Author Rights vs Self-Archiving in Spanish Scientific Journals

The paper analyzes publishers" copyright policies and self-archiving conditions of Spanish scientific journals. Data are extracted from the directory DULCINEA that contains information of 1318 Spanish journals, of which 775 (61%) allow some form of self-archiving to be about 60% of the post-print version and allowing them 87% of the deposit of the version of record. In 72% of journals the deposit can be performed immediately after publication and in 16% after article acceptance. 72% of the journals are freely available without charge to the user this figure raises up to 86% if free access after an embargo is considered. Only 18% of the journals use Creative Commons licenses. The adoption of different open access journals model in Spain is favorable, however there is still a high percentage of journals (39%) that do not provide any information about authors and publishers rights and that difficult or inhibits reuse of published articles.

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

Scientific journals in Brazil and Spain: Alternative publishing models

This paper describes high-quality journals in Brazil and Spain, with an emphasis on the distribution models used. It presents the general characteristics (age, type of publisher, and theme) and analyzes the distribution model by studying the type of format (print or digital), the type of access (open access or subscription), and the technology platform used. The 549 journals analyzed (249 in Brazil and 300 in Spain) are included in the 2011 Web of Science (WoS) and Scopus databases. Data on each journal were collected directly from their websites between March and October 2012. Brazil has a fully open access distribution model (97%) in which few journals require payment by authors thanks to cultural, financial, operational, and technological support provided by public agencies. In Spain, open access journals account for 55% of the total and have also received support from public agencies, although to a lesser extent. These results show that there are systems support of open access in scientific journals other than the"author pays" model advocated by the Finch report for the United Kingdom.

The use of non-animal alternatives in the safety evaluations of cosmetics ingredients by the Scientific Committee on Consumer Safety (SCCS)

In Europe, the safety evaluation of cosmetics is based on the safety evaluation of each individual ingredient. Article 3 of the Cosmetics Regulation specifies that a cosmetic product made available on the market is to be safe for human health when used normally or under reasonably foreseeable conditions. For substances that cause some concern with respect to human health (e.g. colorants, preservatives, UV-filters), safety is evaluated at the Commission level by a scientific committee, presently called the Scientific Committee on Consumer Safety (SCCS). According to the Cosmetics Regulations, in the EU, the marketing of cosmetics products and their ingredients that have been tested on animals for most of their human health effects, including acute toxicity, is prohibited. Nevertheless, any study dating from before this prohibition took effect is accepted for the safety assessment of cosmetics ingredients. The in vitro methods reported in the dossiers summited to the SCCS are here evaluated from the published reports issued by the scientific committee of the Directorate General of Health and Consumers (DG SANCO); responsible for the safety of cosmetics ingredients. The number of studies submitted to the SCCS that do not involve animals is still low and in general the safety of cosmetics ingredients is based on in vivo studies performed before the prohibition.

Research networks and scientific production in Economics: The recent spanish experience

This paper studies Spanish scientific production in Economics from 1994 to 2004. It focuses on aspects that have received little attention in other bibliometric studies, such as the impact of research and the role of scientific collaborations in the publications produced by Spanish universities. Our results show that national research networks have played a fundamental role in the increase in Spanish scientific production in this discipline.

Selecting Scientific Papers for Publication via Citation Auctions

The scientific community has been suffering from peer review for decades. This process (also called refereeing) subjects an author's scientific work or ideas to the scrutiny of one or more experts in the field. Publishers use it to select and screen manuscript submissions, and funding agencies use it to award research funds. The goal is to get authors to meet their discipline's standards and thus achieve scientific objectivity. Publications and awards that haven't undergone peer review are often regarded with suspicion by scholars and professionals in many fields. However, peer review, although universally used, has many drawbacks. We propose replacing peer review with an auction-based approach: the better the submitted paper, the more scientific currency the author likely bid to have it published. If the bid correctly reflects the paper's quality, the author is rewarded in this new scientific currency; otherwise, the author loses this currency. We argue that citations are an appropriate currency for all scientists. We believe that citation auctions encourage scientists to better control their submissions' quality. It also inspire them to prepare more exciting talks for accepted papers and to invite discussion of their results at congresses and conferences and among their colleagues. In the long run, citation auctions could have the power to greatly improve scientific research

Citation auctions as a method to improve selection of scientific papers

This paper describes the basis of citation auctions as a new approach to selecting scientific papers for publication. Our main idea is to use an auction for selecting papers for publication through - differently from the state of the art - bids that consist of the number of citations that a scientist expects to receive if the paper is published. Hence, a citation auction is the selection process itself, and no reviewers are involved. The benefits of the proposed approach are two-fold. First, the cost of refereeing will be either totally eliminated or significantly reduced, because the process of citation auction does not need prior understanding of the paper's content to judge the quality of its contribution. Additionally, the method will not prejudge the content of the paper, so it will increase the openness of publications to new ideas. Second, scientists will be much more committed to the quality of their papers, paying close attention to distributing and explaining their papers in detail to maximize the number of citations that the paper receives. Sample analyses of the number of citations collected in papers published in years 1999-2004 for one journal, and in years 2003-2005 for a series of conferences (in a totally different discipline), via Google scholar, are provided. Finally, a simple simulation of an auction is given to outline the behaviour of the citation auction approach

