Efficient computation of popular phylogenetic tree measures

Given a phylogenetic tree T of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance (MPD) and the Phylogenetic Diversity (PD). In many applications, it is often necessary to compute the expectation and standard deviation of one of these measures over all subsets of tips of T that have a certain size. Unfortunately, existing methods to calculate the expectation and deviation of these measures are inexact and inefficient. We present analytical expressions that lead to efficient algorithms for computing the expectation and the standard deviation of the MPD and the PD. More specifically, our main contributions are • We present efficient algorithms for computing the expectation and the standard deviation of the MPD exactly, in Θ(n) time. • We provide a Θ(n) time algorithm for computing approximately the expectation of the PD and a O(n 2) time algorithm for computing approximately the standard deviation of the PD. We also describe the major computational obstacles that hinder the exact calculation of these concepts. We also describe O(n) time algorithms for evaluating the MPD and PD given a single sample of tips. Having implemented all the presented algorithms, we assess their efficiency experimentally using as a point of reference a standard software package for processing phylogenetic trees. © 2012 Springer-Verlag

Irrigation and Drainage Scheme of the Plain of Arta – Effects on the Rural Landscape and the Wetlands of Amvrakikos’ Natura Area

AbstractAmvrakikos Wetlands National Park is located in the North-West Greece. It is an area of high environmental importance, as it is characterized by a very rich biodiversity. Because of it's importance, the north part of the gulf is protected by Ramsar Convention and is part of the EU NATURA network. The adjacent plain of Arta (most of which is part of the land part of the park), hosts intensively cultivated, irrigated agricultural land and a number of food processing facilities and though it constitutes a major threat for this ecosystem.As water is plentiful and cheap, most farmers over-irrigate using water by the old open canal scheme that covers part of the plain and from numerous drillings most of which are illegal. The main pathways of agricultural pollutants (fertilizers, pesticides etc) are three rivers (Louros, Aracthos and Vovos) and three main draining canals (Salaoras, Fidokastrou and Neochoriou). This presentation, reviews information from several research works of the last 10 years which investigated the effects of agricultural activity to the coastal and the inland natural and rural landscape. Efforts that have been made (installation of measuring - alarming stations, educational sessions for farmers, de-nitrification programs etc) during the same period are also referred

A population level computational model of the basal ganglia that generates parkinsonian local field potential activity

Recordings from the basal ganglia's subthalamic nucleus are acquired via microelectrodes immediately prior to the application of Deep Brain Stimulation (DBS) treatment for Parkinson's Disease (PD) to assist in the selection of the final point for the implantation of the DBS electrode. The acquired recordings reveal a persistent characteristic beta band peak in the power spectral density function of the Local Field Potential (LFP) signals. This peak is considered to lie at the core of the causality-effect relationships of the parkinsonian pathophysiology. Based on LFPs acquired from human subjects during DBS for PD, we constructed a computational model of the basal ganglia on the population level that generates LFPs to identify the critical pathophysiological alterations that lead to the expression of the beta band peak. To this end, we used experimental data reporting that the strengths of the synaptic connections are modified under dopamine depletion. The hypothesis that the altered dopaminergic modulation may affect both the amplitude and the time course of the postsynaptic potentials is validated by the model. The results suggest a pivotal role of both of these parameters to the pathophysiology of PD. © 2009 Springer-Verlag

Effects of planting and structural configurations on human thermal comfort in a schoolyard

Schoolyards are places where children spend a lot of their day. In highly populated Greek cities, schoolyards are usually surrounded by dense and elevated buildings, while the grounds are largely hard surfaces comprising asphalt, concrete, bricks and stone paving. This combination creates considerable thermal discomfort, especially in hot or Mediterranean-type climates. A study exploring the redesign of schoolyards to improve thermal comfort and heat stress conditions is presented in this paper. This included use of a microclimate model ENVI-met (V4), first validated using experimental data and then later applied to different case studies in schoolyards of Volos, a coastal city in central Greece. Microclimate measurements were carried out and thermal comfort and heat stress conditions evaluated by means of the physiologically equivalent temperature (PET, °C). The impact of materials, structures, obstacles, and different tree species on thermal comfort was also assessed. The results of the measured and simulated values were similar, including air temperature, relative humidity, solar radiation and mean radiant temperature (Tmrt). ENVI-met was then used to evaluate different landscape design proposals to improve outdoor human thermal comfort that prevail in schoolyards. © 2017 ISHS