A simple two-module problem to exemplify building-block assembly under crossover

Theoretically and empirically it is clear that a genetic algorithm with crossover will outperform a genetic algorithm without crossover in some fitness landscapes, and vice versa in other landscapes. Despite an extensive literature on the subject, and recent proofs of a principled distinction in the abilities of crossover and non-crossover algorithms for a particular theoretical landscape, building general intuitions about when and why crossover performs well when it does is a different matter. In particular, the proposal that crossover might enable the assembly of good building-blocks has been difficult to verify despite many attempts at idealized building-block landscapes. Here we show the first example of a two-module problem that shows a principled advantage for cross-over. This allows us to understand building-block assembly under crossover quite straightforwardly and build intuition about more general landscape classes favoring crossover or disfavoring it

Analysing co-evolution among artificial 3D creatures

This paper is concerned with the analysis of coevolutionary dynamics among 3D artificial creatures, similar to those introduced by Sims (1). Coevolution is subject to complex dynamics which are notoriously difficult to analyse. We introduce an improved analysis method based on Master Tournament matrices [2], which we argue is both less costly to compute and more informative than the original method. Based on visible features of the resulting graphs, we can identify particular trends and incidents in the dynamics of coevolution and look for their causes. Finally, considering that coevolutionary progress is not necessarily identical to global overall progress, we extend this analysis by cross-validating individuals from different evolutionary runs, which we argue is more appropriate than single-record analysis method for evaluating the global performance of individuals

Evolution of changes in carbon monoxide transfer factor in men with chronic obstructive pulmonary disease

SummaryProgression of chronic obstructive pulmonary disease (COPD) has been studied predominantly by following change in forced expiratory volume in 1s (FEV1) which reflects both primary airway disease and associated alveolar disease. Carbon monoxide transfer (Tlco) (the product of the transfer coefficient Kco and alveolar volume Va) is the only simple, widely available test of alveolar function, but few studies have followed long-term changes in an individual.Seventeen middle-aged men with moderate chronic airflow obstruction (mean FEV1 56% of predicted values) were observed with yearly measurements of FEV1, Tlco and Kco over a mean of 18.9yr. At the end of follow-up FEV1 had fallen to 29% of predicted values. Va, measured by single breath dilution, fell in each man. Kco at recruitment ranged from 41% to 110% predicted and remained >75% predicted in eight men at the end of follow-up supporting a phenotype of COPD with predominant airway disease and little emphysema. Fall in FEV1 was faster (2.03% predicted FEV1/yr) in seven men with low initial Kco<75% pred. than in men with initial Kco>75% pred. (1.14% predicted FEV1/yr, P=0.006).Repeated measurements of CO transfer in an individual should increase the present poor knowledge of the contribution of alveolar disease to the progression of chronic airflow obstruction

Quantum dot emission from site-controlled ngan/gan micropyramid arrays

InxGa1−xN quantum dots have been fabricated by the selective growth of GaN micropyramid arrays topped with InGaN/GaN quantum wells. The spatially, spectrally, and time-resolved emission properties of these structures were measured using cathodoluminescence hyperspectral imaging and low-temperature microphotoluminescence spectroscopy. The presence of InGaN quantum dots was confirmed directly by the observation of sharp peaks in the emission spectrum at the pyramid apices. These luminescence peaks exhibit decay lifetimes of approximately 0.5 ns, with linewidths down to 650 me

Open-Ended Evolutionary Robotics: an Information Theoretic Approach

This paper is concerned with designing self-driven fitness functions for Embedded Evolutionary Robotics. The proposed approach considers the entropy of the sensori-motor stream generated by the robot controller. This entropy is computed using unsupervised learning; its maximization, achieved by an on-board evolutionary algorithm, implements a "curiosity instinct", favouring controllers visiting many diverse sensori-motor states (sms). Further, the set of sms discovered by an individual can be transmitted to its offspring, making a cultural evolution mode possible. Cumulative entropy (computed from ancestors and current individual visits to the sms) defines another self-driven fitness; its optimization implements a "discovery instinct", as it favours controllers visiting new or rare sensori-motor states. Empirical results on the benchmark problems proposed by Lehman and Stanley (2008) comparatively demonstrate the merits of the approach

Genetic Assimilation and Canalisation in the Baldwin Effect

The Baldwin Effect indicates that individually learned behaviours acquired during an organism’s lifetime can influence the evolutionary path taken by a population, without any direct Lamarckian transfer of traits from phenotype to genotype. Several computational studies modelling this effect have included complications that restrict its applicability. Here we present a simplified model that is used to reveal the essential mechanisms and highlight several conceptual issues that have not been clearly defined in prior literature. In particular, we suggest that canalisation and genetic assimilation, often conflated in previous studies, are separate concepts and the former is actually not required for non-heritable phenotypic variation to guide genetic variation. Additionally, learning, often considered to be essential for the Baldwin Effect, can be replaced with a more general phenotypic plasticity model. These simplifications potentially permit the Baldwin Effect to operate in much more general circumstances