Os produtos naturais e a química medicinal moderna

Natural products have been utilized by humans since ancient times and the relief and cure of their diseases was the first purpose for using natural products in medicine. The history of the oriental and occidental civilizations is very rich in examples of the utilization of natural products in medicine and health care. Chinese traditional medicine is one of the most important examples of how natural products can be efficient in the treatment of diseases, and it points to the importance of scientific research on natural products, concerning the discovery of new active chemical entities. The complexity, chemical diversity and biological properties of natural products always fascinated people, and during the last 200 years, this led to the discovery of important new drugs. In the last 30 years, the development of new bioassay techniques, biotechnology methods, bio-guided phytochemical studies, automated high throughput screening and high performance analytical methods, have introduced new concepts and possibilities of rational drug design and drug discovery. In this context, natural products have played an important and decisive role in the development of modern medicinal chemistry.

Inovação & propriedade industrial & indústria química

ABSTRACT The main aim of this paper was to contribute to reflections in Brazil on the need to transfer knowledge held at universities and R&D institutions over to companies, i.e. to transfer scientific knowledge of chemistry to technology. It discusses how the competitiveness of countries is increasingly dependent on their technological capacity. The chemicals industry is a fundamental driver of social, environmental, economic and industrial indicators of sustainable development. In Brazil, the chemicals industry's deficit has grown over the last three decades. Patents are important sources of information because patent documents contain 75% of all technological information available. The National Institute of Industrial Property in Brazil has created a Technology Observatory with the purpose of identifying and analyzing technological information contained in patent documents within the ambit of partnerships with government entities or business associations, in order to support their technology-related decision-making processes. The paper gives examples of ethanol and biotechnology patent documents, including pharmaceuticals, of which there are very few in Brazil. However, a few of the patent applications identified are filed in Brazil, giving the country the opportunity to transform this scientific knowledge into technology by means of partnership agreements with companies. Finally, the paper presents information on the patent applications filed by the world's leading chemicals companies as measured by their revenues, and the respective numbers of patent applications in the last five years in organic chemistry and polymers, sectors in which Brazil is currently dependent on imports for over 50% of its needs. The patent assignees in these sectors in Brazil are also identified, and the paper concludes that Brazil needs to invest in the development of professionals, providing clearly-defined career paths in technology innovation teams at R&D institutions, and to foster more initiatives such as the creation of a new research and innovation entity, EMBRAPII, since investing in science and technology is a prerequisite for knowledge production, industrial property, economic development and, consequently, the competitiveness of the country.

Models, truth and realism: assessing Bas van Fraassen's views on scientific representation

This paper is devoted to an analysis of some aspects of Bas van Fraassen's views on representation. While I agree with most of his claims, I disagree on the following three issues. Firstly, I contend that some isomorphism (or at least homomorphism) between the representor and what is represented is a universal necessary condition for the success of any representation, even in the case of misrepresentation. Secondly, I argue that the so-called "semantic" or "model-theoretic" construal of theories does not give proper due to the role played by true propositions in successful representing practices. Thirdly, I attempt to show that the force of van Fraassen's pragmatic - and antirealist - "dissolution" of the "loss of reality objection" loses its bite when we realize that our cognitive contact with real phenomena is achieved not by representing but by expressing true propositions about them.

Carnap and Kuhn on linguistic frameworks and scientific revolutions

Several recent works in history and philosophy of science have re-evaluated the alleged opposition between the theses put forth by logical empiricists such as Carnap and the so-called "post-positivists", such as Kuhn. Although the latter came to be viewed as having seriously challenged the logical positivist views of science, recent authors (e.g., Friedman, Reisch, Earman, Irzik and Grünberg) maintain that some of the most notable theses of the Kuhnian view of science have striking similarities with some aspects of Carnap's philosophy. Against that reading, Oliveira and Psillos argue that within Carnap's philosophy there is no place for the Kuhnian theses of incommensurability, holism, and theory-ladenness of observations. This paper presents each of those readings and argues that Carnap and Kuhn have non-opposing views on holism, incommensurability, the theory-ladenness of observations, and scientific revolutions. We note at the very end - without dwelling on the point, however - that they come apart on other matters, such as their views on metaphysics and on the context of discovery/justification distinction.

Finna - Opening Access to Cultural Heritage and Scientific Information

Aki Lassilan esitys Europeana työpajassa 20.11.2012 Helsingissä.