Active Contour-Based Segmentation of Head and Neck with Adaptive Atlas Selection

This paper presents automated segmentation of structuresin the Head and Neck (H\&N) region, using an activecontour-based joint registration and segmentation model.A new atlas selection strategy is also used. Segmentationis performed based on the dense deformation fieldcomputed from the registration of selected structures inthe atlas image that have distinct boundaries, onto thepatient's image. This approach results in robustsegmentation of the structures of interest, even in thepresence of tumors, or anatomical differences between theatlas and the patient image. For each patient, an atlasimage is selected from the available atlas-database,based on the similarity metric value, computed afterperforming an affine registration between each image inthe atlas-database and the patient's image. Unlike manyof the previous approaches in the literature, thesimilarity metric is not computed over the entire imageregion; rather, it is computed only in the regions ofsoft tissue structures to be segmented. Qualitative andquantitative evaluation of the results is presented.

Response to the comments on "The formation of Pangea" by D.A. Ruban

The Variscan structures of the Caucasus region are still quite difficult to decipher, they certainly deserved some in depth investigations in the future. Thus, it is right to question any paleogeographic models proposed in that area, as made by D.A. Ruban. We present here the arguments that we used to decide on the distribution of the terranes in that region. The Transcaucasus massif is regarded as pertaining to the Galatian super-terrane, whereas, the Great Caucasus terrane belongs to the Hanseatic ribbon terrane. The latter was a part of Hunia, detached from Laurussia in the Devonian.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

Design, synthesis, and biological and crystallographic evaluation of novel inhibitors of Plasmodium falciparum enoyl-ACP-reductase (PfFabI).

Malaria, a disease of worldwide significance, is responsible for over one million deaths annually. The liver-stage of Plasmodium's life cycle is the first, obligatory, but clinically silent step in malaria infection. The P. falciparum type II fatty acid biosynthesis pathway (PfFAS-II) has been found to be essential for complete liver-stage development and has been regarded as a potential antimalarial target for the development of drugs for malaria prophylaxis and liver-stage eradication. In this paper, new coumarin-based triclosan analogues are reported and their biological profile is explored in terms of inhibitory potency against enzymes of the PfFAS-II pathway. Among the tested compounds, 7 and 8 showed the highest inhibitory potency against Pf enoyl-ACP-reductase (PfFabI), followed by 15 and 3. Finally, we determined the crystal structures of compounds 7 and 11 in complex with PfFabI to identify their mode of binding and to confirm outcomes of docking simulations.

Fine structural variations of alphabeta TCRs selected by vaccination with natural versus altered self-antigen in melanoma patients

Immunotherapy of cancer is often performed with altered "analog" peptide Ags optimized for HLA class I binding, resulting in enhanced immunogenicity, but the induced T cell responses require further evaluation. Recently, we demonstrated fine specificity differences and enhanced recognition of naturally presented Ag by T cells after vaccination with natural Melan-A/MART-1 peptide, as compared with analog peptide. In this study, we compared the TCR primary structures of 1489 HLA-A*0201/Melan-A26-35-specific CD8 T cells derived from both cohorts of patients. Although a strong preference for TRAV12-2 segment usage was present in nearly all patients, usage of particular TRAJ gene segments and CDR3 composition differed slightly after vaccination with natural vs analog peptide. Moreover, TCR β-chain repertoires were broader after natural than analog peptide vaccination. In all patients, we observed a marked conservation of the CDR3β amino acid composition with recurrent sequences centered on a glycyl-leucyl/valyl/alanyl-glycyl motif. In contrast to viral-specific TCR repertoires, such "public" motifs were primarily expressed by nondominant T cell clonotypes, which contrasted with "private" CDR3β signatures frequently found in T cell clonotypes that dominated repertoires of individual patients. Interestingly, no differences in functional avidity were observed between public and private T cell clonotypes. Collectively, our data indicate that T cell repertoires generated against natural or analog Melan-A peptide exhibited slightly distinct but otherwise overlapping and structurally conserved TCR features, suggesting that the differences in binding affinity/avidity of TCRs toward pMHC observed in the two cohorts of patients are caused by subtle structural TCR variations.

