Weighted Shape-based Averaging with Neighborhood Prior Model for Multiple Atlas Fusion-based Medical Image Segmentation

In medical imaging, merging automated segmentations obtained from multiple atlases has become a standard practice for improving the accuracy. In this letter, we propose two new fusion methods: "Global Weighted Shape-Based Averaging" (GWSBA) and "Local Weighted Shape-Based Averaging" (LWSBA). These methods extend the well known Shape-Based Averaging (SBA) by additionally incorporating the similarity information between the reference (i.e., atlas) images and the target image to be segmented. We also propose a new spatially-varying similarity-weighted neighborhood prior model, and an edge-preserving smoothness term that can be used with many of the existing fusion methods. We first present our new Markov Random Field (MRF) based fusion framework that models the above mentioned information. The proposed methods are evaluated in the context of segmentation of lymph nodes in the head and neck 3D CT images, and they resulted in more accurate segmentations compared to the existing SBA.

Store-operated Ca2+ Entry Mediated by Orai1 and TRPC1 Participates to Insulin Secretion in Rat β-Cells.

Store-operated Ca(2+) channels (SOCs) are voltage-independent Ca(2+) channels activated upon depletion of the endoplasmic reticulum Ca(2+) stores. Early studies suggest the contribution of such channels to Ca(2+) homeostasis in insulin-secreting pancreatic β-cells. However, their composition and contribution to glucose-stimulated insulin secretion (GSIS) remains unclear. In this study, endoplasmic reticulum Ca(2+) depletion triggered by acetylcholine (ACh) or thapsigargin stimulated the formation of a ternary complex composed of Orai1, TRPC1, and STIM1, the key proteins involved in the formation of SOCs. Ca(2+) imaging further revealed that Orai1 and TRPC1 are required to form functional SOCs and that these channels are activated by STIM1 in response to thapsigargin or ACh. Pharmacological SOCs inhibition or dominant negative blockade of Orai1 or TRPC1 using the specific pore mutants Orai1-E106D and TRPC1-F562A impaired GSIS in rat β-cells and fully blocked the potentiating effect of ACh on secretion. In contrast, pharmacological or dominant negative blockade of TRPC3 had no effect on extracellular Ca(2+) entry and GSIS. Finally, we observed that prolonged exposure to supraphysiological glucose concentration impaired SOCs function without altering the expression levels of STIM1, Orai1, and TRPC1. We conclude that Orai1 and TRPC1, which form SOCs regulated by STIM1, play a key role in the effect of ACh on GSIS, a process that may be impaired in type 2 diabetes.

Validation of a brief form of the Perceived Neighborhood Social Cohesion questionnaire.

The aim of this study was the validation of a brief form of the Perceived Neighborhood Social Cohesion questionnaire using data from 5065 men from the "Cohort Study on Substance-Use Risk Factors." A 9-item scale covering three factors was proposed. Excellent indices of internal consistency were measured (α = .93). The confirmatory factor analyses resulted in acceptable fit indices supporting measurement invariance across French and German forms. Significant correlations were found between the brief form of the Perceived Neighborhood Social Cohesion questionnaire, and satisfaction and self-reported health, providing evidence of the concurrent validity of the scale. Perceived neighborhood social cohesion, and depression and suicide attempts were negatively associated, sustaining the protective effect of perceived social cohesion.

Validation of French and German versions of a Perceived Neighborhood Social Cohesion questionnaire among young Swiss males, and its relationship with substance use

This study main purpose was the validation of both French and German versions of a Perceived Neighborhood Social Cohesion Questionnaire. The sample group comprised 5065 Swiss men from the "Cohort Study on Substance Use Risk Factors." Multigroup Confirmatory factor analysis showed that a three-factor model fits the data well, which substantiates the generalizability of Perceived Neighborhood Social Cohesion Questionnaire factor structure, regardless of the language. The Perceived Neighborhood Social Cohesion Questionnaire demonstrated excellent homogeneity (α = 95) and split-half reliability (r = .96). The Perceived Neighborhood Social Cohesion Questionnaire was sensitive to community size and participants' financial situation, confirming that it also measures real social conditions. Finally, weak but frequent correlations between Perceived Neighborhood Social Cohesion Questionnaire and alcohol, cigarette, and cannabis dependence were measured.

