Genetic Improvement of Software: a Comprehensive Survey

Genetic improvement (GI) uses automated search to find improved versions of existing software. We present a comprehensive survey of this nascent field of research with a focus on the core papers in the area published between 1995 and 2015. We identified core publications including empirical studies, 96% of which use evolutionary algorithms (genetic programming in particular). Although we can trace the foundations of GI back to the origins of computer science itself, our analysis reveals a significant upsurge in activity since 2012. GI has resulted in dramatic performance improvements for a diverse set of properties such as execution time, energy and memory consumption, as well as results for fixing and extending existing system functionality. Moreover, we present examples of research work that lies on the boundary between GI and other areas, such as program transformation, approximate computing, and software repair, with the intention of encouraging further exchange of ideas between researchers in these fields

The Paranormal is (Still) Normal: The Sociological Implications of a Survey of Paranormal Experiences in Great Britain

Historically, there has been limited sociological interest in the paranormal and no systematic study of reported paranormal experiences. There are also few medium-to-large-scale survey results with nationally representative populations focusing on paranormal experiences. This paper provides details of an exploratory survey conducted in 2009 with a nationally representative sample of 4,096 adults aged 16 years and over across Great Britain. Our findings show that 37% of British adults report at least one paranormal experience and that women, those who are middle-aged or individuals resident in the South West are more likely to report such experiences. These results establish incidence levels of reported paranormal experiences in contemporary Britain. We argue also that they merit a more sustained sociological consideration of the paranormal. In this respect we renew and update the robust justification and call for serious research positioning the paranormal as a social phenomenon, originally proposed well over thirty years ago by Greeley (1975)

Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes.

The pneumococcus is a leading global pathogen and a key virulence factor possessed by the majority of pneumococci is an antigenic polysaccharide capsule ('serotype'), which is encoded by the capsular (cps) locus. Approximately 100 different serotypes are known, but the extent of sequence diversity within the cps loci of individual serotypes is not well understood. Investigating serotype-specific sequence variation is crucial to the design of sequence-based serotyping methodology, understanding pneumococcal conjugate vaccine (PCV) effectiveness and the design of future PCVs. The availability of large genome datasets makes it possible to assess population-level variation among pneumococcal serotypes and in this study 5405 pneumococcal genomes were used to investigate cps locus diversity among 49 different serotypes. Pneumococci had been recovered between 1916 and 2014 from people of all ages living in 51 countries. Serotypes were deduced bioinformatically, cps locus sequences were extracted and variation was assessed within the cps locus, in the context of pneumococcal genetic lineages. Overall, cps locus sequence diversity varied markedly: low to moderate diversity was revealed among serogroups/types 1, 3, 7, 9, 11 and 22; whereas serogroups/types 6, 19, 23, 14, 15, 18, 33 and 35 displayed high diversity. Putative novel and/or hybrid cps loci were identified among all serogroups/types apart from 1, 3 and 9. This study demonstrated that cps locus sequence diversity varied widely between serogroups/types. Investigation of the biochemical structure of the polysaccharide capsule of major variants, particularly PCV-related serotypes and those that appear to be novel or hybrids, is warranted.This work was supported by a Wellcome Trust Biomedical Research Fund award (04992/Z/14/Z) to M. J. C. M., K. A. J., and A. B. B.; a Wellcome Trust career development fellowship (083511/Z/07/Z) to A. B. B; and a University of Oxford John Fell Fund award (123/734) to A. B. B. Core funding for the Sanger Institute was provided by the Wellcome Trust (098051). Funding for the Icelandic vaccine impact study was provided by GlaxoSmithKline Biologicals SA and the Landspítali University Hospital Research Fund to K. G. K., A. H., H. E., S. D. B., and A. B. B

Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.The pneumococcus is a leading pathogen infecting children and adults. Safe, effective vaccines exist, and they work by inducing antibodies to the polysaccharide capsule (unique for each serotype) that surrounds the cell; however, current vaccines are limited by the fact that only a few of the nearly 100 antigenically distinct serotypes are included in the formulations. Within the serotypes, serogroup 6 pneumococci are a frequent cause of serious disease and common colonizers of the nasopharynx in children. Serotype 6E was first reported in 2004 but was thought to be rare; however, we and others have detected serotype 6E among recent pneumococcal collections. Therefore, we analyzed a diverse data set of ∼1,000 serogroup 6 genomes, assessed the prevalence and distribution of serotype 6E, analyzed the genetic diversity among serogroup 6 pneumococci, and investigated whether pneumococcal conjugate vaccine-induced serotype 6A and 6B antibodies mediate the killing of serotype 6E pneumococci. We found that 43% of all genomes were of serotype 6E, and they were recovered worldwide from healthy children and patients of all ages with pneumococcal disease. Four genetic lineages, three of which were multidrug resistant, described ∼90% of the serotype 6E pneumococci. Serological assays demonstrated that vaccine-induced serotype 6B antibodies were able to elicit killing of serotype 6E pneumococci. We also revealed three major genetic clusters of serotype 6A capsular sequences, discovered a new hybrid 6C/6E serotype, and identified 44 examples of serotype switching. Therefore, while vaccines appear to offer protection against serotype 6E, genetic variants may reduce vaccine efficacy in the longer term because of the emergence of serotypes that can evade vaccine-induced immunity

Vernix caseosa as a multi-component defence system based on polypeptides, lipids and their interactions

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldVernix caseosa is a white cream-like substance that covers the skin of the foetus and the newborn baby. Recently, we discovered antimicrobial peptides/proteins such as LL-37 in vernix, suggesting host defence functions of vernix. In a proteomic approach, we have continued to characterize proteins in vernix and have identified 20 proteins, plus additional variant forms. The novel proteins identified, considered to be involved in host defence, are cystatin A, UGRP-1, and calgranulin A, B and C. These proteins add protective functions to vernix such as antifungal activity, opsonizing capacity, protease inhibition and parasite inactivation. The composition of the lipids in vernix has also been characterized and among these compounds the free fatty acids were found to exhibit antimicrobial activity. Interestingly, the vernix lipids enhance the antimicrobial activity of LL-37 in vitro, indicating interactions between lipids and antimicrobial peptides in vernix. In conclusion, vernix is a balanced cream of compounds involved in host defence, protecting the foetus and newborn against infection

Meningococcal carriage in children and young adults : a cross-sectional and longitudinal study, Iceland, 2019 to 2021

BackgroundNeisseria meningitidis is a commensal bacterium which can cause invasive disease. Colonisation studies are important to guide vaccination strategies.AimThe study's aim was to determine the prevalence of meningococcal colonisation, duration of carriage and distribution of genogroups in Iceland.MethodsWe collected samples from 1 to 6-year-old children, 15-16-year-old adolescents and 18-20-year-old young adults. Carriers were sampled at regular intervals until the first negative swab. Conventional culture methods and qPCR were applied to detect meningococci and determine the genogroup. Whole genome sequencing was done on groupable meningococci.ResultsNo meningococci were detected among 460 children, while one of 197 (0.5%) adolescents and 34 of 525 young adults (6.5 %) carried meningococci. Non-groupable meningococci were most common (62/77 isolates from 26/35 carriers), followed by genogroup B (MenB) (12/77 isolates from 6/35 carriers). Genogroup Y was detected in two individuals and genogroup W in one. None carried genogroup C (MenC). The longest duration of carriage was at least 21 months. Serial samples from persistent carriers were closely related in WGS.ConclusionsCarriage of pathogenic meningococci is rare in young Icelanders. Non-groupable meningococci were the most common colonising meningococci in Iceland, followed by MenB. No MenC were found. Whole genome sequencing suggests prolonged carriage of the same strains in persistent carriers.Peer reviewe

Ctenophore population recruits entirely through larval reproduction in the central Baltic Sea

The comb jelly Mertensia ovum, widely distributed in Arctic regions, has recently been discovered in the northern Baltic Sea. We show that M. ovum also exists in the central Baltic but that the population consists solely of small-sized larvae (less than 1.6 mm). Despite the absence of adults, eggs were abundant. Experiments revealed that the larvae were reproductively active. Egg production and anticipated mortality rates suggest a self-sustaining population. This is the first account of a ctenophore population entirely recruiting through larval reproduction (paedogenesis). We hypothesize that early reproduction is favoured over growth to compensate for high predation pressure