Productivity of CNPq Researchers from Different Fields in Biomedical Sciences: The Need for Objective Bibliometric Parameters-A Report from Brazil.

In Brazil, the CNPq (National Council for Scientific and Technological Development) provides grants, funds and fellowships to productive scientists to support their investigations. They are ranked and categorized into four hierarchical levels ranging from PQ 1A (the highest) to PQ 1D (the lowest). Few studies, however, report and analyse scientific productivity in different sub-fields of Biomedical Sciences (BS), e.g., Biochemistry, Pharmacology, Biophysics and Physiology. In fact, systematic comparisons of productivity among the PQ 1 categories within the above sub-fields are lacking in the literature. Here, the scientific productivity of 323 investigators receiving PQ 1 fellowships (A to D levels) in these sub-fields of BS was investigated. The Scopus database was used to compile the total number of articles, citations, h-index values and authorship positions (first-, co- or last-listed author) in the most cited papers by researchers granted CNPq fellowships. We found that researchers from Pharmacology had the best performance for all of the parameters analysed, followed by those in Biochemistry. There was great variability in scientific productivity within the PQ 1A level in all of the sub-fields of BS, but not within the other levels (1B, 1C and 1D). Analysis of the most cited papers of PQ 1(A-D) researchers in Pharmacology revealed that the citations of researchers in the 1C and 1D levels were associated with publications with their senior supervisors, whereas those in the 1B level were less connected with their supervisors in comparison to those in 1A. Taken together, these findings suggest that the scientific performance of PQ 1A researchers in BS is not homogenous. In our opinion, parameters such as the most cited papers without the involvement of Ph.D. and/or post-doctoral supervisors should be used to make decisions regarding any given researcher's fellowship award level.

Developmental biology, the stem cell of biological disciplines.

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

Approaches to verb subcategorization for biomedicine.

Information about verb subcategorization frames (SCFs) is important to many tasks in natural language processing (NLP) and, in turn, text mining. Biomedicine has a need for high-quality SCF lexicons to support the extraction of information from the biomedical literature, which helps biologists to take advantage of the latest biomedical knowledge despite the overwhelming growth of that literature. Unfortunately, techniques for creating such resources for biomedical text are relatively undeveloped compared to general language. This paper serves as an introduction to subcategorization and existing approaches to acquisition, and provides motivation for developing techniques that address issues particularly important to biomedical NLP. First, we give the traditional linguistic definition of subcategorization, along with several related concepts. Second, we describe approaches to learning SCF lexicons from large data sets for general and biomedical domains. Third, we consider the crucial issue of linguistic variation between biomedical fields (subdomain variation). We demonstrate significant variation among subdomains, and find the variation does not simply follow patterns of general lexical variation. Finally, we note several requirements for future research in biomedical SCF lexicon acquisition: a high-quality gold standard, investigation of different definitions of subcategorization, and minimally-supervised methods that can learn subdomain-specific lexical usage without the need for extensive manual work.

Towards a top-domain ontology for linking biomedical ontologies.

In this paper we present the ongoing development and extension work on BioTop--a top-domain ontology for linking biomedical domain ontologies. We start by making the case for the application of a common ontology to interface independent biomedical domain ontologies by introducing a set of more general classes. Then we briefly depict the relation of BioTop to the GENIA ontology as starting point of its initial developement. Afterwards we propose our distinction of ontologies into top, top-domain and domain ones and describe our approach to the integration of the top ontology BFO into BioTop. Then we present our plans to join the OBO and OBO Foundry repository of ontologies and list its admission principles in relation to our ontology. Some actual BioTop interface classes are shown subsequently. We conclude by detailing on some planned BioTop usages in the area of BioNLP and cancer research and show some further intended improvements.

[A problem of truth in biological systematics]. / Problema istiny v biologicheskoi sistematike.

A possibility to put a question of truth of knowledge in biological systematics is studied. It is shown that the problem of truth in reference to systematics is wider than a question of classified information reliability. Prerequisites needed for logically accurate formulation of a definition and criteria of truth are considered. It is shown that such prerequisites are present in taxonomic practice, namely in a process of diagnosis compiling. Philosophical analysis of this work has been carried out. Interpretation of an essence of systematics as classification is connected with use of classical concept of truth (which defines truth as correspondence between knowledge and object) in its undeveloped form. Carried analysis allows supposing that a theory of systematics based on diagnostics rather than on classification would be more prospective. Use of imperfect concept of truth can be seen also in notions that system of taxa must reflect its evolutionary history. Development and modernization of Aristotle's orientation to discovery of the object form can become an alternative to such opinions. An aspiration to achieve the truth is the main motive of systematic work. An influence of this aspiration on a selection of purposes of taxonomic work and theoretical comprehension of its bases is shown. Such features of modern biological systematics as its accessibility for new results, criticism in respect of external morphological characters, and interest in intraspecific variability are connected with this aspiration. This motive comes into contradiction with a tendency to withdraw the problem of truth as such, which takes place in some brunches of theoretic systematics.

¿Irá todo bien? Por un progreso a medida humana / Will everything turn right? For a human measured propers

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