An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim  Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.Location  World-wide.Methods  Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.Results  Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.Main conclusions  By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

Accelerated Microstructure Imaging via Convex Optimisation for regions with multiple fibres (AMICOx)

This paper reviews and extends our previous work to enable fast axonal diameter mapping from diffusion MRI data in the presence of multiple fibre populations within a voxel. Most of the existing mi-crostructure imaging techniques use non-linear algorithms to fit their data models and consequently, they are computationally expensive and usually slow. Moreover, most of them assume a single axon orientation while numerous regions of the brain actually present more complex configurations, e.g. fiber crossing. We present a flexible framework, based on convex optimisation, that enables fast and accurate reconstructions of the microstructure organisation, not limited to areas where the white matter is coherently oriented. We show through numerical simulations the ability of our method to correctly estimate the microstructure features (mean axon diameter and intra-cellular volume fraction) in crossing regions.

Assessment of statistical iterative reconstructions to optimize CT examination protocols for children and young adults

La tomodensitométrie (CT) est une technique d'imagerie dont l'intérêt n'a cessé de croître depuis son apparition dans le début des années 70. Dans le domaine médical, son utilisation est incontournable à tel point que ce système d'imagerie pourrait être amené à devenir victime de son succès si son impact au niveau de l'exposition de la population ne fait pas l'objet d'une attention particulière. Bien évidemment, l'augmentation du nombre d'examens CT a permis d'améliorer la prise en charge des patients ou a rendu certaines procédures moins invasives. Toutefois, pour assurer que le compromis risque - bénéfice soit toujours en faveur du patient, il est nécessaire d'éviter de délivrer des doses non utiles au diagnostic.¦Si cette action est importante chez l'adulte elle doit être une priorité lorsque les examens se font chez l'enfant, en particulier lorsque l'on suit des pathologies qui nécessitent plusieurs examens CT au cours de la vie du patient. En effet, les enfants et jeunes adultes sont plus radiosensibles. De plus, leur espérance de vie étant supérieure à celle de l'adulte, ils présentent un risque accru de développer un cancer radio-induit dont la phase de latence peut être supérieure à vingt ans. Partant du principe que chaque examen radiologique est justifié, il devient dès lors nécessaire d'optimiser les protocoles d'acquisitions pour s'assurer que le patient ne soit pas irradié inutilement. L'avancée technologique au niveau du CT est très rapide et depuis 2009, de nouvelles techniques de reconstructions d'images, dites itératives, ont été introduites afin de réduire la dose et améliorer la qualité d'image.¦Le présent travail a pour objectif de déterminer le potentiel des reconstructions itératives statistiques pour réduire au minimum les doses délivrées lors d'examens CT chez l'enfant et le jeune adulte tout en conservant une qualité d'image permettant le diagnostic, ceci afin de proposer des protocoles optimisés.¦L'optimisation d'un protocole d'examen CT nécessite de pouvoir évaluer la dose délivrée et la qualité d'image utile au diagnostic. Alors que la dose est estimée au moyen d'indices CT (CTDIV0| et DLP), ce travail a la particularité d'utiliser deux approches radicalement différentes pour évaluer la qualité d'image. La première approche dite « physique », se base sur le calcul de métriques physiques (SD, MTF, NPS, etc.) mesurées dans des conditions bien définies, le plus souvent sur fantômes. Bien que cette démarche soit limitée car elle n'intègre pas la perception des radiologues, elle permet de caractériser de manière rapide et simple certaines propriétés d'une image. La seconde approche, dite « clinique », est basée sur l'évaluation de structures anatomiques (critères diagnostiques) présentes sur les images de patients. Des radiologues, impliqués dans l'étape d'évaluation, doivent qualifier la qualité des structures d'un point de vue diagnostique en utilisant une échelle de notation simple. Cette approche, lourde à mettre en place, a l'avantage d'être proche du travail du radiologue et peut être considérée comme méthode de référence.