Characteristics of TCR repertoire associated with successful immune checkpoint therapy responses

Immunotherapies have revolutionized cancer treatment. In particular, immune checkpoint therapy (ICT) leads to durable responses in some patients with some cancers. However, the majority of treated patients do not respond. Understanding immune mechanisms that underlie responsiveness to ICT will help identify predictive biomarkers of response and develop treatments to convert non-responding patients to responding ones. ICT primarily acts at the level of adaptive immunity. The specificity of adaptive immune cells, such as T and B cells, is determined by antigen-specific receptors. T cell repertoires can be comprehensively profiled by high-throughput sequencing at the bulk and single-cell level. T cell receptor (TCR) sequencing allows for sensitive tracking of dynamic changes in antigen-specific T cells at the clonal level, giving unprecedented insight into the mechanisms by which ICT alters T cell responses. Here, we review how the repertoire influences response to ICT and conversely how ICT affects repertoire diversity. We will also explore how changes to the repertoire in different anatomical locations can better correlate and perhaps predict treatment outcome. We discuss the advantages and limitations of current metrics used to characterize and represent TCR repertoire diversity. Discovery of predictive biomarkers could lie in novel analysis approaches, such as network analysis of amino acids similarities between TCR sequences. Single-cell sequencing is a breakthrough technology that can link phenotype with specificity, identifying T cell clones that are crucial for successful ICT. The field of immuno-sequencing is rapidly developing and cross-disciplinary efforts are required to maximize the analysis, application, and validation of sequencing data. Unravelling the dynamic behavior of the TCR repertoire during ICT will be highly valuable for tracking and understanding anti-tumor immunity, biomarker discovery, and ultimately for the development of novel strategies to improve patient outcomes

Multipole Amplitudes of Pion Photoproduction on Nucleons up to 2GeV within Dispersion Relations and Unitary Isobar Model

Two approaches for analysis of pion photo- and electroproduction on nucleons in the resonance energy region are checked at $Q^2=0$ using the results of GWU(VPI) partial-wave analysis of photoproduction data. The approaches are based on dispersion relations and unitary isobar model. Within dispersion relations good description of photoproduction multipoles is obtained up to $W=1.8 GeV$. Within unitary isobar model, modified with increasing energy by incorporation of Regge poles, and with unified Breit-Wigner parametrization of resonance contributions, good description of photoproduction multipoles is obtained up to $W=2 GeV$.Comment: 23 pages, LaTe

A regional water quality model designed for a range of users and for retrofit and re-use

We discuss the motivations for, and software design concepts underpinning, the development of a regional water quality model. The Environmental Management Support System (EMSS) was developed to predict daily fluxes of runoff, total suspended sediment, total nitrogen and total phosphorous through a large-scale river network. It was built using a custom environmental modelling framework called Tarsier, founded on the Borland C++ Builder rapid application development environment. Three autonomous models are integrated within the EMSS, but are loosely coupled so that alternative models could be retrofitted into the system if desired. The three models share common data handling and visualisation routines resident in the Tarsier modelling environment and used in other modelling applications. The EMSS was designed for use by a range of stakeholders with varying levels of computer and technical proficiency. To satisfy their varying needs, we built three different interfaces, suited to ‘expert’, ‘intermediate’ and ‘basic’ users. The interfaces for the latter two groups were developed using interface prototyping methods, resulting in software that suited the user requirements. The object-oriented design employed in the coding of the EMSS has enhanced the extendibility and re-useability of the software. The EMSS development was part of a larger hydrologic modelling initiative aimed at reducing duplication in model building and standardising approaches to model design and delivery. The lessons learned during development of the EMSS have informed our future model development strategy

The rate of cosmic ray showers at large zenith angles: a step towards the detection of ultra-high energy neutrinos by the Pierre Auger Observatory

It is anticipated that the Pierre Auger Observatory can be used to detect cosmic neutrinos of >10^19 eV that arrive at very large zenith angles. However showers created by neutrino interactions close to the detector must be picked out against a background of similar events initiated by cosmic ray nuclei. As a step towards understanding this background, we have made the first detailed analysis of air showers recorded at Haverah Park (an array which used similar detectors to those planned for the Auger Observatory) with zenith angles above 60 degs. We find that the differential shower rate from 60 degs to 80 degs. can be predicted accurately when we adopt the known primary energy spectrum above 10^17 eV and assume the QGSJET model and proton primaries. Details of the calculation are given.Comment: 22 pages, 12 figures, to appear in Astroparticle Physic