Testing differentiation in diploid populations.

We examine the power of different exact tests of differentiation for diploid populations. Since there is not necessarily random mating within populations, the appropriate hypothesis to construct exact tests is that of independent sampling of genotypes. There are two categories of tests, FST-estimator tests and goodness of fit tests. In this latter category, we distinguish "allelic statistics", which account for the nature of alleles within genotypes, from "genotypic statistics" that do not. We show that the power of FST-estimator tests and of allelic goodness of fit tests are similar when sampling is balanced, and higher than the power of genotypic goodness of fit tests. When sampling is unbalanced, the most powerful tests are shown to belong to the allelic goodness of fit group.

Diagnostics VIH tardifs en 2009 en Suisse: motivation a un dépistage systématique du VIH [Late diagnoses of HIV infection in 2009 in Switzerland: towards a universal HIV testing?]

Individuals who are unaware of their HIV infection constitute a fragile and a critical population both from a personal and from a community-based point of view: if the infection is diagnosed too late, the outcome can be complicated by AIDS-defining diseases, whose prognosis may remain unfavourable even after the initiation of a potent antiretroviral therapy. These patients contribute to the virus spreading into the community, owing to a high viral load. It is now necessary to recognise the limits of a risk behaviour and disease-driven HIV screening policy. Since 2006, the American guidelines recommend a routine HIV testing for all patients age 13 to 64 years unless they specifically refuse the test (opt-out). In Switzerland, the recommendations remain so far risk-centred.

Load Testing and Load Rating Eight State Highway Bridges in Iowa, 1999

This main report provides a general discussion of the load testing, structural evaluation, and load rating procedures. Specific details for each bridge are provided in individual report sections. Additional supporting information on load testing, analyses, and load rating are also provided in the attached appendices.

Reproducing the organic matter model of anthropogenic dark earth of Amazonia and testing the ecotoxicity of functionalized charcoal compounds

The objective of this work was to obtain organic compounds similar to the ones found in the organic matter of anthropogenic dark earth of Amazonia (ADE) using a chemical functionalization procedure on activated charcoal, as well as to determine their ecotoxicity. Based on the study of the organic matter from ADE, an organic model was proposed and an attempt to reproduce it was described. Activated charcoal was oxidized with the use of sodium hypochlorite at different concentrations. Nuclear magnetic resonance was performed to verify if the spectra of the obtained products were similar to the ones of humic acids from ADE. The similarity between spectra indicated that the obtained products were polycondensed aromatic structures with carboxyl groups: a soil amendment that can contribute to soil fertility and to its sustainable use. An ecotoxicological test with Daphnia similis was performed on the more soluble fraction (fulvic acids) of the produced soil amendment. Aryl chloride was formed during the synthesis of the organic compounds from activated charcoal functionalization and partially removed through a purification process. However, it is probable that some aryl chloride remained in the final product, since the ecotoxicological test indicated that the chemical functionalized soil amendment is moderately toxic.

Inventory of sparse forest populations using adaptive cluster sampling

Abstract

HIV-1 vaccines and adaptive trial designs.

Developing a vaccine against the human immunodeficiency virus (HIV) poses an exceptional challenge. There are no documented cases of immune-mediated clearance of HIV from an infected individual, and no known correlates of immune protection. Although nonhuman primate models of lentivirus infection have provided valuable data about HIV pathogenesis, such models do not predict HIV vaccine efficacy in humans. The combined lack of a predictive animal model and undefined biomarkers of immune protection against HIV necessitate that vaccines to this pathogen be tested directly in clinical trials. Adaptive clinical trial designs can accelerate vaccine development by rapidly screening out poor vaccines while extending the evaluation of efficacious ones, improving the characterization of promising vaccine candidates and the identification of correlates of immune protection.

Spatial prediction of monthly wind speeds in complex terrain with adaptive general regression neural networks

This paper presents the general regression neural networks (GRNN) as a nonlinear regression method for the interpolation of monthly wind speeds in complex Alpine orography. GRNN is trained using data coming from Swiss meteorological networks to learn the statistical relationship between topographic features and wind speed. The terrain convexity, slope and exposure are considered by extracting features from the digital elevation model at different spatial scales using specialised convolution filters. A database of gridded monthly wind speeds is then constructed by applying GRNN in prediction mode during the period 1968-2008. This study demonstrates that using topographic features as inputs in GRNN significantly reduces cross-validation errors with respect to low-dimensional models integrating only geographical coordinates and terrain height for the interpolation of wind speed. The spatial predictability of wind speed is found to be lower in summer than in winter due to more complex and weaker wind-topography relationships. The relevance of these relationships is studied using an adaptive version of the GRNN algorithm which allows to select the useful terrain features by eliminating the noisy ones. This research provides a framework for extending the low-dimensional interpolation models to high-dimensional spaces by integrating additional features accounting for the topographic conditions at multiple spatial scales. Copyright (c) 2012 Royal Meteorological Society.

Evidence for adaptive radiation from a phylogenetic study of plant defenses.

