Neural-prior stochastic block model

The stochastic block model (SBM) is widely studied as a benchmark for graph clustering aka community detection. In practice, graph data often come with node attributes that bear additional information about the communities. Previous works modeled such data by considering that the node attributes are generated from the node community memberships. In this work, motivated by a recent surge of works in signal processing using deep neural networks as priors, we propose to model the communities as being determined by the node attributes rather than the opposite. We define the corresponding model; we call it the neural-prior SBM. We propose an algorithm, stemming from statistical physics, based on a combination of belief propagation and approximate message passing. We analyze the performance of the algorithm as well as the Bayes-optimal performance. We identify detectability and exact recovery phase transitions, as well as an algorithmically hard region. The proposed model and algorithm can be used as a benchmark for both theory and algorithms. To illustrate this, we compare the optimal performances to the performance of simple graph neural networks

Travelling more over time : making an in-situ exhibit at the Montréal-du-Gers palaeontological site (France

There are more ancient remains in palaeontological sites than in archaeological ones, and the structures of habitat or the traces of human activity are absent. In the Miocene dig of Montréal-du- Gers, remains of mammals, gastropods and pollen have been found, and they have make it possible for scientists to decode the past of the region. Among the fossils extracted, in a good state of conservation, there are four new species. For all these reasons, this site has a high heritage value. Now, it is time to bring this knowledge closer to the public, as well as its process of creation. Therefore, two plannings have been articulated; one for the conditioning and one for interpretive work that will guide the action of the Natural History Museum of Toulouse (Toulouse City Council) about heritage interpretation. The objective of the plan is to develop a geoturism experience, using thematic interpretation and defining the interpretive resources and services to implement in the site. This plan includes a prevision of infrastructures, equipments and media to transmit the message to the visitor in an organized and coherent way.Los yacimientos paleontológicos presentan restos más antiguos que los documentados en yacimientos arqueológicos, y las estructuras de hábitat o las trazas de actividad humana están ausentes. En la excavación miocena de Montréal-du-Gers, han sido recuperados restos de mamíferos, gasterópodos y polen. Estos restos han permitido a los científicos interpretar el pasado de la región. Entre los fósiles recuperados, que están en buen estado de conservación, se encuentran cuatro especies nuevas. Por estas razones, el yacimiento presenta un alto valor patrimonial. Ahora es el momento de transmitir este conocimiento al público, así como su proceso de creación. Para ello, se han puesto en marcha dos planes, uno para el acondicionamiento del yacimiento y el otro para el trabajo interpretativo que guiará las acciones del Museo de Historia Natural de Toulouse (Ayuntamiento de Toulouse) acerca de la interpretación patrimonial. El objetivo del proyecto es desarrollar una experiencia de geoturismo empleando la interpretación temática y definiendo los recursos interpretativos que se deben implementar en el yacimiento. El plan incluye la previsión de infraestructuras, equipamientos y medios para transmitir los contenidos a los visitantes de forma organizada y coherente.Els jaciments paleontològics presenten restes més antigues que les documentades als jaciments arqueològics, i les estructures d'hàbitat o les traces d'activitat humana hi són absents. En l'excavació miocena de Montréal-du-Gers, hi han estat descobertes restes de mamífers, gasteròpodes i pol·len. Aquestes restes han fet possible que els científics poguessin interpretar el passat de la regió. Entre els fòssils recuperats, que es troben en bon estat de conservació, hi ha quatre espècies noves. Per aquestes raons, el jaciment presenta un alt valor patrimonial. Ara és el moment de transmetre aquests coneixements al públic, així com el procés de creació. Per aquesta raó, s'han posat en marxa dos plans, un per condicionar el jaciment i l'altre per fer el treball interpretatiu que guiarà les accions del Museu d'Història Natural de Tolosa (Ajuntament de Tolosa) al voltant de la interpretació patrimonial. L'objectiu del projecte és desenvolupar una experiència de geoturisme emprant la interpretació temàtica i definint els recursos interpretatius que caldrà implementar al jaciment. El pla inclou la previsió d'infraestructures, equipament i mitjans per transmetre els continguts als visitants de forma organitzada i coherent

