About the largest subtree common to several X-trees

Étant donnés plusieursX-arbres, ou arbres phylogénétiques, sur le même ensembleX, nous cherchons à construire un plus grand sous-ensembleY⊂Xtel que les arbres partiels induits surYsoient identiques d’un point de vue topologique, c’est-à-dire indépendamment des longueurs des arêtes. Ce problème, connu sous le nom de MAST (Maximum Agreement SubTree), est NP-Difficile, dans le cas général, dès que le nombre deX-arbres est supérieur à 2. Nous présentons un algorithme approché qui construit un arbre partiel commun maximal. Il est facilement programmable et suffisamment efficace sur une centaine deX-arbres connectant une centaine d’éléments pour évaluer la taille moyenne d’un sous-arbre commun à desX-arbres indépendants. La distribution observée permet d’estimer la taille critique d’un sous-arbre commun et de mesurer la congruence de plusieurs arbres évolutifs.Given severalX-trees or unrooted phylogenetic trees on the same set of taxaX, we look for a largest subsetY⊂Xsuch that al l the partial trees reduced byYare topologically identical. This common subtree is called a MAST for Maximum Agreement SubTree. The problem has polynomial complexity when there are only two trees but generally it is NP-hard for more than two. We introduce a polynomial approximation algorithm for the multiple case, which is easy to implement, very efficient and which produces a maximal common subtree. It begins with the computation of an upper bound for its size and designates elements inXthat cannot belong to a common subtree of a given size. Simulations on random and real data have shown that this heuristic often provides an optimal solution as soon as the number of trees is larger than 5. Then, we develop a statistical study to evaluate the average size of a MAST corresponding to independent trees. The computed distribution allows to estimate the critical size of a MAST to reveal some congruence between trees

Sclerosing encapsulating peritonitis after peritoneal dialysis

Patients with chronic renal failure in use of peritoneal dialysis (PD) are subject to various complications of the renal replacement therapy. We report a rare complication of PD in which the peritoneum, after years of contact with hypertonic dialysate, is gradually replaced by fibrous tissue. This patient had several complications after initiation of PD including a bacterial peritonitis, tertiary hyperparathyroidism (being treated with parathyroidectomy 2) and cholelithiasis (being treated with laparoscopic cholecystectomy). After 8 years of peritoneal dialysis was transferred to hemodialysis by decreasing ultrafiltration and episodes of intestinal sub-occlusion, being diagnosed as sclerosing encapsulating peritonitis (SEP). He is currently on corticotherapy with a significant reduction of symptoms and likely stabilization of the SEP.Pacientes com insuficiência renal crônica terminal em uso de diálise peritoneal (DP) estão sujeitos a diversas complicações da própria terapia de substituição renal. Relatamos uma complicação rara da DP na qual o peritôneo, após anos de contato com a substância hipertônica dialisante, é gradualmente substituído por tecido fibroso. O paciente em questão teve diversas intercorrências após o início da DP, incluindo uma peritonite bacteriana, hiperparatireoidismo terciário (sendo tratado com duas paratireoidectomias) e colelitíase (sendo tratado com colecistectomia videolaparoscópica). Após 8 anos de diálise peritoneal, foi transferido para hemodiálise por diminuição da ultrafiltração e episódios de suboclusão intestinal, sendo diagnosticado como peritonite esclerosante encapsulante (PEE). Atualmente, está em corticoterapia e com diminuição significativa dos sintomas e provável estabilização da PEE.Fundação Lusíada Faculdade de Ciências Médicas de SantosUniversidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM)Universidade de São Paulo Faculdade de Medicina Hospital das ClínicasUNIFESP, EPMSciEL

Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters

International audienceBackground and scope Large networks, such as protein interaction networks, are extremely difficult to analyze as a whole. We developed Clust&See, a Cytoscape plugin dedicated to the identification, visualization and analysis of clusters extracted from such networks. Implementation and performance Clust&See provides the ability to apply three different, recently developed graph clustering algorithms to networks and to visualize: (i) the obtained partition as a quotient graph in which nodes correspond to clusters and (ii) the obtained clusters as their corresponding subnetworks. Importantly, tools for investigating the relationships between clusters and vertices as well as their organization within the whole graph are supplied

