Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems

The amount of genomic and proteomic data that is entered each day into databases and the experimental literature is outstripping the ability of experimental scientists to keep pace. While generic databases derived from automated curation efforts are useful, most biological scientists tend to focus on a class or family of molecules and their biological impact. Consequently, there is a need for molecular class-specific or other specialized databases. Such databases collect and organize data around a single topic or class of molecules. If curated well, such systems are extremely useful as they allow experimental scientists to obtain a large portion of the available data most relevant to their needs from a single source. We are involved in the development of two such databases with substantial pharmacological relevance. These are the GPCRDB and NucleaRDB information systems, which collect and disseminate data related to G protein-coupled receptors and intra-nuclear hormone receptors, respectively. The GPCRDB was a pilot project aimed at building a generic molecular class-specific database capable of dealing with highly heterogeneous data. A first version of the GPCRDB project has been completed and it is routinely used by thousands of scientists. The NucleaRDB was started recently as an application of the concept for the generalization of this technology. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm/ and the NucleaRDB at http://www.receptors.org/NR/.

The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information

The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains 795 full-length homeodomain-containing sequences, 32 experimentally-derived structures and 143 homeo­box loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engine with a graphical user interface is provided to query the component databases and assemble customized data sets. A new feature for this release is the addition of DNA recognition sites for all human homeodomain proteins described in the literature. The Homeodomain Resource is freely available through the World Wide Web at http://genome.nhgri.nih.gov/homeodomain.

The pattern of gene expression in human CD15+ myeloid progenitor cells

We performed a genome-wide analysis of gene expression in primary human CD15+ myeloid progenitor cells. By using the serial analysis of gene expression (SAGE) technique, we obtained quantitative information for the expression of 37,519 unique SAGE-tag sequences. Of these unique tags, (i) 25% were detected at high and intermediate levels, whereas 75% were present as single copies, (ii) 53% of the tags matched known expressed sequences, 34% of which were matched to more than one known expressed sequence, and (iii) 47% of the tags had no matches and represent potentially novel genes. The correct genes were confirmed by application of the generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) technique for high-copy tags with multiple matches. A set of genes known to be important in myeloid differentiation were expressed at various levels and used different spliced forms. This study provides a normal baseline for comparison of gene expression in myeloid diseases. The strategy of using SAGE and GLGI techniques in this study has broad applications to the genome-wide identification of expressed genes.

Molecular genetics of pattern formation in the inner ear: Do compartment boundaries play a role?

The membranous labyrinth of the inner ear establishes a precise geometrical topology so that it may subserve the functions of hearing and balance. How this geometry arises from a simple ectodermal placode is under active investigation. The placode invaginates to form the otic cup, which deepens before pinching off to form the otic vesicle. By the vesicle stage many genes expressed in the developing ear have assumed broad, asymmetrical expression domains. We have been exploring the possibility that these domains may reflect developmental compartments that are instrumental in specifying the location and identity of different parts of the ear. The boundaries between compartments are proposed to be the site of inductive interactions required for this specification. Our work has shown that sensory organs and the endolymphatic duct each arise near the boundaries of broader gene expression domains, lending support to this idea. A further prediction of the model, that the compartment boundaries will also represent lineage-restriction compartments, is supported in part by fate mapping the otic cup. Our data suggest that two lineage-restriction boundaries intersect at the dorsal pole of the otocyst, a convergence that may be critical for the specification of endolymphatic duct outgrowth. We speculate that the patterning information necessary to establish these two orthogonal boundaries may emanate, in part, from the hindbrain. The compartment boundary model of ear development now needs to be tested through a variety of experimental perturbations, such as the removal of boundaries, the generation of ectopic boundaries, and/or changes in compartment identity.

Scale dependence in earthquake phenomena and its relevance to earthquake prediction.

The recent discovery of a low-velocity, low-Q zone with a width of 50-200 m reaching to the top of the ductile part of the crust, by observations on seismic guided waves trapped in the fault zone of the Landers earthquake of 1992, and its identification with the shear zone inferred from the distribution of tension cracks observed on the surface support the existence of a characteristic scale length of the order of 100 m affecting various earthquake phenomena in southern California, as evidenced earlier by the kink in the magnitude-frequency relation at about M3, the constant corner frequency for earthquakes with M below about 3, and the sourcecontrolled fmax of 5-10 Hz for major earthquakes. The temporal correlation between coda Q-1 and the fractional rate of occurrence of earthquakes in the magnitude range 3-3.5, the geographical similarity of coda Q-1 and seismic velocity at a depth of 20 km, and the simultaneous change of coda Q-1 and conductivity at the lower crust support the hypotheses that coda Q-1 may represent the activity of creep fracture in the ductile part of the lithosphere occurring over cracks with a characteristic size of the order of 100 m. The existence of such a characteristic scale length cannot be consistent with the overall self-similarity of earthquakes unless we postulate a discrete hierarchy of such characteristic scale lengths. The discrete hierarchy of characteristic scale lengths is consistent with recently observed logarithmic periodicity in precursory seismicity.