¦Parmi les principaux résultats de ce travail, il a été montré que les algorithmes itératifs statistiques étudiés en clinique (ASIR?, VEO?) ont un important potentiel pour réduire la dose au CT (jusqu'à-90%). Cependant, par leur fonctionnement, ils modifient l'apparence de l'image en entraînant un changement de texture qui pourrait affecter la qualité du diagnostic. En comparant les résultats fournis par les approches « clinique » et « physique », il a été montré que ce changement de texture se traduit par une modification du spectre fréquentiel du bruit dont l'analyse permet d'anticiper ou d'éviter une perte diagnostique. Ce travail montre également que l'intégration de ces nouvelles techniques de reconstruction en clinique ne peut se faire de manière simple sur la base de protocoles utilisant des reconstructions classiques. Les conclusions de ce travail ainsi que les outils développés pourront également guider de futures études dans le domaine de la qualité d'image, comme par exemple, l'analyse de textures ou la modélisation d'observateurs pour le CT.¦-¦Computed tomography (CT) is an imaging technique in which interest has been growing since it first began to be used in the early 1970s. In the clinical environment, this imaging system has emerged as the gold standard modality because of its high sensitivity in producing accurate diagnostic images. However, even if a direct benefit to patient healthcare is attributed to CT, the dramatic increase of the number of CT examinations performed has raised concerns about the potential negative effects of ionizing radiation on the population. To insure a benefit - risk that works in favor of a patient, it is important to balance image quality and dose in order to avoid unnecessary patient exposure.¦If this balance is important for adults, it should be an absolute priority for children undergoing CT examinations, especially for patients suffering from diseases requiring several follow-up examinations over the patient's lifetime. Indeed, children and young adults are more sensitive to ionizing radiation and have an extended life span in comparison to adults. For this population, the risk of developing cancer, whose latency period exceeds 20 years, is significantly higher than for adults. Assuming that each patient examination is justified, it then becomes a priority to optimize CT acquisition protocols in order to minimize the delivered dose to the patient. Over the past few years, CT advances have been developing at a rapid pace. Since 2009, new iterative image reconstruction techniques, called statistical iterative reconstructions, have been introduced in order to decrease patient exposure and improve image quality.¦The goal of the present work was to determine the potential of statistical iterative reconstructions to reduce dose as much as possible without compromising image quality and maintain diagnosis of children and young adult examinations.¦The optimization step requires the evaluation of the delivered dose and image quality useful to perform diagnosis. While the dose is estimated using CT indices (CTDIV0| and DLP), the particularity of this research was to use two radically different approaches to evaluate image quality. The first approach, called the "physical approach", computed physical metrics (SD, MTF, NPS, etc.) measured on phantoms in well-known conditions. Although this technique has some limitations because it does not take radiologist perspective into account, it enables the physical characterization of image properties in a simple and timely way. The second approach, called the "clinical approach", was based on the evaluation of anatomical structures (diagnostic criteria) present on patient images. Radiologists, involved in the assessment step, were asked to score image quality of structures for diagnostic purposes using a simple rating scale. This approach is relatively complicated to implement and also time-consuming. Nevertheless, it has the advantage of being very close to the practice of radiologists and is considered as a reference method.¦Primarily, this work revealed that the statistical iterative reconstructions studied in clinic (ASIR? and VECO have a strong potential to reduce CT dose (up to -90%). However, by their mechanisms, they lead to a modification of the image appearance with a change in image texture which may then effect the quality of the diagnosis. By comparing the results of the "clinical" and "physical" approach, it was showed that a change in texture is related to a modification of the noise spectrum bandwidth. The NPS analysis makes possible to anticipate or avoid a decrease in image quality. This project demonstrated that integrating these new statistical iterative reconstruction techniques can be complex and cannot be made on the basis of protocols using conventional reconstructions. The conclusions of this work and the image quality tools developed will be able to guide future studies in the field of image quality as texture analysis or model observers dedicated to CT.

CT attenuation values of blood and myocardium: rationale for accurate coronary artery calcifications detection with multi-detector CT.

