the replication of HIV-1 at the molecular level. This inhibition was selective, dose-dependent, and nonreciprocal. The closely related simian immunodeficiency provirus also inhibited HIV-1. The selectivity of inhibition was shown by the observation that HIV-2 did not significantly downmodulate the expression of the unrelated murine leukemia virus; neither did the murine leukemia virus markedly affect HIV-1 or HIV-2 expression. Moreover, while HIV-2 potently inhibited HIV-1, the reverse did not happen, thus identifying yet another and remarkable difference between HIV-1 and HIV-2. Mutational analysis of the HIV-2 genome suggested that the inhibition follows a complex pathway, possibly involving multiple genes and redundant mechanisms. Introduction of inactivating mutations into the structural and regulatory/accessory genes did not render the HIV-2 provirus ineffective. Some of the HIV-2 gene defects, such as that of tat and rev genes, were phenotypically transcomplemented by HIV-1. The HIV-2 proviruses with deletions in the putative packaging signal and defective for virus replication were effective in inducing the suppressive phenotype. Though the exact mechanism remains to be defined, the inhibition appeared to be mainly due to an intracellular molecular event because it could not be explained solely on the basis of cell surface receptor mediated interference. The results support the notion that the inhibition likely occurred at the level of viral RNA, possibly involving competition between viral RNAs for some transcriptional factor essential for virus replication. Induction of a cytokine is another possibility. These findings might be relevant to the clinical-epidemiological data suggesting that infection with HIV-2 may offer some protection against HIV-1 infection.

Desenvolvimento de um método para diagnose de falhas na operação de navios transportadores de gás natural liquefeito através de redes bayesianas.

O Gás Natural Liquefeito (GNL) tem, aos poucos, se tornado uma importante opção para a diversificação da matriz energética brasileira. Os navios metaneiros são os responsáveis pelo transporte do GNL desde as plantas de liquefação até as de regaseificação. Dada a importância, bem como a periculosidade, das operações de transporte e de carga e descarga de navios metaneiros, torna-se necessário não só um bom plano de manutenção como também um sistema de detecção de falhas que podem ocorrer durante estes processos. Este trabalho apresenta um método de diagnose de falhas para a operação de carga e descarga de navios transportadores de GNL através da utilização de Redes Bayesianas em conjunto com técnicas de análise de confiabilidade, como a Análise de Modos e Efeitos de Falhas (FMEA) e a Análise de Árvores de Falhas (FTA). O método proposto indica, através da leitura de sensores presentes no sistema de carga e descarga, quais os componentes que mais provavelmente estão em falha. O método fornece uma abordagem bem estruturada para a construção das Redes Bayesianas utilizadas na diagnose de falhas do sistema.

Identifying the role of natural resources in knowledge-based strategies of development

Knowledge has adopted a preferential role in the explanation of development while the evidence about the effect of natural resources in countries’ performance is more controversial in the economic literature. This paper tries to demonstrate that natural resources may positively affect growth in countries with a strong natural resources specialization pattern although the magnitude of these effects depend on the type of resources and on other aspects related to the production and innovation systems. The positive trajectory described by a set of national economies mainly specialized in natural resources and low-tech industries invites us to analyze what is the combination of factors that serves as engine for a sustainable development process. With panel data for the period 1996-2008 we estimate an applied growth model where both traditional factors and other more related to innovation and absorptive capabilities are taken into account. Our empirical findings show that according to the postulates of a knowledge-based approach, a framework that combines physical and intangible factors is more suitable for the definition of development strategies in those prosperous economies dominated by natural resources and connected activities, while the internationalization process of activities and technologies become also a very relevant aspect.

EmotiBlog: a model to learn subjective information detection in the new textual genres of the Web 2.0 -a multilingual and multi-genre approach-

Tesis doctoral con mención europea en procesamiento del lenguaje natural realizada en la Universidad de Alicante por Ester Boldrini bajo la dirección del Dr. Patricio Martínez-Barco. El acto de defensa de la tesis tuvo lugar en la Universidad de Alicante el 23 de enero de 2012 ante el tribunal formado por los doctores Manuel Palomar (Universidad de Alicante), Dr. Paloma Moreda (UA), Dr. Mariona Taulé (Universidad de Barcelona), Dr. Horacio Saggion (Universitat Pompeu Fabra) y Dr. Mike Thelwall (University of Wolverhampton). Calificación: Sobresaliente Cum Laude por unanimidad.