Fusion of Multi-Atlas Segmentations with Spatial Distribution Modeling

In recent years, multi-atlas fusion methods have gainedsignificant attention in medical image segmentation. Inthis paper, we propose a general Markov Random Field(MRF) based framework that can perform edge-preservingsmoothing of the labels at the time of fusing the labelsitself. More specifically, we formulate the label fusionproblem with MRF-based neighborhood priors, as an energyminimization problem containing a unary data term and apairwise smoothness term. We present how the existingfusion methods like majority voting, global weightedvoting and local weighted voting methods can be reframedto profit from the proposed framework, for generatingmore accurate segmentations as well as more contiguoussegmentations by getting rid of holes and islands. Theproposed framework is evaluated for segmenting lymphnodes in 3D head and neck CT images. A comparison ofvarious fusion algorithms is also presented.

Le nombre de reines chez les fourmis et sa conséquence sur l'organisations sociale

Nearly half of all ant species form polygyne societies (cohabitation of more than a single egg-laying queen). These queens are generally smaller and store fewer fat reserves than queens from monogyne colonies. Most queens in polygyne colonies (70-100 pour 100) are inseminated, although this proportion varies among species, and even among populations of the same species. They exhibit mutual tolerance and they all contribute to the reproductive effort of the colony. Nevertheless, their individual fecundity is considerably reduced compared with that of queens from monogyne colonies. This reduction in fecundity seems to be due to some form of mutual inhibition, in some cases the secretion by each female of a substance suppressing egg production in other queens has been implicated. In a few species, queens are organized into a hierarchy such that certain queens lay more eggs than others or even monopolize egg-laying (functional monogyny). Polygyny is linked to a particular life history. It rarely results from the association of several foundresses (primary polygyny). Usually, it is due to the adoption of young queens by an established nest just after a nuptial flight. This secondary polygyny means that the dispersal of the species is limited and is achieved by the budding of a mother nest. Thus colony founding is dependent; with workers accompanying young queens in establishing new colonies. Observation of closely related species exhibiting different social organizations, some monogyne and others polygyne, shows a possible link between queen number and ecological conditions: polygyne forms are more frequent in unstable habitats susceptible to rapid change, such as that caused by human activity. The existence of polygyne societies is an intriguing evolutionary mystery. Research into the origin and maintenance of polygyny focuses on patterns of speciation in relation to queen number and the different theories put forth for the evolution of eusociality, mainly kin selection and mutualism.

Siliceous deep-sea sponge Monorhaphis chuni: A potential paleoclimate archive in ancient animals

The deep-sea sponge Monorhaphis chuni forms giant basal spicules, which can reach lengths of 3 m; they represent the largest biogenic silica structures on Earth that is formed from an individual metazoan. The spicules offer a unique opportunity to record environmental change of past oceanic and climatic conditions. A giant spicule collected in the East China Sea in a depth of 1110 m was investigated. The oxygen isotopic composition and Mg/Ca ratios determined along center-to-surface segments are used as geochemical proxies for the assessment of seawater paleotemperatures. Calculations are based on the assumption that the calculated temperature near the surface of the spicule is identical with the average ambient temperature of 4 degrees C. A seawater temperature of 1.9 degrees C is inferred for the beginning of the lifespan of the Monorhaphis specimen. The temperature increases smoothly to 2.3 degrees C, to be followed by sharply increased and variable temperatures up to 6-10 degrees C. In the outer part of the spicule, the inferred seawater temperature is about 4 degrees C. The lifespan of the spicule can be estimated to 11,000 +/- 3000 years using the long-term trend of the inferred temperatures fitted to the seawater temperature age relationships since the Last Glacial Maximum. Specimens of Monorhaphis therefore represents one the oldest living animals on Earth. The remarkable temperature spikes of the ambient seawater occurring 9500-3100 years B.P. are explained by discharges of hydrothermal fluids in the neighborhood of the spicule. The irregular lamellar organization of the spicule and the elevated Mn concentrations during the high-temperature growth are consistent with a hydrothermal fluid input. (C) 2012 Elsevier B.V. All rights reserved.

Quantifying rates of landscape evolution and tectonic processes by thermochronology and numerical modeling of crustal heat transport using PECUBE

PECUBE is a three-dimensional thermal-kinematic code capable of solving the heat production-diffusion-advection equation under a temporally varying surface boundary condition. It was initially developed to assess the effects of time-varying surface topography (relief) on low-temperature thermochronological datasets. Thermochronometric ages are predicted by tracking the time-temperature histories of rock-particles ending up at the surface and by combining these with various age-prediction models. In the decade since its inception, the PECUBE code has been under continuous development as its use became wider and addressed different tectonic-geomorphic problems. This paper describes several major recent improvements in the code, including its integration with an inverse-modeling package based on the Neighborhood Algorithm, the incorporation of fault-controlled kinematics, several different ways to address topographic and drainage change through time, the ability to predict subsurface (tunnel or borehole) data, prediction of detrital thermochronology data and a method to compare these with observations, and the coupling with landscape-evolution (or surface-process) models. Each new development is described together with one or several applications, so that the reader and potential user can clearly assess and make use of the capabilities of PECUBE. We end with describing some developments that are currently underway or should take place in the foreseeable future. (C) 2012 Elsevier B.V. All rights reserved.