Darwin, les fossiles et les bases de la classification moderne

Depuis l’antiquité, les hommes ont cherché à classer les espèces, manière de décrire le monde et de se l’approprier. A la suite de la systématisation de la nomenclature binominale par Carl von Linné (1758) et jusqu’aux premiers développements des théories évolutionnistes, la classification se veut être le reflet d’une échelle naturelle des êtres avec, bien entendu, une place prépondérante pour l’homme, classé chez les Primates (les premiers), tout au sommet de cette échelle. Avec la parution de L’Origine des espèces de Darwin, l’idée d’évolution, déjà dans l’air depuis les travaux de Lamarck notamment, amène à revoir les principes fondamentaux de la classification : d’une échelle traduisant la position respective des différentes espèces autour d’un monde fixe, créé par la volonté divine, il faut dorénavant y intégrer les fossiles et lire la classification dans une perspective temporelle. La classification doit devenir le reflet de l’histoire du vivant. Il est d’ailleurs symptomatique que la seule figure de L’Origine des espèces soit justement un modèle théorique de phylogénie, c’est-à-dire d’histoire évolutive. Avec cette illustration, les principes de base de la classification moderne sont jetés, mais il faudra attendre les années 1950 et le développement de la cladistique, sous l’impulsion de l’entomologiste allemand Willi Hennig, pour que le rêve de Darwin devienne une réalité.Men have tried to classify species since time immemorial, classification being a means of describing the world and of appropriating it. From Carl von Linne’s system of scientific classification and binominal nomenclature, to the first developments of evolutionary theories, classifications attempted to fashion a natural scale of living beings. Man was, of course, positioned with the Primates (i.e. the first ones) at the top of the tree. After the publication of Darwin’s Origin of Species, the idea of evolution, which had stamped Lamarck’s work (albeit as transformism), led scientists to imagine new ways of classifying the living. Moving away from a vision of classification as fixed and reflecting divine design, Darwin and his followers took fossils into account to redefine classification from a temporal point of view. Classification started then to represent the history of life. The fact that the only illustration in the Origin of Species is a theoretical phylogenetic tree is highly significant: the illustration set up the basis of modern classification, which was developed in the 1950s by Willi Hennig’s phylogenetic systematics, making Darwin’s dream come true

Preimplantation embryo programming: transcription, epigenetics, and culture environment.

Preimplantation development directs the formation of an implantation- or attachment-competent embryo so that metabolic interactions with the uterus can occur, pregnancy can be initiated, and fetal development can be sustained. The preimplantation embryo exhibits a form of autonomous development fueled by products provided by the oocyte and also from activation of the embryo\u27s genome. Despite this autonomy, the preimplantation embryo is highly influenced by factors in the external environment and in extreme situations, such as those presented by embryo culture or nuclear transfer, the ability of the embryo to adapt to the changing environmental conditions or chromatin to become reprogrammed can exceed its own adaptive capacity, resulting in aberrant embryonic development. Nuclear transfer or embryo culture-induced influences not only affect implantation and establishment of pregnancy but also can extend to fetal and postnatal development and affect susceptibility to disease in later life. It is therefore critical to define the basic program controlling preimplantation development, and also to utilize nuclear transfer and embryo culture models so that we may design healthier environments for preimplantation embryos to thrive in and also minimize the potential for negative consequences during pregnancy and post-gestational life. In addition, it is necessary to couple gene expression analysis with the investigation of gene function so that effects on gene expression can be fully understood. The purpose of this short review is to highlight our knowledge of the mechanisms controlling preimplantation development and report how those mechanisms may be influenced by nuclear transfer and embryo culture

SSH adequacy to preimplantation mammalian development: Scarce specific transcripts cloning despite irregular normalisation

