Nanoinformatics approaches for information extraction and text mining in nanomedical research texts

La nanotecnología es un área de investigación de reciente creación que trata con la manipulación y el control de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. A escala nanométrica, los materiales exhiben fenómenos físicos, químicos y biológicos singulares, muy distintos a los que manifiestan a escala convencional. En medicina, los compuestos miniaturizados a nanoescala y los materiales nanoestructurados ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, así como una mejora en la focalización del medicamento hacia la diana terapéutica, revelando así nuevas propiedades diagnósticas y terapéuticas. A su vez, la complejidad de la información a nivel nano es mucho mayor que en los niveles biológicos convencionales (desde el nivel de población hasta el nivel de célula) y, por tanto, cualquier flujo de trabajo en nanomedicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Desafortunadamente, la informática biomédica todavía no ha proporcionado el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, ni ha adaptado sus métodos y herramientas a este nuevo campo de investigación. En este contexto, la nueva área de la nanoinformática pretende detectar y establecer los vínculos existentes entre la medicina, la nanotecnología y la informática, fomentando así la aplicación de métodos computacionales para resolver las cuestiones y problemas que surgen con la información en la amplia intersección entre la biomedicina y la nanotecnología. Las observaciones expuestas previamente determinan el contexto de esta tesis doctoral, la cual se centra en analizar el dominio de la nanomedicina en profundidad, así como en el desarrollo de estrategias y herramientas para establecer correspondencias entre las distintas disciplinas, fuentes de datos, recursos computacionales y técnicas orientadas a la extracción de información y la minería de textos, con el objetivo final de hacer uso de los datos nanomédicos disponibles. El autor analiza, a través de casos reales, alguna de las tareas de investigación en nanomedicina que requieren o que pueden beneficiarse del uso de métodos y herramientas nanoinformáticas, ilustrando de esta forma los inconvenientes y limitaciones actuales de los enfoques de informática biomédica a la hora de tratar con datos pertenecientes al dominio nanomédico. Se discuten tres escenarios diferentes como ejemplos de actividades que los investigadores realizan mientras llevan a cabo su investigación, comparando los contextos biomédico y nanomédico: i) búsqueda en la Web de fuentes de datos y recursos computacionales que den soporte a su investigación; ii) búsqueda en la literatura científica de resultados experimentales y publicaciones relacionadas con su investigación; iii) búsqueda en registros de ensayos clínicos de resultados clínicos relacionados con su investigación. El desarrollo de estas actividades requiere el uso de herramientas y servicios informáticos, como exploradores Web, bases de datos de referencias bibliográficas indexando la literatura biomédica y registros online de ensayos clínicos, respectivamente. Para cada escenario, este documento proporciona un análisis detallado de los posibles obstáculos que pueden dificultar el desarrollo y el resultado de las diferentes tareas de investigación en cada uno de los dos campos citados (biomedicina y nanomedicina), poniendo especial énfasis en los retos existentes en la investigación nanomédica, campo en el que se han detectado las mayores dificultades. El autor ilustra cómo la aplicación de metodologías provenientes de la informática biomédica a estos escenarios resulta efectiva en el dominio biomédico, mientras que dichas metodologías presentan serias limitaciones cuando son aplicadas al contexto nanomédico. Para abordar dichas limitaciones, el autor propone un enfoque nanoinformático, original, diseñado específicamente para tratar con las características especiales que la información presenta a nivel nano. El enfoque consiste en un análisis en profundidad de la literatura científica y de los registros de ensayos clínicos disponibles para extraer información relevante sobre experimentos y resultados en nanomedicina —patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.