Prognostic ability of practitioners of traditional arabic medicine: comparison with Western methods through a relative patient progress scale.

The ancient Greek medical theory based on balance or imbalance of humors disappeared in the western world, but does survive elsewhere. Is this survival related to a certain degree of health care efficiency? We explored this hypothesis through a study of classical Greco-Arab medicine in Mauritania. Modern general practitioners evaluated the safety and effectiveness of classical Arabic medicine in a Mauritanian traditional clinic, with a prognosis/follow-up method allowing the following comparisons: (i) actual patient progress (clinical outcome) compared with what the traditional 'tabib' had anticipated (= prognostic ability) and (ii) patient progress compared with what could be hoped for if the patient were treated by a modern physician in the same neighborhood. The practice appeared fairly safe and, on average, clinical outcome was similar to what could be expected with modern medicine. In some cases, patient progress was better than expected. The ability to correctly predict an individual's clinical outcome did not seem to be better along modern or Greco-Arab theories. Weekly joint meetings (modern and traditional practitioners) were spontaneously organized with a modern health centre in the neighborhood. Practitioners of a different medical system can predict patient progress. For the patient, avoiding false expectations with health care and ensuring appropriate referral may be the most important. Prognosis and outcome studies such as the one presented here may help to develop institutions where patients find support in making their choices, not only among several treatment options, but also among several medical systems.

