Science education and popularization of science in the biomedical area: its role for the future of science and of society

This paper presents the main subjects discussed in the round-table: "Educational Base for Biomedical Research", during the International Symposium on Biomedical Research in the 21st century; two main aspects will be focused: (1) the importance of popularizing science in order to stimulate comprehension of the scientific process and progress, their critical thinking, citizenship and social commitment, mainly in the biomedical area, considering the new advances of knowledge and the resulting technology; (2) the importance to stimulate genuine scientific vocation among young people, by giving them opportunity to early experience scientific environment, throught the hands of well prepared master in a humanistic atmosphere.

Current millennium biotechniques for biomedical research on parasites and host-parasite interactions

The development of biotechnology in the last three decades has generated the feeling that the newest scientific achievements will deliver high standard quality of life through abundance of food and means for successfully combating diseases. Where the new biotechnologies give access to genetic information, there is a common belief that physiological and pathological processes result from subtle modifications of gene expression. Trustfully, modern genetics has produced genetic maps, physical maps and complete nucleotide sequences from 141 viruses, 51 organelles, two eubacteria, one archeon and one eukaryote (Saccharomices cerevisiae). In addition, during the Centennial Commemoration of the Oswaldo Cruz Institute the nearly complete human genome map was proudly announced, whereas the latest Brazilian key stone contribution to science was the publication of the Shillela fastidiosa genomic sequence highlythed on a Nature cover issue. There exists a belief among the populace that further scientific accomplishments will rapidly lead to new drugs and methodological approaches to cure genetic diseases and other incurable ailments. Yet, much evidence has been accumulated, showing that a large information gap exists between the knowledge of genome sequence and our knowledge of genome function. Now that many genome maps are available, people wish to know what are we going to do with them. Certainly, all these scientific accomplishments will shed light on many more secrets of life. Nevertheless, parsimony in the weekly announcements of promising scientific achievements is necessary. We also need many more creative experimental biologists to discover new, as yet un-envisaged biotechnological approaches, and the basic resource needed for carrying out mile stone research necessary for leading us to that "promised land"often proclaimed by the mass media.

Biomedical nanoparticles modulate specific CD4(+) T cell stimulation by inhibition of antigen processing in dendritic cells

Understanding how nanoparticles may affect immune responses is an essential prerequisite to developing novel clinical applications. To investigate nanoparticle-dependent outcomes on immune responses, dendritic cells (DCs) were treated with model biomedical poly(vinylalcohol)-coated super-paramagnetic iron oxide nanoparticles (PVA-SPIONs). PVA-SPIONs uptake by human monocyte-derived DCs (MDDCs) was analyzed by flow cytometry (FACS) and advanced imaging techniques. Viability, activation, function, and stimulatory capacity of MDDCs were assessed by FACS and an in vitro CD4(+) T cell assay. PVA-SPION uptake was dose-dependent, decreased by lipopolysaccharide (LPS)-induced MDDC maturation at higher particle concentrations, and was inhibited by cytochalasin D pre-treatment. PVA-SPIONs did not alter surface marker expression (CD80, CD83, CD86, myeloid/plasmacytoid DC markers) or antigen-uptake, but decreased the capacity of MDDCs to process antigen, stimulate CD4(+) T cells, and induce cytokines. The decreased antigen processing and CD4(+) T cell stimulation capability of MDDCs following PVA-SPION treatment suggests that MDDCs may revert to a more functionally immature state following particle exposure.

Direct analysis of dried blood spots coupled with mass spectrometry: concepts and biomedical applications.

Because of the emergence of dried blood spots (DBS) as an attractive alternative to conventional venous plasma sampling in many pharmaceutical companies and clinical laboratories, different analytical approaches have been developed to enable automated handling of DBS samples without any pretreatment. Associated with selective and sensitive MS-MS detection, these procedures give good results in the rapid identification and quantification of drugs (generally less than 3 min total run time), which is desirable because of the high throughput requirements of analytical laboratories. The objective of this review is to describe the analytical concepts of current direct DBS techniques and to present their advantages and disadvantages, with particular focus on automation capacity and commercial availability. Finally, an overview of the different biomedical applications in which these concepts could be of major interest will be presented.

Convenient synthesis of heterobifunctional poly(ethylene glycol) suitable for the functionalization of iron oxide nanoparticles for biomedical applications.

A straightforward route is proposed for the multi-gram scale synthesis of heterobifunctional poly(ethylene glycol) (PEG) oligomers containing combination of triethyloxysilane extremity for surface modification of metal oxides and amino or azido active end groups for further functionalization. The suitability of these PEG derivatives to be conjugated to nanomaterials was shown by pegylation of ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles (NPs), followed by functionalization with small peptide ligands for biomedical applications.

Evolutionary and biomedical consequences of internal melanins.