—, seguido del desarrollo de mecanismos para estructurar y analizar dicha información automáticamente. Este análisis concluye con la generación de un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento y de test anotados manualmente—, el cual ha sido aplicado a la clasificación de registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nanodrogas y nanodispositivos de aquellos enfocados a testear productos farmacéuticos tradicionales. El presente trabajo pretende proporcionar los métodos necesarios para organizar, depurar, filtrar y validar parte de los datos nanomédicos existentes en la actualidad a una escala adecuada para la toma de decisiones. Análisis similares para otras tareas de investigación en nanomedicina ayudarían a detectar qué recursos nanoinformáticos se requieren para cumplir los objetivos actuales en el área, así como a generar conjunto de datos de referencia, estructurados y densos en información, a partir de literatura y otros fuentes no estructuradas para poder aplicar nuevos algoritmos e inferir nueva información de valor para la investigación en nanomedicina. ABSTRACT Nanotechnology is a research area of recent development that deals with the manipulation and control of matter with dimensions ranging from 1 to 100 nanometers. At the nanoscale, materials exhibit singular physical, chemical and biological phenomena, very different from those manifested at the conventional scale. In medicine, nanosized compounds and nanostructured materials offer improved drug targeting and efficacy with respect to traditional formulations, and reveal novel diagnostic and therapeutic properties. Nevertheless, the complexity of information at the nano level is much higher than the complexity at the conventional biological levels (from populations to the cell). Thus, any nanomedical research workflow inherently demands advanced information management. Unfortunately, Biomedical Informatics (BMI) has not yet provided the necessary framework to deal with such information challenges, nor adapted its methods and tools to the new research field. In this context, the novel area of nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods to solve informational issues at the wide intersection between biomedicine and nanotechnology. The above observations determine the context of this doctoral dissertation, which is focused on analyzing the nanomedical domain in-depth, and developing nanoinformatics strategies and tools to map across disciplines, data sources, computational resources, and information extraction and text mining techniques, for leveraging available nanomedical data. The author analyzes, through real-life case studies, some research tasks in nanomedicine that would require or could benefit from the use of nanoinformatics methods and tools, illustrating present drawbacks and limitations of BMI approaches to deal with data belonging to the nanomedical domain. Three different scenarios, comparing both the biomedical and nanomedical contexts, are discussed as examples of activities that researchers would perform while conducting their research: i) searching over the Web for data sources and computational resources supporting their research; ii) searching the literature for experimental results and publications related to their research, and iii) searching clinical trial registries for clinical results related to their research. The development of these activities will depend on the use of informatics tools and services, such as web browsers, databases of citations and abstracts indexing the biomedical literature, and web-based clinical trial registries, respectively. For each scenario, this document provides a detailed analysis of the potential information barriers that could hamper the successful development of the different research tasks in both fields (biomedicine and nanomedicine), emphasizing the existing challenges for nanomedical research —where the major barriers have been found. The author illustrates how the application of BMI methodologies to these scenarios can be proven successful in the biomedical domain, whilst these methodologies present severe limitations when applied to the nanomedical context. To address such limitations, the author proposes an original nanoinformatics approach specifically designed to deal with the special characteristics of information at the nano level. This approach consists of an in-depth analysis of the scientific literature and available clinical trial registries to extract relevant information about experiments and results in nanomedicine —textual patterns, common vocabulary, experiment descriptors, characterization parameters, etc.—, followed by the development of mechanisms to automatically structure and analyze this information. This analysis resulted in the generation of a gold standard —a manually annotated training or reference set—, which was applied to the automatic classification of clinical trial summaries, distinguishing studies focused on nanodrugs and nanodevices from those aimed at testing traditional pharmaceuticals. The present work aims to provide the necessary methods for organizing, curating and validating existing nanomedical data on a scale suitable for decision-making. Similar analysis for different nanomedical research tasks would help to detect which nanoinformatics resources are required to meet current goals in the field, as well as to generate densely populated and machine-interpretable reference datasets from the literature and other unstructured sources for further testing novel algorithms and inferring new valuable information for nanomedicine.