BACKGROUND: SSH has emerged as a widely used technology to identify genes that are differentially regulated between two biological situations. Because it includes a normalisation step, it is used for preference to clone low abundance differentially expressed transcripts. It does not require previous sequence knowledge and may start from PCR amplified cDNAs. It is thus particularly well suited to biological situations where specific genes are expressed and tiny amounts of RNA are available. This is the case during early mammalian embryo development. In this field, few differentially expressed genes have been characterized from SSH libraries, but an overall assessment of the quality of SSH libraries is still required. Because we are interested in the more systematic establishment of SSH libraries from early embryos, we have developed a simple and reliable strategy based on reporter transcript follow-up to check SSH library quality and repeatability when starting with small amounts of RNA. RESULTS: Four independent subtracted libraries were constructed. They aimed to analyze key events in the preimplantation development of rabbit and bovine embryos. The performance of the SSH procedure was assessed through the large-scale screening of thousands of clones from each library for exogenous reporter transcripts mimicking either tester specific or tester/driver common transcripts. Our results show that abundant transcripts escape normalisation which is only efficient for rare and moderately abundant transcripts. Sequencing 1600 clones from one of the libraries confirmed and extended our results to endogenous transcripts and demonstrated that some very abundant transcripts common to tester and driver escaped subtraction. Nonetheless, the four libraries were greatly enriched in clones encoding for very rare (0.0005% of mRNAs) tester-specific transcripts. CONCLUSION: The close agreement between our hybridization and sequencing results shows that the addition and follow-up of exogenous reporter transcripts provides an easy and reliable means to check SSH performance. Despite some cases of irregular normalisation and subtraction failure, we have shown that SSH repeatedly enriches the libraries in very rare, tester-specific transcripts, and can thus be considered as a powerful tool to investigate situations where small amounts of biological material are available, such as during early mammalian development

Preimplantation development in mammals : how relevant is the mouse model?

La connaissance des évènements moléculaires et cellulaires des premières étapes du développement de l’embryon des mammifères est indispensable à la recherche biomédicale. Les mécanismes mis en jeu, parfois très spécifiques de cette période, font aussi l’objet de nombreuses recherches fondamentales. La souris a longtemps été utilisée comme modèle unique pour l’analyse de ces stades de développement. Les mécanismes qui les régissent et les outils disponibles pour les étudier eKnowledge of the molecular and cellular events of the early stages of mammalian embryo development is essential for biomedical research. The mechanisms involved, sometimes very specific to this period, are also the subject of much basic research. The mouse has long been used as a unique model for the analysis of these stages of development. Its features and the tools available to study it make it a very interesting model, but it is insufficient to represent all mammals and in particular the human embryo

Muséum : un chantier de fouilles au service de la mixité sociale

Le chantier de fouilles paléontologiques mis en place, depuis près de 20 ans, par le muséum d’Histoire naturelle de Toulouse s’inscrit dans une double dynamique sociale et scientifique : le responsable du projet montre ici comment cette activité éducative à destination des adolescents permet à l’établissement de rendre le public acteur de la démarche scientifique tout en assurant sa mission de sauvegarde du patrimoine

Web et musées : le choc des cultures

Face au développement des nouvelles pratiques des internautes (réseaux sociaux), les auteurs proposent quelques pistes innovantes à suivre par les institutions muséales qui souhaiteraient passer d’une logique « vitrine » à une logique « relationnelle » et imaginer des musées co-créatifs dans lesquels le visiteur – intégré comme acteur de la vie du musée et de ses projets – devient membre d’une communauté, à la fois utilisateur et contributeur d’un savoir commun

Frequency of Dental Caries in Four Historical Populations from the Chalcolithic to the Middle Ages

The majority of dental carie studies over the course of historical period underline mainly the prevalence evolution, the role of carbohydrates consumption and the impact of access to dietary resources. The purpose of the present investigation was to compare population samples from two archaeological periods the Chacolithic and Middle Age taking into account the geographical and socio economical situation. The study concerned four archaelogical sites in south west France and population samples an inlander for the Chalcolithic Age, an inlander, an costal and urban for the Middle Age. The materials studied included a total of 127 maxillaries, 103 mandibles and 3316 teeth. Data recorded allowed us to display that the Chalcolithic population sample had the lowest carie percentage and the rural inlander population samples of Middle Age the highest; in all cases molars were teeth most often affected. These ones differences could be explained according to time period, carious lesions were usually less recorded in the Chalcolithic Age than the Middle because of a lesser cultivation of cereals like in les Treilles Chacolithic population sample. In the Middle Age population samples, the rural inland sample Marsan showed the highest frequency of caries and ate more cereal than the coastal Vilarnau and the poor urban St Michel population samples, the first one ate fish and Mediterranean vegetal and fruits and the second one met difficulties to food access, in both cases the consumption of carbohydrates was lesser than Marsan population sample who lived in a geographical land convice to cereals cultivation

