OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

<p>Abstract</p> <p>Background</p> <p>Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.</p> <p>Results</p> <p>OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.</p> <p>Conclusion</p> <p>OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at <url>http://ontodas.nbn.ac.za</url></p

easyDAS: Automatic creation of DAS servers

Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results: Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions: easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.Postprint (published version

Detecting individual gravity modes in the Sun: Chimera or reality?

Over the past 15 years, our knowledge of the interior of the Sun has tremendously progressed by the use of helioseismic measurements. However, to go further in our understanding of the solar core, we need to measure gravity (g) modes. Thanks to the high quality of the Doppler-velocity signal measured by GOLF/SoHO, it has been possible to unveil the signature of the asymptotic properties of the solar g modes, thus obtaining a hint of the rotation rate in the core. However, the quest for the detection of individual g modes is not yet over. In this work, we apply the latest theoretical developments to guide our research using GOLF velocity time series. In contrary to what was thought till now, we are maybe starting to identify individual low-frequency g modes...Comment: Highlight of Astronomy (HoA) proceedings of the JD-11, IAU 2009. 2 pages, 1 figur

Comparison of intraoperative frozen section analysis for sentinel lymph node biopsy during breast cancer surgery for invasive lobular carcinoma and invasive ductal carcinoma

<p>Abstract</p> <p>Background</p> <p>Sentinel lymph node (SLN) biopsy is the standard of care for the surgical assessment of the axilla during breast cancer surgery. However, the diagnostic accuracy of intraoperative frozen section analysis for confirming metastatic involvement of SLNs in cases of invasive lobular carcinoma (ILC) versus that of invasive ductal carcinoma (IDC) has generated controversy secondary to a frequently low-grade cytologic appearance and an often discohesive pattern displayed by metastatic lymph nodes in ILC. In the current report, we present a comparison of intraoperative frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC.</p> <p>Methods</p> <p>We evaluated the results of 131 consecutive cases of ILC from 1997 to 2008 and 133 cases of IDC (selected by a random sequence generator program) from amongst 1163 consecutive cases of IDC from the same time period. All cases had at least one SLN that had both intraoperative frozen section analysis and confirmatory permanent section analysis performed.</p> <p>Results</p> <p>No statistically significant difference was found in the sensitivity (67% vs. 75%, P = 0.385), specificity (100% vs. 100%), accuracy (86% vs. 92%, P = 0.172), false negative rate (33% vs. 25%, P = 0.385), negative predictive value (81% vs. 89%, P = 0.158), and positive predictive value (100% vs. 100%) for frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC.</p> <p>Conclusion</p> <p>Since there was no statistically significant difference in sensitivity, specificity, accuracy, false negative rate, negative predictive value, and positive predictive value between frozen section analysis of SLNs for patients with ILC and IDC, the clinical accuracy of confirming metastatic involvement of SLNs on frozen section analysis for ILC should not be considered inferior to the clinical accuracy for IDC. Therefore, frozen section analysis of all SLNs during breast cancer surgery in patients with ILC should remain the standard of care in order to reduce the risk of the need of a later, separate axillary lymph node dissection.</p

Multilayered Nanostructures Integrated with Emerging Technologies

Surface and interface functionalization are crucial steps to introduce new functionalities in numerous applications, as faster dynamics occur on surfaces rather than bulk. Within this context, the layer-by-layer (LbL) technique is a versatile methodology to controllably form organized nanostructures from the spontaneous adsorption of charged molecules. It enables the assembly of multilayered LbL films on virtually any surface using non-covalent molecular interactions, allowing the nanoengineering of interfaces and creation of multifunctional systems with distinct building blocks (polymers, clays, metal nanoparticles, enzymes, organic macromolecules, etc.). Several applications require thin films on electrodes for sensing/biosensing, and here we explore LbL films deposited on interdigitated electrodes (IDEs) that were 3D-printed using the fusing deposition modeling (FDM) technique. IDEs covered with LbL films can be used to form multisensory systems employed in the analysis of complex liquids transforming raw data into specific patterns easily recognized by computational and statistical methods. We extend the FDM 3D-printing methodology to simplify the manufacturing of electrodes and microchannels, thus integrating an e-tongue system in a microfluidic device. Moreover, the continuous flow within microchannels contributes to faster and more accurate analysis, reducing the amount of sample, waste, and costs

Heme metabolism, oxidative and nitrosative markers in a mouse model of Hemochromatosis: Effect of Isoflurane, ethanol and 5-aminolevulinic acid

Hereditary hemochromatosis (HH) is characterized by iron homeostasis alterations. Association between HH and Porphyria Cutanea Tarda has been reported. The aim was to characterize oxidative and nitrosative stress status and its relationship with heme metabolism in a hemochromatosis mouse model (Hfe-/-), and to evaluate the effects of Isoflurane, ethanol and 5-aminolevulinic acid (ALA). Male and female Hfe−/− and wild-type C57BL/6J mice received Isoflurane (2 ml/kg); ethanol (30%) or ALA (40 mg/kg). In male Hfe-/-, reduced glutathione (GSH) was diminished respect to C57BL/6J mice. Female Hfe-/- showed higher levels of GSH and total antioxidant capacity than male Hfe-/-. Catalase activity was lower in male and female Hfe-/- than in controls. 5-Aminolevulinic acid synthetase activity was higher in male and female Hfe-/- than in controls. In male Hfe-/-, Porphobilinogen deaminase (PBG-D) activity was augmented and Heme oxygenase (HO) activity was diminished probably to avoid iron increase. Isoflurane and ethanol reduced PBG-D and increased HO activities. HO induction would indicate oxidative stress instauration being more striking due to ethanol that also induced Superoxide dismutase activity. Isoflurane reduced Nitric Oxide Synthase expression. ALA altered antioxidant system. In Hfe-/- mice different metabolisms were altered being more affected by the drugs studied. Findings here described would contribute to increase the knowledge about the association between HH and the Porphyrias and about the effects of volatile anaesthetics on different metabolisms in genetic models of Porphyrias and associated diseases.Fil: Buzaleh, Ana Maria. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Houssay. Centro de Invest. Sobre Porfirinas y Porfirias; Argentina. Hospital 12 de Octubre; España. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Moreno Carraledo, Maria. Hospital 12 de Octubre; EspañaFil: Mendez, Manuel. Hospital 12 de Octubre; EspañaFil: Batlle, Alcira Maria del C.. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Houssay. Centro de Invest. Sobre Porfirinas y Porfirias; ArgentinaFil: Enriquez de Salamanca, Rafael. Hospital 12 de Octubre; EspañaFil: Moran Jimenez, Maria Jose. Hospital 12 de Octubre; Españ

MyDas, an extensible Java DAS server

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users. We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details

Dasty3, a WEB framework for DAS

Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification