Bird communities in the buffer lands of Epping Forest

A farmland site in the green-belt buffer lands to the north of Epping Forest was surveyed for bird species across one calendar year. This is the first known effort in this area. The principal focus was upon birds listed on the Farmland Bird Index, but all species encountered were recorded, giving 41 species in total. Diversity and dominance data is presented for the whole year and across seasons. Eleven of the 19 indicator species were registered, and ten of those were present during breeding season. The majority of the missing eight species are red listed and in population decline, but so are some of those recorded. Generalist species were more readily registered. Woodpigeon is the dominant species, from two forms of analysis. The limitations of this survey and next steps are discussed

Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit

Background: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates

[Open peer commentary] Is genomics bad for you?

The plasticity of the genome complicates genetic causation, but should be investigated from a functional perspective. Specific adaptive hypotheses are referenced in the target article, but it is also necessary to explain how the integrity of the genome is maintained despite processes that tend towards its diversification and degradation. These include the accumulation of deleterious changes and intra-genomic conflict

Draft genome sequence of "Candidatus Cronobacter colletis" NCTC 14934T, a new species in the genus Cronobacter

Members of the Cronobacter genus are associated with serious infections in neonates. This is the first report of the draft genome sequence for the newly proposed species Cronobacter colletis

Draft genome sequences of three newly identified species in the genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T

Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described species in the Cronobacter genus, which is associated with serious infections of neonates. This is the first report of draft genome sequences for these species

Draft genome sequence of the earliest Cronobacter sakazakii sequence type 4 strain, NCIMB 8272

The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with severe cases of neonatal meningitis and persistence in powdered infant formula. For genome sequencing of the earliest deposited culture collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272, originally isolated from milk powder in 1950

Draft genome sequence of a meningitic isolate of Cronobacter sakazakii clonal complex 4, strain 8399

The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine sequence types, is associated with severe cases of neonatal meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4) strains have been sequenced. C. sakazakii strain 8399, isolated from a case of neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain

Adult Kittiwake expelling chick from nesting ledge

On 17th June 2021, we witnessed an adult Kittiwake Rissa tridactyla expel a chick from its nesting ledge. The chick fell to its death. We made the observation during our annual monitoring of this species on Lundy. A scan of the colony at 12.13 hrs detected unusual movement in a two-chick nest. One chick, which we designated as the beta chick given its smaller size, was unusually positioned outside the nest away from the alpha chick and the adult, which both remained in the nest. We estimate that the beta chick was about 1–2 days old. The site was such that the floor of the ledge extended well behind the nest to a slightly overhanging back wall, and the chick was scrabbling against this back wall. At 12.25 hrs, in a rapid sequence of movements lasting only seconds, the beta chick turned and moved back in the direction of the nest. As it approached, it came between the adult and a side wall and was then grasped in the adult’s beak and expelled in an upward arc, falling into the sea below. No interactions between the alpha and beta were observed

Arabic Language WEKA-Based Dialect Classifier for Arabic Automatic Speech Recognition Transcripts

This paper describes an Arabic dialect identification system which we developed for the Discriminating Similar Languages (DSL) 2016 shared task. We classified Arabic dialects by using Waikato Environment for Knowledge Analysis (WEKA) data analytic tool which contains many alternative filters and classifiers for machine learning. We experimented with several classifiers and the best accuracy was achieved using the Sequential Minimal Optimization (SMO) algorithm for training and testing process set to three different feature-sets for each testing process. Our approach achieved an accuracy equal to 42.85% which is considerably worse in comparison to the evaluation scores on the training set of 80-90% and with training set 60:40 percentage split which achieved accuracy around 50%. We observed that Buckwalter transcripts from the Saarland Automatic Speech Recognition (ASR) system are given without short vowels, though the Buckwalter system has notation for these. We elaborate such observations, describe our methods and analyse the training dataset

Evolutionary theory and the ultimate-proximate distinction in the human behavioral sciences

To properly understand behavior, we must obtain both ultimate and proximate explanations. Put briefly, ultimate explanations are concerned with why a behavior exists, and proximate explanations are concerned with how it works. These two types of explanation are complementary and the distinction is critical to evolutionary explanation. We are concerned that they have become conflated in some areas of the evolutionary literature on human behavior. This article brings attention to these issues. We focus on three specific areas: the evolution of cooperation, transmitted culture, and epigenetics. We do this to avoid confusion and wasted effort—dangers that are particularly acute in interdisciplinary research. Throughout this article, we suggest ways in which misunderstanding may be avoided in the future