An approach based on Logic Forms and WordNet relationships to Textual Entailment performance

This paper outlines the approach adopted by the PLSI research group at University of Alicante in the PASCAL-2006 second Recognising Textual Entailment challenge. Our system is composed of several components. On the one hand, the first component performs the derivation of the logic forms of the text/hypothesis pairs and, on the other hand, the second component provides us with a similarity score given by the semantic relations between the derived logic forms. In order to obtain this score we apply several measures of similitude and relatedness based on the structure and content of WordNet.

Applying semantic knowledge to the automatic processing of temporal expressions and events in natural language

This paper addresses the problem of the automatic recognition and classification of temporal expressions and events in human language. Efficacy in these tasks is crucial if the broader task of temporal information processing is to be successfully performed. We analyze whether the application of semantic knowledge to these tasks improves the performance of current approaches. We therefore present and evaluate a data-driven approach as part of a system: TIPSem. Our approach uses lexical semantics and semantic roles as additional information to extend classical approaches which are principally based on morphosyntax. The results obtained for English show that semantic knowledge aids in temporal expression and event recognition, achieving an error reduction of 59% and 21%, while in classification the contribution is limited. From the analysis of the results it may be concluded that the application of semantic knowledge leads to more general models and aids in the recognition of temporal entities that are ambiguous at shallower language analysis levels. We also discovered that lexical semantics and semantic roles have complementary advantages, and that it is useful to combine them. Finally, we carried out the same analysis for Spanish. The results obtained show comparable advantages. This supports the hypothesis that applying the proposed semantic knowledge may be useful for different languages.

A "Know-How vs. Know-What" Approach in the Teaching-Learning of Competences in Physical Chemistry

The methodological approach a teacher uses in the competence teaching-learning process determines the way students learn. Knowledge can be acquired from a series of perspectives, mainly: “know-what” (concept), where facts and descriptions of (natural or social) phenomena are pursued; “know-how” (procedure), where methods and procedures for their application are described; and “know-why” (competence), where general principles and laws that explain both the facts and their applications are sought. As all the three cases are interconnected, the boundaries between them are not fully clear and their application uses shared elements. In any case, the depth of student’s acquired competences will be directly affected by the teaching-learning perspective, traditionally aiming to a “know-why” approach for full competence acquisition. In this work, we discuss a suitable teaching-learning methodology for evaluating whether a “know-how”, “know-what” or combined approach seems better for enhancing competence learning in students. We exemplify the method using a selection of formative activities from the Physical Chemistry area in the Grades of Chemistry and Chemical Engineering.

Microwave-Assisted Extraction of Phenolic Compounds from Almond Skin Byproducts (Prunus amygdalus): A Multivariate Analysis Approach

A microwave-assisted extraction (MAE) procedure to isolate phenolic compounds from almond skin byproducts was optimized. A three-level, three-factor Box–Behnken design was used to evaluate the effect of almond skin weight, microwave power, and irradiation time on total phenolic content (TPC) and antioxidant activity (DPPH). Almond skin weight was the most important parameter in the studied responses. The best extraction was achieved using 4 g, 60 s, 100 W, and 60 mL of 70% (v/v) ethanol. TPC, antioxidant activity (DPPH, FRAP), and chemical composition (HPLC-DAD-ESI-MS/MS) were determined by using the optimized method from seven different almond cultivars. Successful discrimination was obtained for all cultivars by using multivariate linear discriminant analysis (LDA), suggesting the influence of cultivar type on polyphenol content and antioxidant activity. The results show the potential of almond skin as a natural source of phenolics and the effectiveness of MAE for the reutilization of these byproducts.

Bio-renewable enantioselective aldol reaction in natural deep eutectic solvents

Among the deep eutectic solvents (DES), natural deep eutectic solvents (NADES) formed by D-glucose and racemic malic acid are suitable media to perform the enantioselective L-proline catalyzed intermolecular aldol reaction, creating simultaneously and selectively a C–C bond and a new stereocenter. The scope of the reaction was found to be broad, with products being obtained with good levels of diastereo- and enantioselectivities. Furthermore, when the reaction was performed at a large scale, the catalyst together with the reaction media can be recovered by simple water extraction and reused at least three times affording similar results. Therefore, the use of NADES as reaction media to carry out a VOC-free selective process has been demonstrated for the first time. The process is clean, cheap, simple and scalable and meets most of the criteria to be considered as a sustainable and bio-renewable process, with the reaction media and catalyst arising directly from Nature.