The adaptive function of melanin located in the integument is well known. Although pigments are also deposited in various internal organs, their function is unclear. A review of the literature revealed that 'internal melanin' protects against parasites, pollutants, low temperature, oxidative stress, hypoxemia and UV light, and is involved in the development and function of organs. Importantly, several studies have shown that the amount of melanin deposited on the external body surface is correlated with the amount located inside the body. This finding raises the possibility that internal melanin plays more important physiological roles in dark than light-colored individuals. Internal melanin and coloration may therefore not evolve independently. This further emphasizes the major role played by indirect selection in evolutionary processes.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

BIMS: Biomedical Information Management System

This final year project presents the design principles and prototype implementation of BIMS (Biomedical Information Management System), a flexible software system which provides an infrastructure to manage all information required by biomedical research projects.The BIMS project was initiated with the motivation to solve several limitations in medical data acquisition of some research projects, in which Universitat Pompeu Fabra takes part. These limitations,based on the lack of control mechanisms to constraint information submitted by clinicians, impact on the data quality, decreasing it.BIMS can easily be adapted to manage information of a wide variety of clinical studies, not being limited to a given clinical specialty. The software can manage both, textual information, like clinical data (measurements, demographics, diagnostics, etc ...), as well as several kinds of medical images (magnetic resonance imaging, computed tomography, etc ...). Moreover, BIMS provides a web - based graphical user interface and is designed to be deployed in a distributed andmultiuser environment. It is built on top of open source software products and frameworks.Specifically, BIMS has been used to represent all clinical data being currently used within the CardioLab platform (an ongoing project managed by Universitat Pompeu Fabra), demonstratingthat it is a solid software system, which could fulfill requirements of a real production environment.

Compositional Data in Biomedical Research

Modern methods of compositional data analysis are not well known in biomedical research.Moreover, there appear to be few mathematical and statistical researchersworking on compositional biomedical problems. Like the earth and environmental sciences,biomedicine has many problems in which the relevant scienti c information isencoded in the relative abundance of key species or categories. I introduce three problemsin cancer research in which analysis of compositions plays an important role. Theproblems involve 1) the classi cation of serum proteomic pro les for early detection oflung cancer, 2) inference of the relative amounts of di erent tissue types in a diagnostictumor biopsy, and 3) the subcellular localization of the BRCA1 protein, and it'srole in breast cancer patient prognosis. For each of these problems I outline a partialsolution. However, none of these problems is \solved". I attempt to identify areas inwhich additional statistical development is needed with the hope of encouraging morecompositional data analysts to become involved in biomedical research

Hand-in-hand advances in biomedical engineering and sensorimotor restoration.

BACKGROUND: Living in a multisensory world entails the continuous sensory processing of environmental information in order to enact appropriate motor routines. The interaction between our body and our brain is the crucial factor for achieving such sensorimotor integration ability. Several clinical conditions dramatically affect the constant body-brain exchange, but the latest developments in biomedical engineering provide promising solutions for overcoming this communication breakdown. NEW METHOD: The ultimate technological developments succeeded in transforming neuronal electrical activity into computational input for robotic devices, giving birth to the era of the so-called brain-machine interfaces. Combining rehabilitation robotics and experimental neuroscience the rise of brain-machine interfaces into clinical protocols provided the technological solution for bypassing the neural disconnection and restore sensorimotor function. RESULTS: Based on these advances, the recovery of sensorimotor functionality is progressively becoming a concrete reality. However, despite the success of several recent techniques, some open issues still need to be addressed. COMPARISON WITH EXISTING METHOD(S): Typical interventions for sensorimotor deficits include pharmaceutical treatments and manual/robotic assistance in passive movements. These procedures achieve symptoms relief but their applicability to more severe disconnection pathologies is limited (e.g. spinal cord injury or amputation). CONCLUSIONS: Here we review how state-of-the-art solutions in biomedical engineering are continuously increasing expectances in sensorimotor rehabilitation, as well as the current challenges especially with regards to the translation of the signals from brain-machine interfaces into sensory feedback and the incorporation of brain-machine interfaces into daily activities.

Time-resolved imaging of the laser forward transfer of liquids

Time-resolved imaging is carried out to study the dynamics of the laser-induced forward transfer of an aqueous solution at different laser fluences. The transfer mechanisms are elucidated, and directly correlated with the material deposited at the analyzed irradiation conditions. It is found that there exists a fluence range in which regular and well-defined droplets are deposited. In this case, laser pulse energy absorption results in the formation of a plasma, which expansion originates a cavitation bubble in the liquid. After the further expansion and collapse of the bubble, a long and uniform jet is developed, which advances at a constant velocity until it reaches the receptor substrate. On the other hand, for lower fluences no material is deposited. In this case, although a jet can be also generated, it recoils before reaching the substrate. For higher fluences, splashing is observed on the receptor substrate due to the bursting of the cavitation bubble. Finally, a discussion of the possible mechanisms which lead to such singular dynamics is also provided.