Self-organized phase transitions in neural networks as a neural mechanism of information processing.

Transitions between dynamically stable activity patterns imposed on an associative neural network are shown to be induced by self-organized infinitesimal changes in synaptic connection strength and to be a kind of phase transition. A key event for the neural process of information processing in a population coding scheme is transition between the activity patterns encoding usual entities. We propose that the infinitesimal and short-term synaptic changes based on the Hebbian learning rule are the driving force for the transition. The phase transition between the following two dynamical stable states is studied in detail, the state where the firing pattern is changed temporally so as to itinerate among several patterns and the state where the firing pattern is fixed to one of several patterns. The phase transition from the pattern itinerant state to a pattern fixed state may be induced by the Hebbian learning process under a weak input relevant to the fixed pattern. The reverse transition may be induced by the Hebbian unlearning process without input. The former transition is considered as recognition of the input stimulus, while the latter is considered as clearing of the used input data to get ready for new input. To ensure that information processing based on the phase transition can be made by the infinitesimal and short-term synaptic changes, it is absolutely necessary that the network always stays near the critical state corresponding to the phase transition point.

Discovery of a brain promoter from the human transferrin gene and its utilization for development of transgenic mice that express human apolipoprotein E alleles.

Transgenic mice carrying heterologous genes directed by a 670-bp segment of the regulatory sequence from the human transferrin (TF) gene demonstrated high expression in brain. Mice carrying the chimeric 0.67kbTF-CAT gene expressed TF-CAT in neurons and glial cells of the nucleus basalis, the cerebrum, corpus callosum, cerebellum, and hippocampus. In brains from two independent TF-CAT transgenic founder lines, copy number of TF-CAT mRNA exceeded the number of mRNA transcripts encoding either mouse endogenous transferrin or mouse endogenous amyloid precursor protein. In two transgenic founder lines, the chloramphenicol acetyltransferase (CAT) protein synthesized from the TF-CAT mRNA was estimated to be 0.10-0.15% of the total soluble proteins of the brain. High expression observed in brain indicates that the 0.67kbTF promoter is a promising director of brain expression of heterologous genes. Therefore, the promoter has been used to express the three common human apolipoprotein E (apoE) alleles in transgenic mouse brains. The apoE alleles have been implicated in the expression of Alzheimer disease, and the human apoE isoforms are reported to interact with different affinities to the brain beta-amyloid and tau protein in vitro. Results of this study demonstrate high expression and production of human apoE proteins in transgenic mouse brains. The model may be used to characterize the interaction of human apoE isoforms with other brain proteins and provide information helpful in designing therapeutic strategies for Alzheimer disease.

Human neoplasms elicit multiple specific immune responses in the autologous host.

Expression of cDNA libraries from human melanoma, renal cancer, astrocytoma, and Hodgkin disease in Escherichia coli and screening for clones reactive with high-titer IgG antibodies in autologous patient serum lead to the discovery of at least four antigens with a restricted expression pattern in each tumor. Besides antigens known to elicit T-cell responses, such as MAGE-1 and tyrosinase, numerous additional antigens that were overexpressed or specifically expressed in tumors of the same type were identified. Sequence analyses suggest that many of these molecules, besides being the target of a specific immune response, might be of relevance for tumor growth. Antibodies to a given antigen were usually confined to patients with the same tumor type. The unexpected frequency of human tumor antigens, which can be readily defined at the molecular level by the serological analysis of autologous tumor cDNA expression cloning, indicates that human neoplasms elicit multiple specific immune responses in the autologous host and provides diagnostic and therapeutic approaches to human cancer.

Análise de grandezas cinemáticas e dinâmicas inerentes à hemiparesia através da descoberta de conhecimento em bases de dados

Em virtude de uma elevada expectativa de vida mundial, faz-se crescente a probabilidade de ocorrer acidentes naturais e traumas físicos no cotidiano, o que ocasiona um aumento na demanda por reabilitação. A terapia física, sob o paradigma da reabilitação robótica com serious games, oferece maior motivação e engajamento do paciente ao tratamento, cujo emprego foi recomendado pela American Heart Association (AHA), apontando a mais alta avaliação (Level A) para pacientes internados e ambulatoriais. No entanto, o potencial de análise dos dados coletados pelos dispositivos robóticos envolvidos é pouco explorado, deixando de extrair informações que podem ser de grande valia para os tratamentos. O foco deste trabalho consiste na aplicação de técnicas para descoberta de conhecimento, classificando o desempenho de pacientes diagnosticados com hemiparesia crônica. Os pacientes foram inseridos em um ambiente de reabilitação robótica, fazendo uso do InMotion ARM, um dispositivo robótico para reabilitação de membros superiores e coleta dos dados de desempenho. Foi aplicado sobre os dados um roteiro para descoberta de conhecimento em bases de dados, desempenhando pré-processamento, transformação (extração de características) e então a mineração de dados a partir de algoritmos de aprendizado de máquina. A estratégia do presente trabalho culminou em uma classificação de padrões com a capacidade de distinguir lados hemiparéticos sob uma precisão de 94%, havendo oito atributos alimentando a entrada do mecanismo obtido. Interpretando esta coleção de atributos, foi observado que dados de força são mais significativos, os quais abrangem metade da composição de uma amostra.