Routines in precision agriculture technology: an action research study

A crop management and precision agriculture software application facilitates the flow of information between disparate software/equipment and the network of individuals that work with them. A new generation of farmers are using precision technology to help them more efficiently manage their roplands. By measuring precisely the way their fields reflect and emit energy at visible and infrared wavelengths, precision farmers can monitor a wide range of variables that affect their crops,such as soil moisture, surface temperature, photosynthetic activity, and weed or pest infestations. Over thirty years have passed since Nelson and Winter put the concept of routines firmly at the center of the analysis of organizational and economic change. Taken as the central unit of analysis, routines would help understand energy and agriculture economy evolution.

Occurrence and analysis of selected pharmaceutical compounds in soil from Spanish agricultural fields

This work describes the analysis of 15 pharmaceutical compounds, belonging to different therapeutic classes (anti-inflammatory/analgesics, lipid regulators, antiepileptics, ?-blockers and antidepressants) and with diverse physical?chemical properties, in Spanish soils with different farmland uses. The studied compounds were extracted from soil by ultrasound-assisted extraction (UAE) and determined, after derivatization, by gas chromatography with mass spectrometric detection (GC?MS). The limits of detection (LODs) ranged from 0.14 ng g?1 (naproxen) to 0.65 ng g?1 (amitriptyline). At least two compounds where detected in all samples, being ibuprofen, salicylic acid, and paracetamol, the most frequently detected compounds. The highest levels found in soil were 47 ng g?1 for allopurinol and 37 ng g?1 for salicylic acid. The influence of the type of crop and the sampling area on the levels of pharmaceuticals in soil, as well as their relationship with soil physical?chemical properties, was studied. The frequent and widespread detection of some of these compounds in agricultural soils show a diffuse contamination, although the low levels found do not pose a risk to the environment or the human health.

Ergodic theorems along sequences and Hardy fields.

Let a(x) be a real function with a regular growth as x --> infinity. [The precise technical assumption is that a(x) belongs to a Hardy field.] We establish sufficient growth conditions on a(x) so that the sequence ([a(n)])(infinity)(n=1) is a good averaging sequence in L2 for the pointwise ergodic theorem. A sequence (an) of positive integers is a good averaging sequence in L2 for the pointwise ergodic theorem if in any dynamical system (Omega, Sigma, m, T) for f [symbol, see text] in L2(Omega) the averages [equation, see text] converge for almost every omicron in. Our result implies that sequences like ([ndelta]), where delta > 1 and not an integer, ([n log n]), and ([n2/log n]) are good averaging sequences for L2. In fact, all the sequences we examine will turn out to be good averaging for Lp, p > 1; and even for L log L. We will also establish necessary and sufficient growth conditions on a(x) so that the sequence ([a(n)]) is good averaging for mean convergence. Note that for some a(x) (e.g., a(x) = log2 x), ([a(n)]) may be good for mean convergence without being good for pointwise convergence.

Rectification and signal averaging of weak electric fields by biological cells.

Oscillating electric fields can be rectified by proteins in cell membranes to give rise to a dc transport of a substance across the membrane or a net conversion of a substrate to a product. This provides a basis for signal averaging and may be important for understanding the effects of weak extremely low frequency (ELF) electric fields on cellular systems. We consider the limits imposed by thermal and "excess" biological noise on the magnitude and exposure duration of such electric field-induced membrane activity. Under certain circumstances, the excess noise leads to an increase in the signal-to-noise ratio in a manner similar to processes labeled "stochastic resonance." Numerical results indicate that it is difficult to reconcile biological effects with low field strengths.