OBJECTIVES: To determine inter-session and intra/inter-individual variations of the attenuations of aortic blood/myocardium with MDCT in the context of calcium scoring. To evaluate whether these variations are dependent on patients' characteristics. METHODS: Fifty-four volunteers were evaluated with calcium scoring non-enhanced CT. We measured attenuations (inter-individual variation) and standard deviations (SD, intra-individual variation) of the blood in the ascending aorta and of the myocardium of left ventricle. Every volunteer was examined twice to study the inter-session variation. The fat pad thickness at the sternum and noise (SD of air) were measured too. These values were correlated with the measured aortic/ventricular attenuations and their SDs (Pearson). Historically fixed thresholds (90 and 130 HU) were tested against different models based on attenuations of blood/ventricle. RESULTS: The mean attenuation was 46 HU (range, 17-84 HU) with mean SD 23 HU for the blood, and 39 HU (10-82 HU) with mean SD 18 HU for the myocardium. The attenuation/SD of the blood were significantly higher than those of the myocardium (p < 0.01). The inter-session variation was not significant. There was a poor correlation between SD of aortic blood/ventricle with fat thickness/noise. Based on existing models, 90 HU threshold offers a confidence interval of approximately 95% and 130 HU more than 99%. CONCLUSIONS: Historical thresholds offer high confidence intervals for exclusion of aortic blood/myocardium and by the way for detecting calcifications. Nevertheless, considering the large variations of blood/myocardium CT values and the influence of patient's characteristics, a better approach might be an adaptive threshold.

Accurate performance of a rat model of schizophrenia in the water maze depends on visual cue availability and stability: a distortion in cognitive mapping abilities?

Rats were treated postnatally (PND 5-16) with BSO (l-buthionine-(S,R)-sulfoximine) in an animal model of schizophrenia based on transient glutathione deficit. The BSO treated rats were impaired in patrolling a maze or a homing table when adult, yet demonstrated preserved escape learning, place discrimination and reversal in a water maze task [37]. In the present work, BSO rats' performance in the water maze was assessed in conditions controlling for the available visual cues. First, in a completely curtained environment with two salient controlled cues, BSO rats showed little accuracy compared to control rats. Secondly, pre-trained BSO rats were impaired in reaching the familiar spatial position when curtains partially occluded different portions of the room environment in successive sessions. The apparently preserved place learning in a classical water maze task thus appears to require the stability and the richness of visual landmarks from the surrounding environment. In other words, the accuracy of BSO rats in place and reversal learning is impaired in a minimal cue condition or when the visual panorama changes between trials. However, if the panorama remains rich and stable between trials, BSO rats are equally efficient in reaching a familiar position or in learning a new one. This suggests that the BSO accurate performance in the water maze does not satisfy all the criteria for a cognitive map based navigation on the integration of polymodal cues. It supports the general hypothesis of a binding deficit in BSO rats.

L'magerie forensique [Forensic imaging].

In recent years, modern techniques of medical imaging such as MDCT (multidetector-computed tomography) and MRI (magnetic resonance imaging) have pioneered post mortem (pm) investigations, especially in forensic medicine. Particularly pm angiography permits investigating the vascular system in a way which is not possible by performing only conventional autopsy. Beside these radiological methods, other modem visualizing techniques like the three dimensional (3D) surface scan have been implemented in order perform reconstructions of complex cases. By the use of pm imaging techniques, more objective and accurate documentations can be realized that permit an increase of quality in forensic investigations.

Geodynamic reconstructions of the South America-Antarctica plate system

The South America-Antarctica plate system shows many oceanic accretionary systems and subduction zones that initiated and then stopped. To better apprehend the evolution of the system, geodynamic reconstructions (global) have been created from Jurassic (165 Ma) to present, following the techniques used at the University of Lausanne. However, additional synthetic magnetic anomalies were used to refine the geodynamics between 33 Ma and present. The reconstructions show the break up of Gondwana with oceanisation between South America (SAM) and Antarctica (ANT), together with the break off of `Andean' geodynamical units (GDUs). We propose that oceanisation occurs also east and south of the Scotian GDUs. Andean GDUs collide with other GDUs crossing the Pacific. The west coast of SAM and ANT undergo a subsequent collision with all those GDUs between 103 Ma and 84 Ma, and the Antarctic Peninsula also collides with Tierra del Fuego. The SAM-ANT plate boundary experienced a series of extension and shortening with large strike-slip component, culminating with intra-oceanic subduction leading to the presence of the `V-' and anomalies in the Weddell Sea. From 84 Ma, a transpressive collision takes place in the Scotia region, with active margin to the east. As subduction propagates northwards into an old and dense oceanic crust, slab roll-back initiates, giving rise to the western Scotia Sea and the Powell Basin opening. The Drake Passage opens. As the Scotian GDUs migrate eastwards, there is enough space for them to spread and allow a north-south divergence with a spreading axis acting simultaneously with the western Scotia ridge. Discovery Bank stops the migration of South Orkney and `collides with' the SAM-ANT spreading axis, while the northern Scotian GDUs are blocked against the Falkland Plateau and the North-East Georgia Rise. The western and central Scotia and the Powell Basin spreading axes must cease, and the ridge jumps to create the South Sandwich Islands Sea. The Tierra del Fuego-Patagonia region has always experienced mid-oceanic ridge subduction since 84 Ma. Slab window location is also presented (57-0 Ma), because of its important implication for heat flux and magmatism. (C) 2011 Elsevier Ltd. All rights reserved.