Defining secretion processes in astrocytes

During the last decade, evidence that release of chemical transmitters from astrocytes might modulate neuronal activity (the so-called "gliotransmission") occurs in situ has been extensively provided. Nevertheless, gliotransmission remains a highly debated topic because of the lack of direct morphological and functional evidence. Here we provided new information supporting gliotransmission, by i) deepen knowledge about specific properties of regulated secretion of glutamatergic SLMVs, and ii) investigating the involvement of astrocytes in the transmission of dopamine, a molecule whose interaction with astrocytes is likely to occur, but it's still not proven.¦VGLUT-expressing glutamatergic SLMVs have been previously identified both in situ and in vitro, but description of kinetics of release were still lacking. To elucidate this issue, we took advantage of fluorescent tools (styryl dyes and pHluorin) and adapted experimental paradigms and analysis methods previously developed to study exo-endocytosis and recycling of glutamatergic vesicles at synapses. Parallel use of EPIfluorescence and total internal reflection (TIRF) imaging allowed us to find that exo-endocytosis processes in astrocytes are extremely fast, with kinetics in the order of milliseconds, able to sustain and follow neuronal signalling at synapses. Also, exocytosis of SLMVs is under the control of fast, localized Ca2+ elevations in close proximity of SLMVs and endoplasmatic reticulum (ER) tubules, the intracellular calcium stores. Such complex organization supports the fast stimulus-secretion coupling we described; localized calcium elevations have been recently observed in astrocytes in situ, suggesting that these functional microdomains might be present in the intact tissue. In the second part of the work, we investigated whether astrocytes possess some of the benchmarks of brain dopaminergic cells. It's been known for years that astrocytes are able to metabolize monoamines by the enzymes MAO and COMT, but to date no clear information that glial cells are able to uptake and store monoamines have been provided. Here, we identified a whole apparatus for the storage, degradation and release of monoamines, at the ultrastructural level. Electron microscopy immunohistochemistry allowed us to visualize VMAT2- and dopamine-positive intracellular compartments within astrocytic processes, i.e. dense -core granules and cisterns. These organelles might be responsible for dopamine release and storage, respectively; interestingly, this intracellular distribution is reminiscent of VMAT2 expression in dendrites if neurons, where dopamine release is tonic and plays a role in the regulation of its a basal levels, suggesting that astrocytic VMAT2 is involved in the homeostasis of dopamine in healthy brains of adult mammals.¦Durant cette dernière décennie, de nombreux résultats sur le relâchement des transmetteurs par les astrocytes pouvant modulé l'activité synaptique (gliotransmission) ont été fournis. Néanmoins, la gliotransmission reste un processus encore très débattu, notamment à cause de l'absence de preuves directes, morphologique et fonctionnelle démontrant ce phénomène. Nous présentons dans nos travaux de nombreux résultats confortant l'hypothèse de la gliotransmission, dont i) une étude approfondie sur les propriétés spatiales et temporelles de la sécrétion régulée du glutamate dans les astrocytes, et ii) une étude sur la participation des astrocytes dans la transmission de la dopamine, une neuromodulateur dont l'interaction avec les astrocytes est fortement probable, mais qui n'a encore jamais été prouvée. L'expression des petites vésicules (SLMVs - Synaptic Like Micro Vesicles) glutamatergiques exprimant les transporteurs vésiculaires du glutamate (VGLUTs) dans les astrocytes a déjà été prouvé tant in situ qu'in vitro. Afin de mettre en évidence les propriétés précises de la sécrétion de ces organelles, nous avons adapté à nos études des méthodes expérimentales conçues pour observer les processus de exocytose et endocytose dans les neurones. Les résolutions spatiale et temporelle obtenues, grâce a l'utilisation en parallèle de l'épi fluorescence et de la fluorescence a onde évanescente (TIRF), nous ont permis de montrer que la sécrétion régulée dans les astrocytes est un processus extrêmement rapide (de l'ordre de la milliseconde) et qu'elle est capable de soutenir et de suivre la transmission de signaux entre neurones. Nous avons également découvert que cette sécrétion a lieu dans des compartiments subcellulaires particuliers où nous observons la présence du reticulum endoplasmique (ER) ainsi que des augmentations rapides de calcium. Cette organisation spatiale complexe pourrait être la base morphologique du couplage rapide entre le stimulus et la sécrétion. Par ailleurs, plusieurs études récentes in vivo semblent confirmer l'existence de ces compartiments. Depuis des années nous savons que les astrocytes sont capables de métaboliser les monoamines par les enzymes MAO et COMT. Nous avons donc fourni de nouvelles preuves concernant la présence d'un appareil de stockage dans les astrocytes participant à la dégradation et la libération de monoamines au niveau ultrastructurelle. Grâce à la microscopie électronique, nous avons découvert la présence de compartiments intracellulaires exprimant VMAT2 dans les processus astrocytaires, sous forme de granules et des citernes. Ces organelles pourraient donc être responsables à la fois du relâchement et du stockage de la dopamine. De manière surprenante, cette distribution intracellulaire est similaire aux dendrites des neurones exprimant VMAT2, où la dopamine est libérée de façon tonique permettant d'agir sur la régulation de ses niveaux de base. Ces résultats, suggèrent une certaine participation des VMAT2 présents dans les astrocytes dans le processus d'homéostase de la dopamine dans le cerveau.¦A de nombreuses reprises, dans des émissions scientifiques ou dans des films, il est avancé que les hommes n'utilisent que 10% du potentiel de leur cerveau. Cette légende provient probablement du fait que les premiers chercheurs ayant décrit les cellules du cerveau entre le XIXème et le XXeme siècle, ont montré que les neurones, les cellules les plus connues et étudiées de cet organe, ne représentent seulement que 10% de la totalité des cellules composant du cerveau. Parmi les 90% restantes, les astrocytes sont sans doute les plus nombreuses. Jusqu'au début des années 90, les astrocytes ont été plutôt considérés peu plus que du tissu conjonctif, ayant comme rôles principaux de maintenir certaines propriétés physiques du cerveau et de fournir un support métabolique (énergie, environnement propre) aux neurones. Grace à la découverte que les astrocytes ont la capacité de relâcher des substances neuro-actives, notamment le glutamate, le rôle des astrocytes dans le fonctionnement cérébral a été récemment reconsidérée.¦Le rôle du glutamate provenant des astrocytes et son impact sur la fonctionnalité des neurones n'a pas encore été totalement élucidé, malgré les nombreuses publications démontrant l'importance de ce phénomène en relation avec différentes fonctions cérébrales. Afin de mieux comprendre comment les astrocytes sont impliqués dans la transmission cérébrale, nous avons étudié les propriétés spatio-temporelles de cette libération grâce à l'utilisation des plusieurs marqueurs fluorescents combinée avec différentes techniques d'imagerie cellulaires. Nous avons découvert que la libération du glutamate par les astrocytes (un processus maintenant appelé "gliotransmission") était très rapide et contrôlée par des augmentations locales de calcium. Nous avons relié ces phénomènes à des domaines fonctionnels subcellulaires morphologiquement adaptés pour ce type de transmission. Plus récemment, nous avons concentré nos études sur un autre transmetteur très important dans le fonctionnement du cerveau : la dopamine. Nos résultats morphologiques semblent indiquer que les astrocytes ont la capacité d'interagir avec ce transmetteur, mais d'une manière différente comparée au glutamate, notamment en terme de rapidité de transmission. Ces résultats suggèrent que le astrocytes ont la capacité de modifier leurs caractéristiques et de s'adapter à leur environnement par rapport aux types de transmetteur avec lequel ils doivent interagir.

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience.

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.