Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$

Transiting exoplanets from the CoRoT space mission VIII. CoRoT-7b: the first Super-Earth with measured radius

We report the discovery of very shallow (DF/F = 3.4 10-4), periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which we interpret as due to the presence of a transiting companion. We describe the 3-colour CoRoT data and complementary ground-based observations that support the planetary nature of the companion. Methods. We use CoRoT color information, good angular resolution ground-based photometric observations in- and out- of transit, adaptive optics imaging, near-infrared spectroscopy and preliminary results from Radial Velocity measurements, to test the diluted eclipsing binary scenarios. The parameters of the host star are derived from optical spectra, which were then combined with the CoRoT light curve to derive parameters of the companion. We examine carefully all conceivable cases of false positives, and all tests performed support the planetary hypothesis. Blends with separation larger than 0.40 arcsec or triple systems are almost excluded with a 8 10-4 risk left. We conclude that, as far as we have been exhaustive, we have discovered a planetary companion, named CoRoT-7b, for which we derive a period of 0.853 59 +/- 3 10-5 day and a radius of Rp = 1.68 +/- 0.09 REarth. Analysis of preliminary radial velocity data yields an upper limit of 21 MEarth for the companion mass, supporting the finding. CoRoT-7b is very likely the first Super-Earth with a measured radius.Comment: Accepted in Astronomy and Astrophysics; typos and language corrections; version sent to the printer w few upgrade

Changes in the flexion relaxation response induced by lumbar muscle fatigue

<p>Abstract</p> <p>Background</p> <p>The flexion relaxation phenomenon (FRP) is an interesting model to study the modulation of lumbar stability. Previous investigations have explored the effect of load, angular velocity and posture on this particular response. However, the influence of muscular fatigue on FRP parameters has not been thoroughly examined. The objective of the study is to identify the effect of erector spinae (ES) muscle fatigue and spine loading on myoelectric silence onset and cessation in healthy individuals during a flexion-extension task.</p> <p>Methods</p> <p>Twenty healthy subjects participated in this study and performed blocks of 3 complete trunk flexions under 4 different experimental conditions: no fatigue/no load (1), no fatigue/load (2), fatigue/no load(3), and fatigue/load (4). Fatigue was induced according to the Sorenson protocol, and electromyographic (EMG) power spectral analysis confirmed that muscular fatigue was adequate in each subject. Trunk and pelvis angles and surface EMG of the ES L2 and L5 were recorded during a flexion-extension task. Trunk flexion angle corresponding to the onset and cessation of myoelectric silence was then compared across the different experimental conditions using 2 × 2 repeated-measures ANOVA.</p> <p>Results</p> <p>Onset of myoelectric silence during the flexion motion appeared earlier after the fatigue task. Additionally, the cessation of myoelectric silence was observed later during the extension after the fatigue task. Statistical analysis also yielded a main effect of load, indicating a persistence of ES myoelectric activity in flexion during the load condition.</p> <p>Conclusion</p> <p>The results of this study suggest that the presence of fatigue of the ES muscles modifies the FRP. Superficial back muscle fatigue seems to induce a shift in load-sharing towards passive stabilizing structures. The loss of muscle contribution together with or without laxity in the viscoelastic tissues may have a substantial impact on post fatigue stability.</p

Evolution through segmental duplications and losses : A Super-Reconciliation approach

The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes

Load and speed effects on the cervical flexion relaxation phenomenon

<p>Abstract</p> <p>Background</p> <p>The flexion relaxation phenomenon (FRP) represents a well-studied neuromuscular response that occurs in the lumbar and cervical spine. However, the cervical spine FRP has not been investigated extensively, and the speed of movement and loading effects remains to be characterized. The objectives of the present study were to evaluate the influence of load and speed on cervical FRP electromyographic (EMG) and kinematic parameters and to assess the measurement of cervical FRP kinematic and EMG parameter repeatability.</p> <p>Methods</p> <p>Eighteen healthy adults (6 women and 12 men), aged 20 to 39 years, participated in this study. They undertook 2 sessions in which they had to perform a standardized cervical flexion/extension movement in 3 phases: complete cervical flexion; the static period in complete cervical flexion; and extension with return to the initial position. Two different rhythm conditions and 3 different loading conditions were applied to assess load and speed effects. Kinematic and EMG data were collected, and dependent variables included angles corresponding to the onset and cessation of myoelectric silence as well as the root mean square (RMS) values of EMG signals. Repeatability was examined in the first session and between the 2 sessions.</p> <p>Results</p> <p>Statistical analyses revealed a significant load effect (P < 0.001). An augmented load led to increased FRP onset and cessation angles. No load × speed interaction effect was detected in the kinematics data. A significant load effect (P < 0.001) was observed on RMS values in all phases of movement, while a significant speed effect (P < 0.001) could be seen only during the extension phase. Load × speed interaction effect was noted in the extension phase, where higher loads and faster rhythm generated significantly greater muscle activation. Intra-session and inter-session repeatability was good for the EMG and kinematic parameters.</p> <p>Conclusions</p> <p>The load increase evoked augmented FRP onset and cessation angles as well as heightened muscle activation. Such increments may reflect the need to enhance spinal stability under loading conditions. The kinematic and EMG parameters showed promising repeatability. Further studies are needed to assess kinematic and EMG differences between healthy subjects and patients with neck pain.</p

One size does not fit all: local determinants of measles vaccination in four districts of Pakistan

Common factors are associated with vaccination. However, despite common factors the pattern of variables related to measles vaccination differs between and within districts. In this study children were more likely to receive measles vaccination if their mother had any formal education, if she knew at least one vaccine preventable disease, and if she had not heard of any bad effects of vaccination. In rural areas, living within 5 km of a vaccination facility or in a community visited by a vaccination team were factors associated with vaccination, as was the mother receiving information about vaccinations