The Effect of Discovery Systems on Online Journal Usage: A Longitudinal Study

Many academic libraries are implementing discovery services as a way of giving their users a single comprehensive search option for all library resources. These tools are designed to change the research experience, yet very few studies have investigated the impact of discovery service implementation. This study examines one aspect of that impact by asking whether usage of publisher-hosted journal content changes after implementation of a discovery tool. Libraries that have begun using the four major discovery services have seen an increase in usage of this content, suggesting that for this particular type of material, discovery services have a positive impact on use. Though all discovery services significantly increased usage relative to a no discovery service control group, some had a greater impact than others, and there was extensive variation in usage change among libraries using the same service. Future phases of this study will look at other types of content.

A model driven framework for geographic knowledge discovery

Geographic knowledge discovery (GKD) is the process of extracting information and knowledge from massive georeferenced databases. Usually the process is accomplished by two different systems, the Geographic Information Systems (GIS) and the data mining engines. However, the development of those systems is a complex task due to it does not follow a systematic, integrated and standard methodology. To overcome these pitfalls, in this paper, we propose a modeling framework that addresses the development of the different parts of a multilayer GKD process. The main advantages of our framework are that: (i) it reduces the design effort, (ii) it improves quality systems obtained, (iii) it is independent of platforms, (iv) it facilitates the use of data mining techniques on geo-referenced data, and finally, (v) it ameliorates the communication between different users.

EmotiBlog: towards a finer-grained sentiment analysis and its application to opinion mining

Comunicación presentada en las IV Jornadas TIMM, Torres (Jaén), 7-8 abril 2011.

Application of Text Summarization techniques to the Geographical Information Retrieval task

Automatic Text Summarization has been shown to be useful for Natural Language Processing tasks such as Question Answering or Text Classification and other related fields of computer science such as Information Retrieval. Since Geographical Information Retrieval can be considered as an extension of the Information Retrieval field, the generation of summaries could be integrated into these systems by acting as an intermediate stage, with the purpose of reducing the document length. In this manner, the access time for information searching will be improved, while at the same time relevant documents will be also retrieved. Therefore, in this paper we propose the generation of two types of summaries (generic and geographical) applying several compression rates in order to evaluate their effectiveness in the Geographical Information Retrieval task. The evaluation has been carried out using GeoCLEF as evaluation framework and following an Information Retrieval perspective without considering the geo-reranking phase commonly used in these systems. Although single-document summarization has not performed well in general, the slight improvements obtained for some types of the proposed summaries, particularly for those based on geographical information, made us believe that the integration of Text Summarization with Geographical Information Retrieval may be beneficial, and consequently, the experimental set-up developed in this research work serves as a basis for further investigations in this field.

Tackling redundancy in text summarization through different levels of language analysis

One of the main challenges to be addressed in text summarization concerns the detection of redundant information. This paper presents a detailed analysis of three methods for achieving such goal. The proposed methods rely on different levels of language analysis: lexical, syntactic and semantic. Moreover, they are also analyzed for detecting relevance in texts. The results show that semantic-based methods are able to detect up to 90% of redundancy, compared to only the 19% of lexical-based ones. This is also reflected in the quality of the generated summaries, obtaining better summaries when employing syntactic- or semantic-based approaches to remove redundancy.

World Map Showing Routes of Exploration and Discovery, 1790 (Image 1 of 8) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Chart of the world on Mercators projection : exhibiting all the new discoveries to the present time, with the tracks of the most distinguished navigators since the year 1700 carefully collected from the best charts, maps, voyages, &c. extant and regulated from the accurate astronomical observations made in three voyages performed under the command of Captn. James Cook in the years 1768, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79 & 80, compiled and published by A. Arrowsmith, geographer; by permission of Simon McTavish Esq[r] is correctly delineated the discoveries of Mr. McKenzie laid down from his original journal in the year 1789. It was published by A. Arrowsmith, April 1, 1790. Scale [ca. 1:20,000,000]. This layer is image 1 of 8 total images of the seven sheet source map. Covers portions of eastern Asia, Siberia, Russia, Pacific Islands, and western portions of Canada and the United States including Alaska. The image inside the map neatline is georeferenced to the surface of the earth and fit to a non-standard 'World Mercator' projection, with the central meridian at 180 degrees west. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. Note: The central meridian of this map is not the same as the Prime Meridian and may wrap the International Date Line or overlap itself when displayed in GIS software. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, and more. Relief shown by hachures. Depths shown by soundings. Includes routes, locations, and dates of James Cook's voyages. This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection and the Harvard University Library as part of the Open Collections Program at Harvard University project: Organizing Our World: Sponsored Exploration and Scientific Discovery in the Modern Age. Maps selected for the project correspond to various expeditions and represent a range of regions, originators, ground condition dates, scales, and purposes.