Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.

MOTIVATION: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. RESULTS: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. AVAILABILITY: download section of the Bgee website http://bgee.unil.ch/

Improving the performance of positive selection inference by filtering unreliable alignment regions.

Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is expected to increase the accuracy of positive selection inference, such filtering may also significantly decrease the power of the test, as positively selected regions are fast evolving, and those same regions are often those that are difficult to align. Here, we used realistic simulations that mimic sequence evolution of HIV-1 genes to test the hypothesis that the performance of positive selection inference using codon models can be improved by removing unreliable alignment regions. Our study shows that the benefit of removing unreliable regions exceeds the loss of power due to the removal of some of the true positively selected sites.

Effects of Different Postural Conditions on Handwriting Variability

During their career, forensic document examiners will inevitably be confronted with handwriting carried out under unusual conditions (UnC). A questioned document signed on top of a car or on a vertical surface like a wall are two examples. These atypical circumstances may give rise to more variability of the signatures or written words, in particular if the body was in non-traditional writing position without the traditional support. Few studies were devoted to handwriting variability under unusual writing conditions. The current study investigates whether individual variability changes with special writing conditions. In a previous study (Sciacca & al, 2009), we found that eight repetitions were sufficient to obtain a correct estimation of the variance. In the present study, twelve subjects were asked to write two word sets eight times in upper and eight times in lower case, under different conditions : sitting and writing on a horizontal (usual condition UC) or vertical support; and standing, kneeling or laying while writing on a horizontal or vertical support (unusual conditions UnC). Words were written on a pen tablet, normalized in space and time and then averaged. The variance of the eight words was measured under all conditions. Results showed only an increase in variability under the laying and kneeling / vertical UnC. Within the five other postural conditions tested, handwriting was shown to be very stable.

Kinematics and dynamic complexity of postural transitions in frail elderly subjects.

The aim of this study was to propose a methodology allowing a detailed characterization of body sit-to-stand/stand-to-sit postural transition. Parameters characterizing the kinematics of the trunk movement during sit-to-stand (Si-St) postural transition were calculated using one initial sensor system fixed on the trunk and a data logger. Dynamic complexity of these postural transitions was estimated by fractal dimension of acceleration-angular velocity plot. We concluded that this method provides a simple and accurate tool for monitoring frail elderly and to objectively evaluate the efficacy of a rehabilitation program.

Tibial component positioning in total knee arthroplasty: bone coverage and extensor apparatus alignment.

Correct positioning of the tibial component in total knee arthroplasty (TKA) must take into account both an optimal bone coverage (defined by a maximal cortical bearing with posteromedial and anterolateral support) and satisfactory patellofemoral tracking. Consequently, a compromise position must be found by the surgeon during the operation to simultaneously meet these two requirements. Moreover, tibial tray positioning depends upon the tibial torsion, which has been shown to act mainly in the proximal quarter of the tibia. Therefore, the correct application of the tibial tray is also theoretically related to the level of bone resection. In this study, we first quantified the torsional profile given by an optimal bone coverage for a symmetrical tibial tray design and for an asymmetrical one. Then, for the two types of tibial trays, we measured the angle difference between optimal bone coverage and an alignment on the middle of the tibial tubercule. Results showed that the values of the torsional profile given by the symmetrical tray were more scattered than those from the asymmetrical one. However, determination of the mean differential angle between the position providing optimal bone coverage and the one providing the best patellofemoral tracking indicated that the symmetrical prosthetic tray offered the best compromise between these two requirements. Although the tibiofemoral joint is known to be asymmetric in both shape and dimension, the asymmetrical tray chosen in this study was found to fulfill this compromise with more difficulty.

Automatic recognition of postural allocations.

A significant part of daily energy expenditure may be attributed to non-exercise activity thermogenesis and exercise activity thermogenesis. Automatic recognition of postural allocations such as standing or sitting can be used in behavioral modification programs aimed at minimizing static postures. In this paper we propose a shoe-based device and related pattern recognition methodology for recognition of postural allocations. Inexpensive technology allows implementation of this methodology as a part of footwear. The experimental results suggest high efficiency and reliability of the proposed approach.

An intramedullary alignment guide lodging within the femoral canal during total knee arthroplasty: a case report.

The usual complications of total knee arthroplasty include thrombo-embolism, infection, and loosening. We report an unusual and potentially serious complication of an intramedullary guide lodging within the femoral canal during the procedure. Considering the risk of fracture and additional exposure, the guide was not removed and was cut in situ. The rest of the operation was completed successfully and the patient made an uneventfully recovery.

Grabbing your ear: rapid auditory-somatosensory multisensory interactions in low-level sensory cortices are not constrained by stimulus alignment.

Multisensory interactions are observed in species from single-cell organisms to humans. Important early work was primarily carried out in the cat superior colliculus and a set of critical parameters for their occurrence were defined. Primary among these were temporal synchrony and spatial alignment of bisensory inputs. Here, we assessed whether spatial alignment was also a critical parameter for the temporally earliest multisensory interactions that are observed in lower-level sensory cortices of the human. While multisensory interactions in humans have been shown behaviorally for spatially disparate stimuli (e.g. the ventriloquist effect), it is not clear if such effects are due to early sensory level integration or later perceptual level processing. In the present study, we used psychophysical and electrophysiological indices to show that auditory-somatosensory interactions in humans occur via the same early sensory mechanism both when stimuli are in and out of spatial register. Subjects more rapidly detected multisensory than unisensory events. At just 50 ms post-stimulus, neural responses to the multisensory 'whole' were greater than the summed responses from the constituent unisensory 'parts'. For all spatial configurations, this effect followed from a modulation of the strength of brain responses, rather than the activation of regions specifically responsive to multisensory pairs. Using the local auto-regressive average source estimation, we localized the initial auditory-somatosensory interactions to auditory association areas contralateral to the side of somatosensory stimulation. Thus, multisensory interactions can occur across wide peripersonal spatial separations remarkably early in sensory processing and in cortical regions traditionally considered unisensory.

Hypobaric versus normobaric hypoxia: same effects on postural stability?

AIMS: To test the hypothesis that postural stability would be more affected during acute exposure in hypobaric (HH) than in normobaric (NH) hypoxia.¦METHODS: In separate trials, 12 subjects stood on a posturographic platform for two successive 25.6 sec tests in three conditions: eyes open (EO), eyes closed (EC), and verbal dual task (DT). Ambient pressure in O(2) was matched between HH and NH at 1700 and 3000 m, respectively.¦RESULTS: Compared to NH, the length of Centre of Pression trajectory in Y-axis was increased (p<0.05) in HH for EO at 1700 m, EC at 1700 and 3000 m, and for DT at 1700 m, whereas the variance of speed of CoP was decreased (p<0.05) in EO, EC, and DT at 1700 m. Compared to normobaric normoxia (NN; 400 m), the surface of CoP trajectory was increased (p<0.05) in HH in EO and EC at 3000 m.¦CONCLUSIONS: HH deteriorated postural stability in the antero-posterior plane, for the variance of speed and the surface of CoP in 3 conditions, whereas no difference was observed between NH and NN. These results suggest that hypobaria instead of hypoxia per se plays an important role to the altered balance classically reported in altitude.

Alterations in Postural Control during the World's Most Challenging Mountain Ultra-Marathon

We investigated postural control (PC) effects of a mountain ultra-marathon (MUM): a 330-km trail run with 24000 m of positive and negative change in elevation. PC was assessed prior to (PRE), during (MID) and after (POST) the MUM in experienced ultra-marathon runners (n = 18; finish time = 126+/-16 h) and in a control group (n = 8) with a similar level of sleep deprivation. Subjects were instructed to stand upright on a posturographic platform over a period of 51.2 seconds using a double-leg stance under two test conditions: eyes open (EO) and eyes closed (EC). Traditional measures of postural stability (center of pressure trajectory analysis) and stabilogram-diffusion analysis (SDA) parameters were analysed. For the SDA, a significantly greater short-term effective diffusion was found at POST compared with PRE in the medio-lateral (ML; Dxs) and antero-posterior (AP) directions (Dys) in runners (p<0.05) The critical time interval (Ctx) in the ML direction was significantly higher at MID (p<0.001) and POST (p<0.05) than at PRE in runners. At MID (p<0.001) and POST (p<0.05), there was a significant difference between the two groups. The critical displacement (Cdx) in the ML was significantly higher at MID and at POST (p<0.001) compared with PRE for runners. A significant difference in Cdx was observed between groups in EO at MID (p<0.05) and POST (p<0.005) in the ML direction and in EC at POST in the ML and AP directions (p<0.05). Our findings revealed significant effects of fatigue on PC in runners, including, a significant increase in Ctx (critical time in ML plan) in EO and EC conditions. Thus, runners take longer to stabilise their body at POST than at MID. It is likely that the mountainous characteristics of MUM (unstable ground, primarily uphill/downhill running, and altitude) increase this fatigue, leading to difficulty in maintaining balance.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.