Geochemical compositions of Neogene phosphatic brachiopods: Implications for ancient environmental and marine conditions

Isotopic and trace element compositions of Miocene and Pliocene phosphatic brachiopods (Lingulidae and Discinidae) from southern North Sea, the Central Paratethys and the Atlantic coast of Europe were investigated in order to trace past environmental conditions and marine connections between the northern boreal and the southern subtropical-tropical marine basins. The North Sea genus Glottidia yielded low epsilon(Nd) and high delta O-18(PO4) values through the Mio-Pliocene indicating cold habitat temperature where the local seawater was dominated by the Atlantic Ocean. In contrast, the Middle Miocene Lingulidae and Discinidae of the Paratethys inhabited warm subtropical seawater with the possible influence of the Indian Ocean via the Mediterranean, as supported by their average epsilon(Nd) value of -8.3. The combined geochemical data support a thermal and marine separation of the Paratethys from the North Sea with no direct connection or major exchange of water from the Miocene onwards. The temperature in the Paratethys was very similar to that inferred from brachiopods from the Middle Miocene of western France, but the seawater epsilon(Nd) value here is identical to that of contemporaneous Atlantic Ocean. A Late Miocene lingulid brachiopod from southern Portugal has a high delta O-18(PO4), similar to the specimens investigated from the North Sea, reflecting either a deep water habitat or formation after the onset of major global cooling that resulted in an increased delta O-18 value of seawater. The epsilon(Nd) value of -8.4 for this site is compatible with an influence of Mediterranean outflow. (C) 2012 Elsevier B.V. All rights reserved.

Effects of colonization asymmetries on metapopulation persistence.

Ocean currents, prevailing winds, and the hierarchical structures of river networks are known to create asymmetries in re-colonization between habitat patches. The impacts of such asymmetries on metapopulation persistence are seldom considered, especially rarely in theoretical studies. Considering three classical models (the island, the stepping stone and the distance-dependent model), we explore how metapopulation persistence is affected by (i) asymmetry in dispersal strength, in which the colonization rate between two patches differs in direction, and (ii) asymmetry in connectivity, in which the overall colonization pattern displays asymmetry (circulating or dendritic networks). Viability can be drastically reduced when directional bias in dispersal strength is higher than 25%. Re-colonization patterns that allow for strong local connectivity provide the highest persistence compared to systems that allow circulation. Finally, asymmetry has relatively weak effects when metapopulations maintain strong general connectivity.