About the largest subtree common to several phylogenetic trees

International audienceGiven several phylogenetic trees on the same set of taxa X, we look for a largest subset Y in X such that all the partial trees reduced by Y are identical. The problem has polynomial complexity when there are only two trees but it is NP-hard for more than two. We introduce a polynomial approximation algorithm for the multiple case, which is easy to implement, very efficient and which produces a maximal common subtree. It begins with the computation of an upper bound for its size and designates elements in X that cannot belong to a common subtree of a given size. Simulations on random and real data have shown that this heuristic always provides an optimal solution as soon as the number of taxa is lower than 100. Then, we develop a statistical study to determine the critical size of a MAST to be significant, that is corresponding to non-independant trees

Peritonite esclerosante encapsulante pós-diálise peritoneal Sclerosing encapsulating peritonitis after peritoneal dialysis

Pacientes com insuficiência renal crônica terminal em uso de diálise peritoneal (DP) estão sujeitos a diversas complicações da própria terapia de substituição renal. Relatamos uma complicação rara da DP na qual o peritôneo, após anos de contato com a substância hipertônica dialisante, é gradualmente substituído por tecido fibroso. O paciente em questão teve diversas intercorrências após o início da DP, incluindo uma peritonite bacteriana, hiperparatireoidismo terciário (sendo tratado com duas paratireoidectomias) e colelitíase (sendo tratado com colecistectomia videolaparoscópica). Após 8 anos de diálise peritoneal, foi transferido para hemodiálise por diminuição da ultrafiltração e episódios de suboclusão intestinal, sendo diagnosticado como peritonite esclerosante encapsulante (PEE). Atualmente, está em corticoterapia e com diminuição significativa dos sintomas e provável estabilização da PEE.Patients with chronic renal failure in use of peritoneal dialysis (PD) are subject to various complications of the renal replacement therapy. We report a rare complication of PD in which the peritoneum, after years of contact with hypertonic dialysate, is gradually replaced by fibrous tissue. This patient had several complications after initiation of PD including a bacterial peritonitis, tertiary hyperparathyroidism (being treated with parathyroidectomy 2) and cholelithiasis (being treated with laparoscopic cholecystectomy). After 8 years of peritoneal dialysis was transferred to hemodialysis by decreasing ultrafiltration and episodes of intestinal sub-occlusion, being diagnosed as sclerosing encapsulating peritonitis (SEP). He is currently on corticotherapy with a significant reduction of symptoms and likely stabilization of the SEP

Segetal plant conservation in arable fields: functional role, farmers’ perception and farming systems

International audienceSegetal plants, or “messicoles” as they are known in French, are weedy inhabitants of wheat crops (mainly winter cereals). The national list of segetal species includes 102 taxa; of which 7 are extinct, 52 threatened, 30 to be kept under close observation and 12 abundant. Data on their distribution indicates that they are mostly in decline due to intensive farming systems. As their survival is intrinsically linked to farming systems, we need to improve knowledge on their relationships with land management in order to establish a sound scientific basis for protection tools, to support and guide farmer conservation measures and to disseminate concerns for segetal biodiversity to agro-environmental policymakers. We propose to examine: 1) the relationships between the abundance and/or the segetal richness (flora sampling) and farmer practices (farm evaluation conducted using the “Dialecte” software) in several farms in different regions, especially in segetal-rich areas; 2) the potential ecosystem service provision as resources for foraging insects through identification of the pollen of segetal plants and their abundance in pollen traps fixed on bee hives; 3) the perception of segetals (e.g. as troublesome weeds, or anecdotal biodiversity, or beautiful floral component of the landscape, or plant for services, etc) by professional actors (farmers, technical advisers, actors of biodiversity preservation initiatives, regional collectivity and regulatory authorities, etc) to identify ways of thinking that underlay the diversity of discourses and present practices about them. Joining national efforts for similar goal and participatory approach could help European Community to adopt agro-environmental measures towards biodiversity conservation without cutting productivity

How rare arable weeds are descriptors of low farming intensification?

International audienceRecent emphasis has been placed on the rapid destruction of the planet’s biodiversity in allhabitats. Rare arable weeds, also known as segetal plants, are threatened species, mostly indecline due to intensive farming systems. However, the presence of these species is intrinsicallylinked to agroecosystems. Their survival is apparently related to low-input agronomic practices.Could these weeds therefore be good descriptors of low agricultural intensification and be goodindicators of high environmental field value? We propose to examine the relationships between thefarming systems and weed flora sampling in the same fields