BlastR--fast and accurate database searches for non-coding RNAs.

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.

Meta-analysis based SVM classification enables accurate detection of Alzheimer's disease across different clinical centers using FDG-PET and MRI.

The application of support vector machine classification (SVM) to combined information from magnetic resonance imaging (MRI) and [F18]fluorodeoxyglucose positron emission tomography (FDG-PET) has been shown to improve detection and differentiation of Alzheimer's disease dementia (AD) and frontotemporal lobar degeneration. To validate this approach for the most frequent dementia syndrome AD, and to test its applicability to multicenter data, we randomly extracted FDG-PET and MRI data of 28 AD patients and 28 healthy control subjects from the database provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) and compared them to data of 21 patients with AD and 13 control subjects from our own Leipzig cohort. SVM classification using combined volume-of-interest information from FDG-PET and MRI based on comprehensive quantitative meta-analyses investigating dementia syndromes revealed a higher discrimination accuracy in comparison to single modality classification. For the ADNI dataset accuracy rates of up to 88% and for the Leipzig cohort of up to 100% were obtained. Classifiers trained on the ADNI data discriminated the Leipzig cohorts with an accuracy of 91%. In conclusion, our results suggest SVM classification based on quantitative meta-analyses of multicenter data as a valid method for individual AD diagnosis. Furthermore, combining imaging information from MRI and FDG-PET might substantially improve the accuracy of AD diagnosis.

Is accurate perception of body image associated with appropriate weight-control behavior among adolescents of the Seychelles

BACKGROUND: We examined body image perception and its association with reported weight-control behavior among adolescents in the Seychelles.METHODS: We conducted a school-based survey of 1432 students aging 11-17 years in the Seychelles. Perception of body image was assessed using both a closed-ended question (CEQ) and Stunkard's pictorial silhouettes (SPS). Voluntary attempts to change weight were also assessed.RESULTS: A substantial proportion of the overweight students did not consider themselves as overweight (SPS: 24%, CEQ: 34%), and a substantial proportion of the normal-weight students considered themselves as too thin (SPS: 29%, CEQ: 15%). Logistic regression analysis showed that students with an accurate weight perception were more likely to have appropriate weight-control behavior.CONCLUSIONS: We found that substantial proportions of students had an inaccurate perception of their weight and that weight perception was associated with weight-control behavior. These findings point to forces that can drive the upwards overweight trends.

F+0 renography in neonates and infants younger than 6 months: an accurate method to diagnose severe obstructive uropathy.