Linking genetic and species diversities in a community of freshwater gastropods

Summary Biodiversity is usually studied through species or genetic diversities. To date, these two levels of diversity have remained the independent .fields of investigations of community ecologists and population geneticists. However, recent joint analyses of species and genetic diversities have suggested that common processes may underlie the two levels. Positive correlations between species diversity and genetic diversity may arise when the effects of drift and migration overwhelm selective effects. The first goal of this thesis was to make a joint investigation of the patterns of species and genetic diversity in a community of freshwater gastropods living in a floodplain habitat. The second goal was to determine, as far as possible, the relative influences of the processes underlying the patterns observed at each level. In chapter 2 we investigate the relative influences of different evolutionary forces in shaping the genetic structure of Radix balthica populations. Results revealed that the structure inferred using quantitative traits was lower or equal to the one inferred using neutral molecular markers. Consequently, the pattern of structure observed could be only due to random drift, possibly to uniform selection, but definitely not to selection for local optima. In chapter 3, we analyze the temporal variation of species and genetic diversities in five localities. An extended period of drought occurred at the end of the study period leading to decay of both species and genetic diversities. This parallel loss of diversity following a natural perturbation highlighted the role sometimes predominant of random drift over selection on patterns of biodiversity in a floodplain habitat. In chapter 4, we compare the spatial genetic structures of two sympatric species: Radix balthica and Planorbis carinatus. We found that R. balthica populations are weakly structured and have moderate to high values of gene diversity. In contrast, P. carinatus populations are highly structured and poorly diverse. Then we measured correlations between various indices of species and genetic diversity using genetic data .from the two species. We found only one significant correlation: between species richness and gene diversity of P. carinatus. This result highlights the .need to use genetic date from more than one species to infer correlations between species and genetic diversities. Overall, this thesis provided new insights into the common processes underlying patterns of species and genetic diversity. Résumé La biodiversité est généralement étudiée au niveau de la diversité génétique ou spécifique. Ces deux niveaux sont restés jusqu'à maintenant les domaines d'investigation séparés des généticiens des populations et des écologistes des communautés. Cependant, des analyses conjointes des diversités génétique et spécifique ont récemment suggéré que des processus similaires pouvaient influencer ces deux niveaux. Des corrélations positives entre les diversités génétique et spécifique pourraient être dues aux effets de migration et de dérive qui dominent les effets sélectifs. Le premier but de cette thèse était de faire une étude conjointe des diversités génétique et spécifique dans une communauté de gastéropodes d'eau douce. Le second objectif était de déterminer les influences relatives des différents processus liés à chaque niveau de diversité. Dans le chapitre 2 nous cherchons à déterminer quelles forces évolutives influencent la structure génétique de quatre populations de Radix balthica. La structure mesurée sur des traits quantitatifs s'est révélée être plus faible ou égale à celle mesurée avec des marqueurs moléculaires neutres. La structure observée pourrait ainsi être due uniquement à la dérive génétique, potentiellement à la sélection uniforme, mais en aucun cas à la sélection locale pour différents optima. Dans le chapitre 3 nous analysons la variation temporelle des diversités génétique et spécifique dans cinq localités. Une récente période de sécheresse a causé une diminution parallèle des deux niveaux de diversité. Cette perturbation à mis en évidence le rôle parfois prépondérant de la dérive par rapport à celui de la sélection dans le déterminisme de la biodiversité dans un écosytème alluvial. Dans le chapitre 4, nous comparons la structure génétique spatiale de deux espèces vivant en sympatrie : Radix balthica et Planorbis carinatus. Les populations de R. balthica sont peu structurées et présentent un niveau de diversité relativement élevé alors que celles de P. carinatus sont fortement structurées et peu diversifiées. Nous avons ensuite mesuré différentes corrélations entre les diversités génétique et spécifique, mais la seule relation significative a été trouvée entre la richesse spécifique et la diversité génétique de P. carinatus. Ainsi, cette thèse a permis de découvrir de nouveaux aspects des processus qui influencent en parallèle la diversité aux niveaux génétique et spécifique.

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

Delayed presentation of deep penetrating trauma to the subaxial cervical spine.

PURPOSE: To present a rare case of deep penetrating neck trauma in which a retained foreign body in the cervical spine (a broken knife blade) resulted in delayed radicular injury. We describe the surgical management using a retrojugular approach. CASE REPORT: Our patient sustained a stab wound to the supraclavicular triangle from a small pocketknife. He was initially managed in a local hospital by simple primary wound closure without any radiological examinations, and was discharged home. The patient re-consulted in a delayed fashion with mild local persistent neck pain. Subsequent radiological investigations revealed a foreign body (the broken blade of a pocket knife) embedded in the left neural foramen between the C6 and C7 vertebrae penetrating the disc space. The blade was lying between the left C7 nerve root and the ipsilateral vertebral artery (VA) at the transition of V1 and V2 segments. Initial neurological evaluation was normal. Some days later, the patient developed a delayed left C7 radicular deficit. We undertook urgent exploration along the wound corridor through a retrojugular, transforaminal approach with successful removal of the blade. DISCUSSION: To our knowledge, this is a unique case where a retained foreign body penetrated the soft tissues of the neck, embedding deep in the vertebral column without vascular, aerodigestive or significant primary neurological injury, while causing delayed neck pain and delayed onset radicular injury. We describe our surgical management for removal of the retained blade. The retrojugular approach gives excellent access to all of the important anatomical structures of the neck from an anterolateral approach.