Erratum. Maternal ageing impairs mitochondrial DNA kinetics during early embryogenesis in mice

STUDY QUESTION: Does ageing affect the kinetics of the mitochondrial pool during oogenesis and early embryogenesis? SUMMARY ANSWER: While we found no age-related change during oogenesis, the kinetics of mitochondrial DNA content and the expression of the factors involved in mitochondrial biogenesis appeared to be significantly altered during embryogenesis. WHAT IS KNOWN ALREADY: Oocyte mitochondria are necessary for embryonic development. The morphological and functional alterations of mitochondria, as well as the qualitative and quantitative mtDNA anomalies, observed during ovarian ageing may be responsible for the alteration of oocyte competence and embryonic development. STUDY DESIGN, SIZE, DURATION: The study, conducted from November 2016 to November 2017, used 40 mice aged 5-8 weeks and 45 mice aged 9-11 months (C57Bl6/CBA F(1)). A total of 488 immature oocytes, with a diameter ranging from 20 μm to more than 80 μm, were collected from ovaries, and 1088 mature oocytes or embryos at different developmental stages (two PN, one-cell, i.e. syngamy, two-cell, four-cell, eight-cell, morula and blastocyst) were obtained after ovarian stimulation and, for embryos, mating. PARTICIPANTS/MATERIALS, SETTING, METHODS: Mitochondrial DNA was quantified by quantitative PCR. We used quantitative reverse transcriptase PCR (RT-PCR) (microfluidic method) to study the relative expression of three genes involved in the key steps of embryogenesis, i.e. embryonic genome activation (HSPA1) and differentiation (CDX2 and NANOG), two mtDNA genes (CYB and ND2) and five genes essential for mitochondrial biogenesis (PPARGC1A, NRF1, POLG, TFAM and PRKAA). The statistical analysis was based on mixed linear regression models applying a logistic link function (STATA v13.1 software), with values of P < 0.05 being considered significant. MAIN RESULTS AND THE ROLE OF CHANCE: During oogenesis, there was a significant increase in oocyte mtDNA content (P < 0.0001) without any difference between the two groups of mice (P = 0.73). During the first phase of embryogenesis, i.e. up to the two-cell stage, embryonic mtDNA decreased significantly in the aged mice (P < 0.0001), whereas it was stable for young mice (young/old difference P = 0.015). The second phase of embryogenesis, i.e. between the two-cell and eight-cell stages, was characterized by a decrease in embryonic mtDNA for young mice (P = 0.013) only (young/old difference P = 0.038). During the third phase, i.e. between the eight-cell and blastocyst stage, there was a significant increase in embryonic mtDNA content in young mice (P < 0.0001) but not found in aged mice (young/old difference P = 0.002). We also noted a faster expression of CDX2 and NANOG in the aged mice than in the young mice during the second (P = 0.007 and P = 0.02, respectively) and the third phase (P = 0.01 and P = 0.008, respectively) of embryogenesis. The expression of mitochondrial genes CYB and ND2 followed similar kinetics and was equivalent for both groups of mice, with a significant increase during the third phase (P < 0.01). Of the five genes involved in mitochondrial biogenesis, i.e. PPARGC1A, NRF1, POLG, TFAM and PRKAA, the expression of three genes decreased significantly during the first phase only in young mice (NRF1, P = 0.018; POLGA, P = 0.002; PRKAA, P = 0.010), with no subsequent difference compared to old mice. In conclusion, during early embryogenesis in the old mice, we suspect that the lack of a replicatory burst before the two-cell stage, associated with the early arrival at the minimum threshold value of mtDNA, together with the absence of an increase of mtDNA during the last phase, might potentially deregulate the key stages of early embryogenesis. LARGE SCALE DATA: N/A. LIMITATIONS, REASONS FOR CAUTION: Because of the ethical impossibility of working on a human, this study was conducted only on a murine model. As superovulation was used, we cannot totally exclude that the differences observed were, at least partially, influenced by differences in ovarian response between young and old mice. WIDER IMPLICATIONS OF THE FINDINGS: Our findings suggest a pathophysiological explanation for the link observed between mitochondria and the deterioration of oocyte quality and early embryonic development with age. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the University of Angers, France, by the French national research centres INSERM and the CNRS and, in part, by PHASE Division, INRA. There are no competing interests