The three-dimensional wake behind an obstacle on a flat plate

Three dimensional incompressible wake behind blunt obstacle located at leading edge of flat plat

Tools and collaborative environments for bioinformatics research

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies

Comportamiento inusual de un ejemplar de tortuga boba joven liberado en el Mar de Alborán

Un individuo juvenil de tortuga boba con problemas de flotabilidad fue capturado en el Mar de Alborán (Mar Mediterráneo, sur de España). Fue liberado 14 meses después de su curación. Seis días después de la liberación, la tortuga fue vista nadando a 42 km del punto de liberación, con un comportamiento inusual. Por este motivo fue recapturada y liberada de nuevo, a 95 millas náuticas de la costa cerca de la Isla de Alborán. Diez días más tarde, la tortuga llegó a la playa, cerca de donde se la había mantenido en cautividad. En la presente nota se discuten estos hechos en el contexto de la alteración de la conducta y la habituación de las tortugas en libertad. Los estudios centrados en la captura, marcaje y recaptura de las tortugas marinas, por ejemplo, deben de abordarse con cautela, ya que la manipulación de estos animales podría modificar su comportamiento habitual. Palabras claves: Tortuga marina, Captura–marcado–recaptura, Posliberación, Mar Mediterráneo.A juvenile loggerhead turtle with buoyancy problems was captured in the Alboran Sea (Mediterranean Sea, south of Spain) and released 14 months later after healing. Six days after the release, the turtle was seen swimming 42 km from the point of release, displaying unusual behaviour. We re–captured and released it again, 95 nautical miles offshore, near the Alboran Island. Ten days later the turtle arrived at the beach close to where it had been maintained in captivity. We discuss these findings in the context of behavioural alteration and habituation in released sea turtles. Capture–mark–recapture studies of sea turtles should be approached with caution as manipulated animals may modify their usual behaviour. Key words: Sea turtle, Captivity, Capture–mark–recapture, Post–release, Mediterranean Sea.Un individuo juvenil de tortuga boba con problemas de flotabilidad fue capturado en el Mar de Alborán (Mar Mediterráneo, sur de España). Fue liberado 14 meses después de su curación. Seis días después de la liberación, la tortuga fue vista nadando a 42 km del punto de liberación, con un comportamiento inusual. Por este motivo fue recapturada y liberada de nuevo, a 95 millas náuticas de la costa cerca de la Isla de Alborán. Diez días más tarde, la tortuga llegó a la playa, cerca de donde se la había mantenido en cautividad. En la presente nota se discuten estos hechos en el contexto de la alteración de la conducta y la habituación de las tortugas en libertad. Los estudios centrados en la captura, marcaje y recaptura de las tortugas marinas, por ejemplo, deben de abordarse con cautela, ya que la manipulación de estos animales podría modificar su comportamiento habitual. Palabras claves: Tortuga marina, Captura–marcado–recaptura, Posliberación, Mar Mediterráneo

Fluoxetine effects assessment on the life cycle of aquatic invertebrates

International audienceFluoxetine is a serotonin re-uptake inhibitor, generally used as an antidepressant. It is suspected to provoke substantial effects in the aquatic environment. This study reports the effects of fluoxetine on the life cycle of four invertebrate species, Daphnia magna, Hyalella azteca and the snail Potamopyrgus antipodarum exposed to fluoxetine spiked-water and the midge Chironomus riparius exposed to fluoxetine-spiked sediments. For D. magna, a multi-generational study was performed with exposition of newborns from exposed organisms. Effects of fluoxetine could be found at low measured concentrations (around 10 micro g l(-1)), especially for parthenogenetic reproduction of D. magna and P. antipodarum. For daphnids, newborns length was impacted by fluoxetine and the second generation of exposed individuals showed much more pronounced effects than the first one, with a NOEC of 8.9 micro g l(-1). For P. antipodarum, significant decrease of reproduction was found for concentrations around 10 micro g l(-1). In contrast, we found no effect on the reproduction of H. azteca but a significant effect on growth, which resulted in a NOEC of 33 micro g l(-1), expressed in nominal concentration. No effect on C. riparius could be found for measured concentrations up to 59.5 mg kg(-1). General mechanistic energy-based models showed poor relevance for data analysis, which suggests that fluoxetine targets specific mechanisms of reproduction

Mining microarray datasets aided by knowledge stored in literature

DNA microarray technology produces large amounts of data. For data mining of these datasets, background information on genes can be helpful. Unfortunately most information is stored in free text. Here, we present an approach to use this information for DNA microarray data mining

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

<p>Abstract</p> <p>Background</p> <p>In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL.</p> <p>Results</p> <p>To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available.</p> <p>Conclusion</p> <p>This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.</p

First record of the harp seal (Pagophilus groenlandicus) extralimital presence in the Mediterranean Sea

The stranding of a harp seal on the beach in the municipality of Motril (southern Spain) represents the first record of this species in the Mediterranean Sea and the southernmost known report. It was a male which reached the beach very tired and sick, dying after two hours on the sand. The specimen presented three species of epibionts. This is the second species of Arctic seal recorded in the Mediterranean SeaPeer reviewe

Ambiguity of human gene symbols in LocusLink and MEDLINE: creating an inventory and a disambiguation test collection

Genes are discovered almost on a daily basis and new names have to be found. Although there are guidelines for gene nomenclature, the naming process is highly creative. Human genes are often named with a gene symbol and a longer, more descriptive term; the short form is very often an abbreviation of the long form. Abbreviations in biomedical language are highly ambiguous, i.e., one gene symbol often refers to more than one gene.Using an existing abbreviation expansion algorithm,we explore MEDLINE for the use of human gene symbols derived from LocusLink. It turns out that just over 40% of these symbols occur in MEDLINE, however, many of these occurrences are not related to genes. Along the process of making an inventory, a disambiguation test collection is constructed automatically