The Use of Humor in Therapy : Research-Based Training Recommendations

Despite its essential and universal nature, humor has historically received limited attention from the behavioral sciences, particularly as compared to other affective experiences like anger and sadness. Some authors (e.g., Bell & Malhi, 2009; Provine, 2000a; Roeckelein, 2002) suggest that this is because researchers have traditionally failed to "take humor seriously" and, according to O'Connell (cited in Roeckelein, 2002), have too often pursued its study in a piecemeal manner lacking scientific rigor, resulting in "no comprehensive network of facts about the development and purposes of humor in human existence" (p. 1). Roeckelein (2002) found not a single mention of humor, laughter, wit, comedy, or theories relating to these topics in introductory psychology textbooks published between 1930 and 1996.While research interest in the area has grown, especially over the last decade, it remains an elusive and nebulous topic, more likely to be examined in specialty psychology texts (e.g., social psychology and child development) than general ones (Martin, 2007; Roeckelein, 2002). Organizations (e.g., The International Society for Humor Studies; The Association for the Advancement of Therapeutic Humor), journals (e.g., Humor: International Journal of Humor Research) and internet phenomena such as "The Humor Project" (www.humorproiect.com) have made great strides in integrating information about humor from discreet fields such as the arts and humanities, biological and social sciences, education, and business management. Still, the therapeutic potential of humor remains a relatively young subject of serious scientific inquiry (Marci, Moran, & Orr, 2004; Sala, Krupat, & Roter, 2002). While humor does make appearances in self-help books and publications addressing clinical applications, these sources are much ...

Competence profile differences among graduates from different academic subject fields: implications for improving students’ education

The aim of a university education is the intellectual development of citizens, and the training of professionals for their subsequent entry into the workforce. However, this entry into the workforce, following the theoretical education usually provided by the university, implies that students have to manage this difficult transition by themselves. Society, in a continual process of transformation, requires of universities that they adjust, adapting the education they offer to comply with the demands of society and the workplace. Socio-emotional skills would seem to have influence predicting professional performance. These skills also influence job-finding and employability. Consequently, providing teachers with an education in socioemotional competences is becoming a necessary task within universities, and the majority of teaching staff consider these skills to be fundamental to the personal and socio-emotional development of students. The objective of our proposed work is to establish the characteristic profile of competences of a sample of teachers in training, and compare it with the competences profile of graduate students belonging to the fields of law sciences, social sciences, humanities, science and technology, and health. Starting from results, implications will be derived for the development of generic competences of socio-emotional type in the framework of the European Frame of Higher Education.

The autonomy of the EU legal order and the law-making activities of international organizations. Some examples regarding the Council most recent practice. Research Papers in Law 03/2012

[Introduction.] It is generally believed that while the principle of the autonomy of the EU legal order, in the sense of constitutional and institutional autonomy that is to say what concerns the autonomous decision-making of the EU, has been clearly strengthened by the most recent jurisprudence of the Court of Justice (eg. Moxplant3, Intertanko or the Kadi/Al Baraakat judgements or the Opinion 1/2009 of the CJEU etc.) as well as, in my opinion, in many aspects by the Treaty of Lisbon, it is still valid to add that the principle of a favourable approach, stemming from the Court jurisprudence, for the enhanced openness of the EU legal order to international law has remained equally important for the EU4. On the other hand, it should be also seen that in a globalized world, and following the increased role of the EU as an international actor, its indispensable and crucial role concerning the creation of world (legal) order in many policy fields ( for example let's think about the G20 issues, the global economic and financial crisis, the role of the EU in promoting and protecting human rights worldwide, the implementation of the multilateral or regional conventional law, developed in the framework the UN (e.g. in the field of agriculture or environment etc) or what concerns the Kyoto process on climate change or the conservation of marine biological resources at international level etc), it seems reasonable and justified to submit that the influence, for example, of the law-making activities of the main stakeholder international organizations in the mentioned policy-areas on the EU (especially on the development of its constantly evolving legal order) or vice-versa the influence of the EU law-making practice on these international organizations is significant, in many aspects mutually interdependent and more and more remarkable. This tendency of the 21st century doesn't mean, however, in my view, that the notion of the autonomy of the EU legal order would have been weakened by this increasing interaction between international law and EU law over the passed years. This contribution is going to demonstrate and prove these departuring points by giving some concrete examples from the most recent practice of the Council (all occuring either in the second half of 2009 or after the entry into force of the Lisbon Treaty), and which relate to two very important policy areas in the EU, namely the protection of human rights and the Common Fishery Policy.

Industries and Citizens’ Groups Networks in EU Food Policy: The Emergence of ‘Unholy Alliances’ in Multilevel Governance? Brugges Political Research Paper No. 30, September 2013

Food policy is one the most regulated policy fields at the EU level. ‘Unholy alliances’ are collaborative patterns that temporarily bring together antagonistic stakeholders behind a common cause. This paper deals with such ‘transversal’ co-operations between citizens’ groups (NGOs, consumers associations…) and economic stakeholders (food industries, retailers…), focusing on their ambitions and consequences. This paper builds on two case studies that enable a more nuanced view on the perspectives for the development of transversal networks at the EU level. The main findings are that (i) the rationale behind the adoption of collaborative partnerships actually comes from a case-by-case cost/benefit analysis leading to hopes of improved access to institutions; (ii) membership of a collaborative network leads to a learning process closely linked to the network’s performance; and (iii) coalitions can have a better reception — rather than an automatic better access — depending on several factors independent of the stakeholders themselves.

With or without you...judging politically in the field of Area of Freedom, Security and Justice? Research Papers in Law, 3/2007

From the Introduction. The study of the European Court of Justice’s (ECJ) case law of the regarding the Area of Freedom Security and Justice (AFSJ) is fascinating in many ways.1 First, almost the totality of the relevant case law is extremely recent, thereby marking the first ‘foundational’ steps in this field of law. This is the result of the fact that the AFSJ was set up by the Treaty of Amsterdam in 1997 and only entered into force in May 1999.2 Second, as the AFSJ is a new field of EU competence, it sets afresh all the fundamental questions – both political and legal – triggered by European integration, namely in terms of: a) distribution of powers between the Union and its member states, b) attribution of competences between the various EU Institutions, c) direct effect and supremacy of EU rules, d) scope of competence of the ECJ, and e) measure of the protection given to fundamental rights. The above questions beg for answers which should take into account both the extremely sensible fields of law upon which the AFSJ is anchored, and the EU’s highly inconvenient three-pillar institutional framework.3 Third, and as a consequence of the above, the vast majority of the ECJ’s judgments relating to the AFSJ are a) delivered by the Full Court or, at least, the Grand Chamber, b) with the intervention of great many member states and c) often obscure in content. This is due to the fact that the Court is called upon to set the foundational rules in a new field of EU law, often trying to accommodate divergent considerations, not all of which are strictly legal.4 Fourth, the case law of the Court relating to the AFSJ, touches upon a vast variety of topics which are not necessarily related to one another. This is why it is essential to limit the scope of this study. The content of, and steering for, the AFSJ were given by the Tampere European Council, in October 1999. According to the Tampere Conclusions, the AFSJ should consist of four key elements: a) a common immigration and asylum policy, b) judicial cooperation in both civil and penal matters, c) action against criminality and d) external action of the EU in all the above fields. Moreover, the AFSJ is to a large extent based on the Schengen acquis. The latter has been ‘communautarised’5 by the Treaty of Amsterdam and further ‘ventilated’ between the first and third pillars by decisions 1999/435 and 1999/436.6 Judicial cooperation in civil matters, mainly by means of international conventions (such as the Rome Convention of 1981 on the law applicable to contractual obligations) and regulations (such as (EC) 44/20017 and (EC) 1348/20008) also form part of the AFSJ. However, the relevant case law of the ECJ will not be examined in the present contribution.9 Similarly, the judgments of the Court delivered in the course of Article 226 EC proceedings against member states, will be omitted.10 Even after setting aside the above case law and notwithstanding the fact that the AFSJ only dates as far back as May 1999, the judgments of the ECJ are numerous. A simple (if not simplistic) categorisation may be between, on the one hand, judgments which concern the institutional setting of the AFSJ (para. 2) and, on the other, judgments which are related to some substantive AFSJ policy (para. 3).

