Effective communication in tropical forests: Song transmission and the singing behaviour of Rufous-and-white Wrens (Thryothorus rufalbus)

This thesis examines sound transmission and the communication behaviour of Neotropical Rufous-and-white Wrens. A song transmission experiment revealed strong effects of distance, signaller perch height, and sex on song degradation, minor effects of receiver perch height, and mixed effects of microhabitat. An examination of fine structure of Rufous-and-white Wren song in relation to habitat did not show a strong effect of microhabitat on song structure, although it did quantitatively validate the use of song type classes in this species. A field study of perch height selection in Rufous-and-white Wrens showed that they use elevated song posts, which were shown to provide a song propagation benefit. Males perch higher than females, which may be related to a more active territorial defence or mate guarding role for male song. This is the first sound transmission-based investigation of effective communication in both sexes of a tropical duetting species

Individual variation and lek-based vocal distinctiveness in songs of the screaming piha (Lipaugus Vociferans), A suboscine songbird

One long-standing ornithological paradigm holds that song learning in oscine songbirds has a cultural component, whereas suboscine songbirds inherit songs genetically. Recent studies reveal that suboscine song may be more variable and complex than previously realized. Several suboscine species show marked individual variation in their songs-variation that may play a role in individual recognition and neighbor-stranger discrimination-and a few suboscine species show indications of song learning. We investigated individual variation in the vocalizations of a suboscine passerine, the Screaming Piha (Lipaugus vociferans), from recordings of 26 males at four lek sites along the Tambopata River in Peru. Male Screaming Piha songs consist of quiet introductory syllables followed by two explosively loud syllables that sound like an emphatic pee haw. We used three complementary methods to examine variation in song characteristics. Spectrogram cross-correlation revealed significant consistency within individual males and variability among males. Analysis of fine structural characteristics revealed that all measured song features were significantly less variable within individuals than among individuals. Canonical discriminant analysis based on these 13 song features correctly classified 93.2% of songs by individual and 76.4% of songs by lek site. Our results indicate that there is sufficient consistency in song features within males and sufficient variation among males for identification of individuals on the basis of songs and, to a lesser extent, that song features vary with the lek site of the singer. We conclude that Screaming Pihas sing songs that are individually distinctive and bear a lek signature. © 2008 by The American Ornithologists\u27 Union. All rights reserved

Validity of a self-report survey tool measuring the nutrition and physical activity environment of primary schools

Background: Valid tools measuring characteristics of the school environment associated with the physical activity and dietary behaviours of children are needed to accurately evaluate the impact of initiatives to improve school environments. The aim of this study was to assess the validity of Principal self-report of primary school healthy eating and physical activity environments. Methods: Primary school Principals (n = 42) in New South Wales, Australia were invited to complete a telephone survey of the school environment; the School Environment Assessment Tool – SEAT. Equivalent observational data were collected by pre-service teachers located within the school. The SEAT, involved 65 items that assessed food availability via canteens, vending machines and fundraisers and the presence of physical activity facilities, equipment and organised physical activities. Kappa statistics were used to assess agreement between the two measures. Results: Almost 70% of the survey demonstrated moderate to almost perfect agreement. Substantial agreement was found for 10 of 13 items assessing foods sold for fundraising, 3 of 6 items assessing physical activity facilities of the school, and both items assessing organised physical activities that occurred at recess and lunch and school sport. Limited agreement was found for items assessing foods sold through canteens and access to small screen recreation. Conclusions: The SEAT provides researchers and policy makers with a valid tool for assessing aspects of the school food and physical activity environment

Reviving WHAAM! a comparative evaluation of cleaning systems for the conservation treatment of Roy Lichtenstein's iconic painting

Abstract Roy Lichtenstein's Whaam! (1963) is an iconic artwork in Tate's collection (T00897). Over the past 50 years, the painting has been on almost continuous display and had accrued a layer of deposited soiling, which resulted in the dampening of Lichtenstein's vibrant colours and the masking of numerous subtleties across the painting surface. This paper outlines the design and execution of an optimal soiling removal strategy for this challenging work; utilising collaborative, practice-based research. The conservation treatment employed was derived through an iterative process that reflected and supported the conservation decision-making process. The research strands included: technical and art historical investigations to determine the materials and construction of Whaam! and to define the aims of the conservation treatment; preparation of accelerated aged and artificially soiled test (mock-up) paint samples based on contemporary equivalent materials and a comparative evaluation of a range of established and novel soil-removal systems, followed by further tailoring for use on the work of art. The range of cleaning systems evaluated included free-solvents, gels and emulsifiers; which were documented using star diagrams, digital microscopy and infrared spectroscopy. After a rigorous process of assessment and refinement, the strategy taken forward to Whaam! included the use of a polyvinyl alcohol-based polymeric hydrogel (Nanorestore Gel® Peggy 6), uploaded with tailored aqueous solutions. This process facilitated a low risk, controlled and even-removal of the soiling layer, enabling the successful treatment of this sensitive painting for the first time in the painting's history

UniProt: the Universal Protein knowledgebase

To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss‐Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross‐references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss‐Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross‐references). For convenient sequence searches, UniProt also provides several non‐redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniPro

The Universal Protein Resource (UniProt)

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two week

The Universal Protein Resource (UniProt): an expanding universe of protein information

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/database

The Universal Protein Resource (UniProt)

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks

The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assembliess

Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes