Determining species tree topologies from clade probabilities under the coalescent

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy consensus algorithm, which consecutively accepts the most probable clades compatible with previously accepted clades, can be used for this second stage, this method is known to be statistically inconsistent under the multispecies coalescent model. This raises the question of whether it is theoretically possible to reconstruct the species tree from known probabilities of clades on gene trees. We investigate clade probabilities arising from the multispecies coalescent model, with an eye toward identifying features of the species tree. Clades on gene trees with probability greater than 1/3 are shown to reflect clades on the species tree, while those with smaller probabilities may not. Linear invariants of clade probabilities are studied both computationally and theoretically, with certain linear invariants giving insight into the clade structure of the species tree. For species trees with generic edge lengths, these invariants can be used to identify the species tree topology. These theoretical results both confirm that clade probabilities contain full information on the species tree topology and suggest future directions of study for developing statistically consistent inference methods from clade frequencies on gene trees.Comment: 25 pages, 2 figure

Distribution of Kingella kingae Capsular Serotypes in France Assessed by a Multiplex PCR Assay on Osteoarticular Samples

International audienceno abstrac

Experimental validation of a patient-specific model of orthotic action in adolescent idiopathic scoliosis

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record.PURPOSE: Personalized modeling of brace action has potential in improving brace efficacy in adolescent idiopathic scoliosis (AIS). Model validation and simulation uncertainty are rarely addressed, limiting the clinical implementation of personalized models. We hypothesized that a thorough validation of a personalized finite element model (FEM) of brace action would highlight potential means of improving the model. METHODS: Forty-two AIS patients were included retrospectively and prospectively. Personalized FEMs of pelvis, spine and ribcage were built from stereoradiographies. Brace action was simulated through soft cylindrical pads acting on the ribcage and through displacements applied to key vertebrae. Simulation root mean squared errors (RMSEs) were calculated by comparison with the actual brace action (quantified through clinical indices, vertebral positions and orientations) observed in in-brace stereoradiographies. RESULTS: Simulation RMSEs of Cobb angle and vertebral apical axial rotation was lower than measurement uncertainty in 79 % of the patients. Pooling all patients and clinical indices, 87 % of the indices had lower RMSEs than the measurement uncertainty. CONCLUSIONS: In-depth analysis suggests that personalization of spinal functional units mechanical properties could improve the simulation's accuracy, but the model gave good results, thus justifying further research on its clinical application

Congenital tibial deficiencies: Treatment using the Ilizarov's external fixator

SummaryIntroductionCongenital longitudinal deficiency of the tibia is a rare and often syndromic anomaly. Amputation is usually the preferred treatment option in complete absence of the tibia; however, a conservative management might be implemented in partial forms or in case of amputation refusal. Our experience with the Ilizarov fixator, convinced us this device was the best suited for progressive correction of lower limbs length discrepancies and articular or bone angular limb deformities (ALD). The aim of this study is to highlight the interest of the Ilizarov fixator in the multistage conservative treatment of congenital tibial deficiencies.Material and methodsA retrospective study was conducted in nine patients suffering from Type I or II congenital tibial deficiencies (Jones) and sequentially managed using the Ilizarov technique. The functional outcome after treatment completion was then clinically assessed.ResultsThe different stages of correction were recorded for each individual patient. Patients were assessed at a mean follow-up of 18,3 years (4–32 years). The mean maximum knee flexion was 35° (0°–90°) in type I deficiencies and 118° (90°–140°) in type II deficiencies. One patient underwent amputation and a bilateral knee arthrodesis was performed in another case.DiscussionFew series in the literature report a comparable length of follow-up period in the conservative management of severe congenital tibial deficiencies. In our study, the Ilizarov fixator provided satisfactory progressive corrections of severe congenital tibial deficiencies.Level of EvidenceLevel IV therapeutic retrospective study

A method to localize gamma-ray bursts using POLAR

The hard X-ray polarimeter POLAR aims to measure the linear polarization of the 50-500 keV photons arriving from the prompt emission of gamma-ray bursts (GRBs). The position in the sky of the detected GRBs is needed to determine their level of polarization. We present here a method by which, despite of the polarimeter incapability of taking images, GRBs can be roughly localized using POLAR alone. For this purpose scalers are attached to the output of the 25 multi-anode photomultipliers (MAPMs) that collect the light from the POLAR scintillator target. Each scaler measures how many GRB photons produce at least one energy deposition above 50 keV in the corresponding MAPM. Simulations show that the relative outputs of the 25 scalers depend on the GRB position. A database of very strong GRBs simulated at 10201 positions has been produced. When a GRB is detected, its location is calculated searching the minimum of the chi2 obtained in the comparison between the measured scaler pattern and the database. This GRB localization technique brings enough accuracy so that the error transmitted to the 100% modulation factor is kept below 10% for GRBs with fluence Ftot \geq 10^(-5) erg cm^(-2) . The POLAR localization capability will be useful for those cases where no other instruments are simultaneously observing the same field of view.Comment: 13 pages, 10 figure

Does the Spine Surgeon’s Experience Affect Fracture Classification, Assessment of Stability, and Treatment Plan in Thoracolumbar Injuries?