We studied the response to F+0 renography and the relative and absolute individual kidney function in neonates and &lt; 6-mo-old infants before and after surgery for unilateral ureteropelvic junction obstruction (UJO). METHODS: The results obtained at diagnosis and after pyeloplasty for 9 children (8 boys, 1 girl; age range, 0.8-5.9 mo; mean age +/- SD, 2.4 +/- 1.5 mo) with proven unilateral UJO (i.e., affected kidney [AK]) and an unremarkable contralateral kidney (i.e., normal kidney [NK]) were evaluated and compared with a control group of 10 children (6 boys, 4 girls; age range, 0.8-2.8 mo; mean age, 1.5 +/- 0.7 mo) selected because of symmetric renal function, absence of vesicoureteral reflux or infection, and an initially dilated but not obstructed renal pelvis as proven by follow-up. Renography was performed for 20 min after injection of (123)I-hippuran (OIH) (0.5-1.0 MBq/kg) immediately followed by furosemide (1 mg/kg). The relative and absolute renal functions and the response to furosemide were measured on background-subtracted and depth-corrected renograms. The response to furosemide was quantified by an elimination index (EI), defined as the ratio of the 3- to 20-min activities: An EI &gt; or = 3 was considered definitively normal and an EI &lt; or = 1 definitively abnormal. If EI was equivocal (1 &lt; EI &lt; 3), the response to gravity-assisted drainage was used to differentiate AKs from NKs. Absolute separate renal function was measured by an accumulation index (AI), defined as the percentage of (123)I-OIH (%ID) extracted by the kidney 30-90 s after maximal cardiac activity. RESULTS: All AKs had definitively abnormal EIs at diagnosis (mean, 0.56 +/- 0.12) and were significantly lower than the EIs of the NKs (mean, 3.24 +/- 1.88) and of the 20 control kidneys (mean, 3.81 +/- 1.97; P &lt; 0.001). The EIs of the AKs significantly improved (mean, 2.81 +/- 0.64; P &lt; 0.05) after pyeloplasty. At diagnosis, the AIs of the AKs were significantly lower (mean, 6.31 +/- 2.33 %ID) than the AIs of the NKs (mean, 9.43 +/- 1.12 %ID) and of the control kidneys (mean, 9.05 +/- 1.17 %ID; P &lt; 0.05). The AIs of the AKs increased at follow-up (mean, 7.81 +/- 2.23 %ID) but remained lower than those of the NKs (mean, 10.75 +/- 1.35 %ID; P &lt; 0.05). CONCLUSION: In neonates and infants younger than 6 mo, (123)I-OIH renography with early furosemide injection (F+0) allowed us to reliably diagnose AKs and to determine if parenchymal function was normal or impaired and if it improved after surgery.

Evaluation de la qualité de vie après prélèvement de la veine fémorale superficielle lors de reconstructions infra-inguinales [Quality of life after superficial femoral vein harvest for infra-inguinal reconstructions]

BACKGROUND: The superficial femoral vein (SFV) is a well-established alternative conduit for infra-inguinal reconstructivenous hypertension after SFV harvest may however result in significant morbidity. This study reports the efficiency of SFV as conduit for infra-inguinal reconstructions and characterize the anatomic and physiologic changes in harvest limbs and their relationship to the development of venous complications. METHODS: From May 1999 through November 2003, 23 SFV were harvested from 21 patients undergoing infra-inguinal reconstructions. Bypasses were controlled by regular duplex-ultrasound. The venous morbidity was assessed by measurements of leg circumferences, strain-gauge plethysmography and quality of life, investigated by the VEINES-QOL scale. RESULTS: At a mean follow-up of 10.4 months (range 1-56), primary, secondary patency and limb salvage rates of infra-inguinal bypasses using SFV are 71.4%, 76.2% and 85.7% respectively. No patient had major venous claudication. Oedema was significantly present in nine patients. Strain-gauge plethysmography showed outflow obstruction in all patients. The VEINES-QOL assessment showed no limitation in social and domestic activity, moderate complain about leg heaviness despite presence of oedema. CONCLUSION: The SFV harvest is a reliable conduit for infra-inguinal reconstructions and results in moderate venous morbidity in terms of functional consequences and quality of life.

Integration of olfactory information in a spatial representation enabling accurate arm choice in the radial arm maze

The aim of the present study was to determine whether and how rats can use local olfactory cues for spatial orientation. Rats were trained in an eight-arm radial maze under different conditions as defined by the presence or absence of supplementary olfactory cues marking each arm, the availability of distant visuospatial information, and the illumination of the maze (light or darkness). The different visual conditions were designed to dissociate among the effects of light per se and those of visuospatial cues, on the use of olfactory cues for accurate arm choice. Different procedures with modifications of the arrangement of olfactory cues were used to determine if rats formed a representation of the spatial configuration of the olfactory cues and if they could rely on such a representation for accurate arm choice in the radial maze. The present study demonstrated that the use of olfactory cues to direct arm choice in the radial arm maze was critically dependent on the illumination conditions and implied two different modes of processing of olfactory information according to the presence or the absence of light. Olfactory cues were used in an explicit manner and enabled accurate arm choice only in the absence of light. Rats, however, had an implicit memory of the location of the olfactory cues and formed a representation of the spatial position of these cues, whatever the lighting conditions. They did not memorize the spatial configuration of the olfactory cues per se but needed these cues to be linked to the external spatial frame of reference.