Tracking the ghost of coevolution in specific plant-insect interactions : the case of the pollination system between the globeflower Trollius europaeus and seven european Chiastocheta flies

This study aims at understanding the evolutionary processes at work in specialized species interactions. Prom the macroevolutionary perspective, coevolution among specialized taxa was proposed to be one of the major processes generating biodiversity. We challenge this idea from the theoretical and practical perspective and through a literature review and show that the major hypotheses linking coevolutionary process with macroevolutionary patterns do not necessarily predict lineage co diversification and parallel speciation, limit¬ing the utility of the comparative phylogenenetic approach for investigating coevolution¬ary processes. We also point to the rarity of observed long-term coevolutionary dynamics among lineages and propose that coevolution rather occurs in shorter timescales, followed by ecological fitting. Prom the empirical point, we focus on the nursery pollination interaction between the European globeflower Trollius europaeus (Ranunculaceae) and its associated Chiastocheta flies (Anthomyiidae; Diptera) as a model system of evolution and maintenance of special¬ized interactions. The flies are obligate parasites of the seeds, but also pollinate the plant - it was thus proposed that both species are mutually dependent. Contrasting with the paradigm used for two decades of research on this system, we show that the female fitness component of the plant is similar in the populations with and without Chiastocheta. The plant is thus not exclusively dependent on the flies for reproduction. We discuss this result in the context of the factors responsible for the evolution of mutualistic systems. Understanding the evolution of a biological system requires understanding of its phylo- genetic context. Previous studies showed large mismatch between mtDNA phylogeny and morphological taxonomy in Chiastocheta. By using a large set of RAD-sequencing loci, we delineate the species limits that are congruent with morphology, and show that the discordance is best explained by the scenario of mitochondrial capture among fly species. Finally, we examine this system from a phylogeographic perspective, and identify the lack of congruence in spatial genetic structures of the plant and associated insects across their whole geographic range. The flies show lower numbers of spatial genetic groups than the plant, indicating that not all of the plant réfugia were shared by all the fly species or that the migration dynamics homogenized some of the groups. The incongruence in spatial genetic patterns indicates that fly migrations were largely independent from the genetic background of the plant, following rather a scenario of resource tracking, without the signature of coevolutionary process at this scale. Indeed, while the flies require the plant to survive climatic oscillations, the opposite is not true. Eventually, we show that there is no phylogenetic signal of spatial genetic structures, meaning that neither histories nor life- history traits are shared among closely related species and that species are characterized by unique trajectories of their genes. -- Cette étude vise à comprendre les processus évolutifs à l'oeuvre au sein d'interactions en¬tre espèces spécialisées. Du point de vue macroévolutif, la coévolution entre les taxons spécialisée a été considérée comme l'un des principaux processus générateur de biodiversité. Nous contestons cette idée du point de vue théorique et pratique à travers une revue de la littérature. Nous montrons que les hypothèses majeures reliant les processus coévolutifs avec les patterns de diversité au niveau macroévolutif ne prédisent pas nécessairement la co- diversification des lignées et leur spéciation parallèle, ce qui limite l'utilité de l'approche de phylogénie comparative pour étudier les processus coévolutifs . Nous rappelons également le peu d'exemples de dynamique coévolutive à long terme et proposons que la coévolution se produit plutôt dans des intervalles courts, suivis d'ajustements écologiques. Du point empirique, nous nous concentrons sur l'interaction de pollinisation entre le Trolle d'Europe Trollius europaeus (Ranunculaceae) et ses pollinisateurs associés, du genre Chiastocheta (Anthomyiidae; Diptera) en tant que système-modèle pour étudier l'évolution et le maintien des interactions spécialisées. Les mouches sont des parasites obligatoires des semences, mais pollinisent également la plante. Il a donc été proposé que les deux espèces soient mutuellement dépendantes. Contrastant avec le paradigme utilisé pendant deux décennies de recherche sur ce système, nous montrons, que la composante de fitness femelle de la plante est similaire dans les populations avec et sans Chiastocheta. La plante ne dépend donc pas exclusivement de son interaction avec les mouches pour la reproduction. Nous discutons de ce résultat dans le contexte des facteurs responsables de l'évolution des systèmes mutualistes. Comprendre l'évolution d'un système biologique nécessite la compréhension de son con- texte phylogénétique. Des études antérieures ont montré, chez Chiastocheta, de grandes disparités entre les phylogénies obtenues à partir d'ADN mitochondrial et la taxonomie basée sur les critères morphologiques. En utilisant un grand nombre de loci obtenus par RAD-sequencing, nous traçons les limites des espèces, qui concordent avec les car¬actéristiques morphologies, et montrons que la discordance s'explique en fait par un scénario de capture mitochondriale entre espèces de mouches. Enfin, nous examinons le système d'un point de vue phylogéographique, et identi¬fions les incohérences entre structurations génétiques spatiales de la plante et des insectes associés dans toute leur aire de distribution géographique. Les mouches présentent un nombre de groupes génétiques inférieur à la plante, indiquant que tous les refuges de la plante n'étaient pas partagés par toutes les espèces de mouches ou que les dynamiques migratoires ont homogénéisés certains des groupes chez les mouches. Les différences ob¬servées dans les patrons de structuration génétique spatiale indique que les migrations et dispersions des mouches ont été indépendantes du contexte génétique de la plante, et ces dernières ont été uniquement tributaires de la disponibilité des ressources, sans qu'il n'y ait de signature du processus de coévolution à cette échelle. En effet, tandis que les mouches ont besoin de la plante pour survivre aux oscillations climatiques, le contraire n'est pas exact. Finalement, nous montrons qu'il n'y a pas de signal phylogénétique des structurations génétiques spatiales chez les mouches, ce qui signifie que ni l'histoire, ni les traits d'histoire de vie ne sont partagés entre les espèces phylogénétiquement proches et que les espèces sont caractérisées par des trajectoires uniques de leurs gènes.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Qualitative, quantitative and temporal study of cutting agents for cocaine and heroin over 9 years