One signature of adaptive radiation is a high level of trait change early during the diversification process and a plateau toward the end of the radiation. Although the study of the tempo of evolution has historically been the domain of paleontologists, recently developed phylogenetic tools allow for the rigorous examination of trait evolution in a tremendous diversity of organisms. Enemy-driven adaptive radiation was a key prediction of Ehrlich and Raven's coevolutionary hypothesis [Ehrlich PR, Raven PH (1964) Evolution 18:586-608], yet has remained largely untested. Here we examine patterns of trait evolution in 51 North American milkweed species (Asclepias), using maximum likelihood methods. We study 7 traits of the milkweeds, ranging from seed size and foliar physiological traits to defense traits (cardenolides, latex, and trichomes) previously shown to impact herbivores, including the monarch butterfly. We compare the fit of simple random-walk models of trait evolution to models that incorporate stabilizing selection (Ornstein-Ulenbeck process), as well as time-varying rates of trait evolution. Early bursts of trait evolution were implicated for 2 traits, while stabilizing selection was implicated for several others. We further modeled the relationship between trait change and species diversification while allowing rates of trait evolution to vary during the radiation. Species-rich lineages underwent a proportionately greater decline in latex and cardenolides relative to species-poor lineages, and the rate of trait change was most rapid early in the radiation. An interpretation of this result is that reduced investment in defensive traits accelerated diversification, and disproportionately so, early in the adaptive radiation of milkweeds.

C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.

Phenotypic convergence is a widespread and well-recognized evolutionary phenomenon. However, the responsible molecular mechanisms remain often unknown mainly because the genes involved are not identified. A well-known example of physiological convergence is the C4 photosynthetic pathway, which evolved independently more than 45 times [1]. Here, we address the question of the molecular bases of the C4 convergent phenotypes in grasses (Poaceae) by reconstructing the evolutionary history of genes encoding a C4 key enzyme, the phosphoenolpyruvate carboxylase (PEPC). PEPC genes belong to a multigene family encoding distinct isoforms of which only one is involved in C4 photosynthesis [2]. By using phylogenetic analyses, we showed that grass C4 PEPCs appeared at least eight times independently from the same non-C4 PEPC. Twenty-one amino acids evolved under positive selection and converged to similar or identical amino acids in most of the grass C4 PEPC lineages. This is the first record of such a high level of molecular convergent evolution, illustrating the repeatability of evolution. These amino acids were responsible for a strong phylogenetic bias grouping all C4 PEPCs together. The C4-specific amino acids detected must be essential for C4 PEPC enzymatic characteristics, and their identification opens new avenues for the engineering of the C4 pathway in crops.

Probabilistic algorithms for blind adaptive multiuser detection

In this paper, two probabilistic adaptive algorithmsfor jointly detecting active users in a DS-CDMA system arereported. The first one, which is based on the theory of hiddenMarkov models (HMM’s) and the Baum–Wech (BW) algorithm,is proposed within the CDMA scenario and compared withthe second one, which is a previously developed Viterbi-basedalgorithm. Both techniques are completely blind in the sense thatno knowledge of the signatures, channel state information, ortraining sequences is required for any user. Once convergencehas been achieved, an estimate of the signature of each userconvolved with its physical channel response (CR) and estimateddata sequences are provided. This CR estimate can be used toswitch to any decision-directed (DD) adaptation scheme. Performanceof the algorithms is verified via simulations as well as onexperimental data obtained in an underwater acoustics (UWA)environment. In both cases, performance is found to be highlysatisfactory, showing the near–far resistance of the analyzed algorithms.

Statistical reference criteria for adaptive signal processing in digital communications

A general criterion for the design of adaptive systemsin digital communications called the statistical reference criterionis proposed. The criterion is based on imposition of the probabilitydensity function of the signal of interest at the outputof the adaptive system, with its application to the scenario ofhighly powerful interferers being the main focus of this paper.The knowledge of the pdf of the wanted signal is used as adiscriminator between signals so that interferers with differingdistributions are rejected by the algorithm. Its performance isstudied over a range of scenarios. Equations for gradient-basedcoefficient updates are derived, and the relationship with otherexisting algorithms like the minimum variance and the Wienercriterion are examined.

Testing of Vacuum Drum Filter

Tämän diplomityön tavoitteena oli testata ja optimoida erään alipainerumpusuodattimen toimivuutta, ja lisäksi maksimoida tuottavuus ja vertailla erilaisten pesumenetelmientehokkuutta. Testilietteiden ¿ rautarikasteen ja täyteainepastan ¿ karakterisointi oli myös tärkeää. Kirjallisuusosassa tarkasteltiin lyhyesti neste-kiintoaine-erotuksen teoriaa, erityisesti alipainesuodatusta ja alipainerumpusuodattimia. Lisäksi käsiteltiin kapillaarisuodatuksen toimintaperiaatteita sekä selvitettiin kaivosteollisuuden veden talteenottokeinoja, kiintoainejäämien käsittelymenetelmiä ja Chilen kaivosteollisuuden nykytilaa. Työn kokeellinen osa suoritettiin käyttämällä raskaita ja kiintoainepitoisuuksiltaan korkeita lietteitä, eli rautarikastetta ja täyteainepastaa. Kokeet suoritettiin erityisellä alipainerumpusuodattimella, joka oli muokattu perinteisestäpäältä syötettävästä alipainerumpusuodattimesta. Kokeissa tutkittiin pyörimisnopeuden ja erilaisten pesumenetelmien vaikutusta kakun kosteuteen ja suodatuskapasiteettiin. Koelietteiden karakterisointi suoritettiin analysoimalla partikkelikokojakauma, kiintoainepitoisuus, metallipitoisuus ja koostumus. Kokeiden perusteella havaittiin, että rummun pyörimisnopeudella ja lietteen kiintoainepitoisuudella on merkittävä vaikutus suodatuskapasiteettiin ja kakun kosteuspitoisuuteen. Havaittiin myös, että kakun kosteuspitoisuuksissa ja rummun suodatuskapasiteeteissa oli eroja, kun verrattiin eri suodatinväliaineen pesumenetelmiä. Täten oikean pesumenetelmän valinta on tärkeää, ja sillä pystytään lisäämään suodatinväliaineen käyttöikää.