Study Design: Prospective survey-based study. Objectives: The AO Spine thoracolumbar injury classification has been shown to have good reproducibility among clinicians. However, the influence of spine surgeons’ clinical experience on fracture classification, stability assessment, and decision on management based on this classification has not been studied. Furthermore, the usefulness of varying imaging modalities including radiographs, computed tomography (CT) and magnetic resonance imaging (MRI) in the decision process was also studied. Methods: Forty-one spine surgeons from different regions, acquainted with the AOSpine classification system, were provided with 30 thoracolumbar fractures in a 3-step assessment: first radiographs, followed by CT and MRI. Surgeons classified the fracture, evaluated stability, chose management, and identified reasons for any changes. The surgeons were divided into 2 groups based on years of clinical experience as \u3c10 years (n = 12) and \u3e10 years (n = 29). Results: There were no significant differences between the 2 groups in correctly classifying A1, B2, and C type fractures. Surgeons with less experience hadmore correct diagnosis in classifyingA3 (47.2% vs 38.5%in step 1, 73.6% vs 60.3% in step 2 and 77.8% vs 65.5% in step 3), A4 (16.7% vs 24.1% in step 1, 72.9% vs 57.8% in step 2 and 70.8% vs 56.0%in step3) and B1 injuries (31.9% vs 20.7% in step 1, 41.7% vs 36.8% in step 2 and 38.9% vs 33.9% in step 3). In the assessment of fracture stability and decision on treatment, the less and more experienced surgeons performed equally. The selection of a particular treatment plan varied in all subtypes except in A1 and C type injuries. Conclusion: Surgeons’ experience did not significantly affect overall fracture classification, evaluating stability and planning the treatment. Surgeons with less experience had a higher percentage of correct classification in A3 and A4 injuries. Despite variations between them in classification, the assessment of overall stability and management decisions were similar between the 2 groups. © The Author(s) 2017

The Development of a Universally Accepted Sacral Fracture Classification: A Survey of AOSpine and AOTrauma Members.

Study Design Survey study. Objective To determine the global perspective on controversial aspects of sacral fracture classifications. Methods While developing the AOSpine Sacral Injury Classification System, a survey was sent to all members of AOSpine and AOTrauma. The survey asked four yes-or-no questions to help determine the best way to handle controversial aspects of sacral fractures in future classifications. Chi-square tests were initially used to compare surgeons\u27 answers to the four key questions of the survey, and then the data was modeled through multivariable logistic regression analysis. Results A total of 474 surgeons answered all questions in the survey. Overall 86.9% of respondents felt that the proposed hierarchical nature of injuries was appropriate, and 77.8% of respondents agreed that that the risk of neurologic injury is highest in a vertical fracture through the foramen. Almost 80% of respondents felt that the separation of injuries based on the integrity of L5-S1 facet was appropriate, and 83.8% of surgeons agreed that a nondisplaced sacral U fracture is a clinically relevant entity. Conclusion This study determines the global perspective on controversial areas in the injury patterns of sacral fractures and demonstrates that the development of a comprehensive and universally accepted sacral classification is possible

Normal Range of Patellar Tendon Elasticity Using the Sharewave Elastography Technique: An In Vivo Study in Normal Volunteers

In-vivo investigation of tendon mechanical properties in healthy subjects using Shear Wave Elastography (SWE) techniques is a relatively new field of study. This work aims to evaluate the elastic properties of the patellar tendon in various knee range of flexion. Twenty healthy adult subjects were enrolled in the study. Shear wave speed (SWS) in the patellar tendon was measured in three different positions: Knee extended, knee semi-flexed (30°), and knee flexed (90°). Mean shear modulus was 50.9 +- 33.1 kPa in knee extension position, 137.5 +- 50.7 kPa in 30° flexion position, and 226.5 +- 60.3 kPa in 90° flexion position. The lowest shear modulus was obtained at rest with the knee in a fully extended position. These results are in agreement with those previously reported on Achilles tendon and triceps muscles. Shear modulus values obtained in our study could be considered as baseline values for further investigations in adults