Ocean acidification compromises a planktic calcifier with implications for global carbon cycling

Anthropogenically-forced changes in ocean chemistry at both the global and regional scale have the potential to negatively impact calcifying plankton, which play a key role in ecosystem functioning and marine carbon cycling. We cultured a globally important calcifying marine plankter (the foraminifer, Globigerina bulloides) under an ecologically relevant range of seawater pH (7.5 to 8.3 total scale). Multiple metrics of calcification and physiological performance varied with pH. At pH \u3e 8.0, increased calcification occurred without a concomitant rise in respiration rates. However, as pH declined from 8.0 to 7.5, calcification and oxygen consumption both decreased, suggesting a reduced ability to precipitate shell material accompanied by metabolic depression. Repair of spines, important for both buoyancy and feeding, was also reduced at pH \u3c 7.7. The dependence of calcification, respiration, and spine repair on seawater pH suggests that foraminifera will likely be challenged by future ocean conditions. Furthermore, the nature of these effects has the potential to actuate changes in vertical transport of organic and inorganic carbon, perturbing feedbacks to regional and global marine carbon cycling. The biological impacts of seawater pH have additional, important implications for the use of foraminifera as paleoceanographic indicators

Flavor-symmetry Breaking with Charged Probes

We discuss the recombination of brane/anti-brane pairs carrying $D3$ brane charge in $AdS_5 \times S^5$. These configurations are dual to co-dimension one defects in the ${\cal N}=4$ super-Yang-Mills description. Due to their $D3$ charge, these defects are actually domain walls in the dual gauge theory, interpolating between vacua of different gauge symmetry. A pair of unjoined defects each carry localized $(2+1)$ dimensional fermions and possess a global $U(N)\times U(N)$ flavor symmetry while the recombined brane/anti-brane pairs exhibit only a diagonal U(N). We study the thermodynamics of this flavor-symmetry breaking under the influence of external magnetic field.Comment: 21 pages, 10 figure

Changing assessment practice in engineering: how can understanding lecturer perspectives help?

Assessment in engineering disciplines is typically oriented to demonstrating competence in specific tasks. Even where assessments are intended to have a formative component, little priority may be given to feedback. Engineering departments are often criticized, by their students and by external quality reviewers, for paying insufficient attention to formative assessment. The e3an project set out to build a question bank of peer-reviewed questions for use within electrical and electronic engineering. As a part of this process, a number of engineers from disparate institutions were required to work together in teams, designing a range of assessments for their subject specialisms. The project team observed that lecturers were especially keen to develop formative assessment but that their understanding of what might be required varied considerably. This paper describes the various ways in which the processes of the project have engaged lecturers in actively identifying and developing their conceptions of teaching, learning and assessment in their subject. It reports on an interview study that was conducted with a selection of participants. It is concluded that lecturers' reflections on and understanding of assessment are closely related to the nature of the subject domain and that it is essential when attempting to improve assessment practice to start from the perspective of lecturers in the discipline

Quantifying full phenological event distributions reveals simultaneous advances, temporal stability and delays in spring and autumn migration timing in long-distance migratory birds

Acknowledgements We thank all Fair Isle Bird Observatory staff and volunteers for help with data collection and acknowledge the foresight of George Waterston and Ken Williamson in instigating the observatory and census methodology. We thank all current and previous directors of Fair Isle Bird Observatory Trust for their contributions, particularly Dave Okill and Mike Wood for their stalwart support for the long-term data collection and for the current analyses. Dawn Balmer and Ian Newton provided helpful guidance on manuscript drafts. We thank Ally Phillimore and two anonymous referees for helpful comments. This study would have been impossible without the Fair Isle community's invaluable support and patience over many decades, which is very gratefully acknowledged. WTSM and JMR designed and undertook analyses, wrote the paper and contributed to data collection and compilation, MB contributed to analysis and editing, all other authors oversaw and undertook data collection and compilation and contributed to editing.Peer reviewedPostprin

Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome

The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor $\textit{Xenopus}$ is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish ($\textit{Polyodon spathula}$). Validation of a subset reveals expression in developing ampullary organs of transcription factor genes critical for hair cell development, and genes essential for glutamate release at hair cell ribbon synapses, suggesting close developmental, physiological and evolutionary links between non-teleost electroreceptors and hair cells. We identify an ampullary organ-specific proneural transcription factor, and candidates for the voltage-sensing L-type Ca$_v$ channel and rectifying K$_v$ channel predicted from skate (cartilaginous fish) ampullary organ electrophysiology. Overall, our results illuminate ampullary organ development, physiology and evolution.Biotechnology and Biological Sciences Research Council (BB/F00818X/1), Leverhulme Trust (RPG-383), Fisheries Society of the British Isles (Research Grant), National Science Foundation (IOS 1557857, IOS 1144965

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Inverse magnetic catalysis in dense holographic matter

We study the chiral phase transition in a magnetic field at finite temperature and chemical potential within the Sakai-Sugimoto model, a holographic top-down approach to (large-N_c) QCD. We consider the limit of a small separation of the flavor D8-branes, which corresponds to a dual field theory comparable to a Nambu-Jona Lasinio (NJL) model. Mapping out the surface of the chiral phase transition in the parameter space of magnetic field strength, quark chemical potential, and temperature, we find that for small temperatures the addition of a magnetic field decreases the critical chemical potential for chiral symmetry restoration - in contrast to the case of vanishing chemical potential where, in accordance with the familiar phenomenon of magnetic catalysis, the magnetic field favors the chirally broken phase. This "inverse magnetic catalysis" (IMC) appears to be associated with a previously found magnetic phase transition within the chirally symmetric phase that shows an intriguing similarity to a transition into the lowest Landau level. We estimate IMC to persist up to 10^{19} G at low temperatures.Comment: 42 pages, 11 figures, v3: extended discussion; new appendix D; references added; version to appear in JHE

Systematic review of studies generating individual participant data on the efficacy of drugs for treating soil-transmitted helminthiases and the case for data-sharing

Preventive chemotherapy and transmission control (PCT) by mass drug administration is the cornerstone of the World Health Organization (WHO)’s policy to control soil-transmitted helminthiases (STHs) caused by Ascaris lumbricoides (roundworm), Trichuris trichiura (whipworm) and hookworm species (Necator americanus and Ancylostama duodenale) which affect over 1 billion people globally. Despite consensus that drug efficacies should be monitored for signs of decline that could jeopardise the effectiveness of PCT, systematic monitoring and evaluation is seldom implemented. Drug trials mostly report aggregate efficacies in groups of participants, but heterogeneities in design complicate classical meta-analyses of these data. Individual participant data (IPD) permit more detailed analysis of drug efficacies, offering increased sensitivity to identify atypical responses potentially caused by emerging drug resistance