Lateral transfer in Stochastic Dollo models

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages and obtain an improved fit over the corresponding model without lateral transfer.Comment: Improvements suggested by reviewer

Towards declarative diagnosis of constraint programs over finite domains

The paper proposes a theoretical approach of the debugging of constraint programs based on a notion of explanation tree. The proposed approach is an attempt to adapt algorithmic debugging to constraint programming. In this theoretical framework for domain reduction, explanations are proof trees explaining value removals. These proof trees are defined by inductive definitions which express the removals of values as consequences of other value removals. Explanations may be considered as the essence of constraint programming. They are a declarative view of the computation trace. The diagnosis consists in locating an error in an explanation rooted by a symptom.Comment: In M. Ronsse, K. De Bosschere (eds), proceedings of the Fifth International Workshop on Automated Debugging (AADEBUG 2003), September 2003, Ghent. cs.SE/030902

Localisation and mobility of trace metal in silver fir needles

Trace metals (TM: Co, Ni, Cu, Zn, Cd, and Pb) as well as Al, Mn, and Fe content was measured in needles of a remote silver fir stand in the south of France. TM localisation and behaviour in needles was evaluated by measuring total and internal content of needles of different ages. Measured concentrations fell within background values. Al, Fe, Co, and Pb were trapped in wax following atmospheric particulate deposition. Contrasting accumulation and migration behaviours of the different elements studied were observed. The wax contained less than 10% Mn, Al, Ni, Co, and Zn and 15–45% Fe, Cu, and Cd in the young needles. Lead was mostly located in the wax (50–80%), and this proportion decreased with needle age. Only the internal content of Pb and Fe increased significantly with needle age. Finally, due to atmospheric deposition accumulation, higher input fluxes of Fe, Cu, Cd, and Pb can be expected in forest soil

The importance of biomass net uptake for a trace metal budget in a forest stand in north-eastern France

The trace metal (TM: Cd, Cu, Ni, Pb and Zn) budget (stocks and annual fluxes) was evaluated in a forest stand (silver fir, Abies alba Miller) in north-eastern France. Trace metal concentrations were measured in different tree compartments in order to assess TM partitioning and dynamics in the trees. Inputs included bulk deposition, estimated dry deposition and weathering. Outputs were leaching and biomass exportation. Atmospheric deposition was the main input flux. The estimated dry deposition accounted for about 40% of the total trace metal deposition. The relative importance of leaching (estimated by a lumped parameter water balance model, BILJOU) and net biomass uptake (harvesting) for ecosystem exportation depended on the element. Trace metal distribution between tree compartments (stem wood and bark, branches and needles) indicated that Pb was mainly stored in the stem, whereas Zn and Ni, and to a lesser extent Cd and Cu, were translocated to aerial parts of the trees and cycled in the ecosystem. For Zn and Ni, leaching was the main output flux (N95% of the total output) and the plot budget (input–output) was negative, whereas for Pb the biomass net exportation represented 60% of the outputs and the budget was balanced. Cadmium and Cu had intermediate behaviours, with 18% and 30% of the total output relative to biomass exportation, respectively, and the budgets were negative. The net uptake by biomass was particularly important for Pb budgets, less so for Cd and Cu and not very important for Zn and Ni in such forest stands

Automatic Repair of Buggy If Conditions and Missing Preconditions with SMT

We present Nopol, an approach for automatically repairing buggy if conditions and missing preconditions. As input, it takes a program and a test suite which contains passing test cases modeling the expected behavior of the program and at least one failing test case embodying the bug to be repaired. It consists of collecting data from multiple instrumented test suite executions, transforming this data into a Satisfiability Modulo Theory (SMT) problem, and translating the SMT result -- if there exists one -- into a source code patch. Nopol repairs object oriented code and allows the patches to contain nullness checks as well as specific method calls.Comment: CSTVA'2014, India (2014