The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Unifying some higher-order statistic-based methods for errors-in-variables model identification ⋆

In this paper, the problem of identifying linear discrete-time systems from noisy input and output data is addressed. Several existing methods based on higher-order statistics are presented. It is shown that they stem from the same set of equations and can thus be united from the viewpoint of extended instrumental variable methods. A numerical example is presented which confirms the theoretical results. Some possible extensions of the methods are then given. Key words: System identification; errors-in-variables; instrumental variable; higher-order statistics.

Two-way communication for programming and measurement in a miniature implantable stimulator.

Implantable stimulators are needed for chronic electrical stimulation of nerves and muscles in experimental studies. The device described exploits the versatility of current microcontrollers for stimulation and communication in a miniature implant. Their standard outputs can provide the required selectable constant-current sources. In this device, pre-programmed stimulation paradigms were selected by transcutaneous light pulses. The potential of a programmable integrated circuit (PIC) was thus exploited. Implantable devices must be biocompatible. A novel encapsulation method that require no specialised equipment and that used two classical encapsulants, silicone and Teflon was developed. It was tested for implantation periods of up to four weeks. A novel way to estimate electrode impedance in awake animals is also presented. It was thus possible to follow the evolution of the nerve-electrode interface and, if necessary, to adjust the stimulation parameters. In practice, the electrode voltage at the end of a known constant-current pulse was measured by the PIC. The binary coded value was then indicated to the user as a series of muscle twitches that represented the binary value of the impedance measurement. This neurostimulator has been successfully tested in vitro and in vivo. Thresholds and impedance values were chronically monitored following implantation of a self-sizing spiral cuff electrode. Impedance variations in the first weeks could reflect morphological changes usually observed after the implantation of such electrodes

Experimental and analytical analyses of the cutting process in the deep hole drilling with BTA (Boring Trepanning Association) system

This paper deals with analysis of the cutting process, on a macro and micro scale, in the deep hole drilling with BTA system. An experimental procedure is developed to highlight the impact of cutting speed and feed rate on the cutting process when machining the 18MND5 steel. Parameters based on dimensional characteristics of chips are introduced to quantify the morphology of chips generated by central, intermediate and external inserts of the complex BTA drilling tool. From observation of the chips morphology (flat, curved and spiral) and the measurement of the chips width, the provenance of each chip with respect to cutting inserts is identified. Then, the Chip Compression Ratio is evaluated for each cutting condition, indicating the amount of plastic strain in chips. Thanks to the introduction of a new parameter, denoted as Chip Fragmentation Ratio, it is found that the cutting speed has a little influence, compared to the feed rate, on the chips size. Based on this quantitative analysis, the optimal range of cutting conditions for the BTA deep hole drilling is discussed. It is mentioned that although increasing the feed rate promotes the chips fragmentation and increases the material removal rate (increasing productivity), an upper limit is to determine to prevent excessive flank wear. Also, the cutting speed should be limited to avoid excessive crater wear

Radiocarbon dating application to modern musical instruments: an interdisciplinary study

International audienceRelics dating: why not follow the example of dating of modern music instrument, combining the sharpest 14C technology and independent expertise?Dating historical relics partly meets the same issue than dating modern music instruments dated between the 16th and 19th century. For both woody relics and music instrument, dendrochronology might not be carried out due to a too short tree-rings record and 14C dating might a priori be ignored for historical periods as a 14C physical measurement might result into several equiprobable age ranges. Several samplings and independent expertise are then required to make a well-considered choice between these intervals. Owing to the new generation of 14C dating instruments, sampling without affecting the instrument or relics integrity is now possible. The interdisciplinary framework allows combining any ante quem or post quem information on the age of relics or music instruments. To illustrate this approach, we will draw on an on-going project of modern music instruments gathering radiocarbon dating specialists and the museum curators. Our goal is to deepen the scientific knowledge about the origin and the long history of use and restoration of instruments kept at the Musée de la musique. As an example, an Indian rudra-vina (E.997.24.1) was dated from the end of the 17th century. Transcription of 14C activity measured on two sub-samples yields four equiprobable calibrated date ranges. The comparison with a Govardhan’s picturial representation of a similar rudra-vina allows to determine the most likely date range: [AD 1650-1683]. Likewise, a second example comes from a stringed Hindustani instrument named kinnari-veena. It was supposedly dated from the 18th century according to Musée's curators because of its organological features. The dating, based on 7 sub-samples, has brought to light a very likely restoration of the upper-nut whereas all other components are contemporaneous of the instrument manufacturing. The results obtained allow to reveal additions or changes (successive layers of history) since they emerged from the instrument factories. The relics made of wood, bones or textile can also take benefit of such a multidisciplinary approach already applied on music instruments with composite constitutions