Current Problems of Social Europe. Research Papers in Law, 7/2007

From the Introduction. The main difficulty of Theology lies in the fact that the very existence of its subject-matter, God, may be put into question. Talking about Social Europe has something of a theological dimension. The aim of this article is to contribute into the debate, by putting into perspective some of the latest manifestations of social Europe. The need for the pursuance of social policies at the European level is now more pressing than ever (para 2). The EU, however, as it now stands, is the direct evolutionary result of the predominantly economic entity created back in 1957. This explains that the social policies pursued at the European level are piecemeal and often impregnated with market concerns (para. 3). From an instrumental point of view, EU social policy is being pursued concomitantly by secondary legislation (hard law) in the fields where the EU does have the relevant competences and by softer means of cooperation (soft law) in several other fields. Hard law has given the occasion to the European Court of Justice (ECJ), in a series of recent judgments, of putting to the fore the concept of a ‘social market’ (para. 4). Soft cooperation has been formalised into the infamous Lisbon Strategy and has been the main object of experimentation with the open method of coordination (OMC) (para. 5). The advances achieved in the above ways, however, do not offer firm answers to basic questions concerning the future development of the European social identity (para. 6)

Casual but Smart: The Court’s new clothes in the Area of Freedom Security and Justice (AFSJ) after the Lisbon Treaty. Research Papers in Law, 2/2008

Introduction. Unintended as it was, the European Court of Justice (ECJ, the Court, the Court of the EU) has played an extremely important role in the construction of the Area of Freedom Security and Justice (AFSJ). The AFSJ was set up by the Treaty of Amsterdam in 1997 and only entered into force in May 1999. The fact that this is a new field of EU competence, poses afresh all the fundamental questions – both political and legal – triggered by European integration, namely in terms of: a) distribution of powers between the Union and its Member States, b) attribution of competences between the various EU Institutions, c) direct effect and supremacy of EU rules, d) scope of competence of the ECJ, and e) extent of the protection given to fundamental rights. The above questions have prompted judicial solutions which take into account both the extremely sensible fields of law upon which the AFSJ is anchored, and the EU’s highly inconvenient three-pillar institutional framework.1 The ECJ is the body whose institutional role is to benefit most from this upcoming ‘depilarisation’, possibly more than that of the European Parliament. This structure is on the verge of being abandoned, provided the Treaty of Lisbon enters into force.2 However spectacular this formal boost of the Court’s competence, the changes in real terms are not going to be that dramatic. This apparent contradiction is explained, to a large extent, by the fact that the Court has in many ways ‘provoked’, or even ‘anticipated’, the depilarisation of its own jurisdictional role, already under the existing three-pillar structure. Simply put, under the new – post Treaty of Lisbon – regime, the Court will have full jurisdiction over all AFSJ matters, as those are going to be fully integrated in what is now the first pillar. Some limitations will continue to apply, however, while a special AFSJ procedure will be institutionalised. Indeed, if we look into the new Treaty we may identify general modifications to the Court’s structure and jurisdiction affecting the AFSJ (section 2), modifications in the field of the AFSJ stemming from the abolition of the pillar structure (section 3) and, finally, some rules specifically applicable to the AFSJ (section 4).

1980 Annual Status Report: Training and Education (Multiannual Programme of the Joint Research Centre 1980-1983). EUR 7261 EN, 1981

The Education and Training Programme has been set up in recognition of the growing importance of continuing education in modern technological society. It is designed to improve the dissemination of scientific and technical knowledge in subjects related to the research activities of the JRC, to the potential external users: industries, public bodies, research and educational organizations, etc. . . Moreover, owing to the number and the quality of specialists of the various fields covered by the courses who are brought to Ispra as lecturers or participants, this programme plays an important role in the integration of the research teams of the JRC with the European scientific world, and in. the development of contacts and ties between European scientists active in a given field.

The analytical description of a multicomponent plasma in high-frequency fields. Contract no. AF 30(602)-2077.

"RADC TN 61-150.