Forensic laboratories mainly focus on the qualification and the quantitation of the illicit drug under analysis as both aspects are used for judiciary purposes. Therefore, information related to cutting agents (adulterants and diluents) detected in illicit drugs is limited in the forensic literature. This article discusses the type and frequency of adulterants and diluents detected in more than 6000 cocaine specimens and 3000 heroin specimens, confiscated in western Switzerland from 2006 to 2014. The results show a homogeneous and quite unchanging adulteration for heroin, while for cocaine it could be characterised as heterogeneous and relatively dynamic. Furthermore, the results indicate that dilution affects more cocaine than heroin. Therefore, the results provided by this study tend to reveal differences between the respective structures of production or distribution of cocaine and heroin. This research seeks to promote the systematic analysis of cutting agents by forensic laboratories. Collecting and processing data related to the presence of cutting agents in illicit drug specimens produces relevant information to understand and to compare the structure of illicit drug markets.

Investigating the functions of subregions within anterior hippocampus.

Previous functional MRI (fMRI) studies have associated anterior hippocampus with imagining and recalling scenes, imagining the future, recalling autobiographical memories and visual scene perception. We have observed that this typically involves the medial rather than the lateral portion of the anterior hippocampus. Here, we investigated which specific structures of the hippocampus underpin this observation. We had participants imagine novel scenes during fMRI scanning, as well as recall previously learned scenes from two different time periods (one week and 30 min prior to scanning), with analogous single object conditions as baselines. Using an extended segmentation protocol focussing on anterior hippocampus, we first investigated which substructures of the hippocampus respond to scenes, and found both imagination and recall of scenes to be associated with activity in presubiculum/parasubiculum, a region associated with spatial representation in rodents. Next, we compared imagining novel scenes to recall from one week or 30 min before scanning. We expected a strong response to imagining novel scenes and 1-week recall, as both involve constructing scene representations from elements stored across cortex. By contrast, we expected a weaker response to 30-min recall, as representations of these scenes had already been constructed but not yet consolidated. Both imagination and 1-week recall of scenes engaged anterior hippocampal structures (anterior subiculum and uncus respectively), indicating possible roles in scene construction. By contrast, 30-min recall of scenes elicited significantly less activation of anterior hippocampus but did engage posterior CA3. Together, these results elucidate the functions of different parts of the anterior hippocampus, a key brain area about which little is definitely known.