InterPro in 2022.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction

Strain field analysis on Montserrat (W.I.) as tool for assessing permeable flow paths in the magmatic system of Soufrière Hills Volcano

Strain dilatometers have been operated on the volcanic island of Montserrat (West Indies) for more than a decade and have proven to be a powerful technique to approach short-term dynamics in the deformational field in response to pressure changes in the magmatic system of the andesitic dome-building Soufrière Hills Volcano (SHV). We here demonstrate that magmatic activity in each of the different segments of the SHV magmatic system (shallow dyke-conduit, upper and lower magma chambers) generates a characteristic strain pattern that allows the identification of operating sources in the plumbing system based on a simple scheme of amplitude ratios. We use this method to evaluate strain data from selected Vulcanian explosions and gas emission events that occurred at SHV between 2003 and 2012. Our results show that the events were initiated by a short phase of contraction of either one or both magma chambers and a simultaneous inflation of the shallow feeder system. The initial phase of the events usually lasted only tens to hundreds of seconds before the explosion/gas emission started and the system recovered. The short duration of this process points at rapid transport of fluids rather than magma ascent to generate the pressure changes. We suggest the propagation of tensile hydraulic fractures as viable mechanism to provide a pathway for fluid migration in the magmatic system at the observed time scale. Fluid mobilization was initiated by a sudden destabilization of large pockets of already segregated fluid in the magma chambers. Our study demonstrates that geodetic observables can provide unprecedented insights into complex dynamic processes within a magmatic system commonly assessed by theoretical modeling and petrologic observations. Key Points Strain data analysis from explosions/degassing events at Soufriere Hills Volcano Pressure release deep within the magmatic system sec-min prior to events Rapid gas rise from magma reservoir to surface via tensile hydraulic fractures © 2014. American Geophysical Union. All Rights Reserved

Hosts and hostages: Mass immigration and the power of hospitality in post-war British and Caribbean literature

This article examines the challenge to colonialist centre-periphery relations in post-war novels by white British and Caribbean writers. Concentrating on the relationship between political debates surrounding mass immigration and the marginalization of non-white migrants within British communities, I analyse texts that depict the threshold of the home as the politicized site of racial tension, namely Sam Selvon’s The Lonely Londoners (1956), V.S. Naipaul’s The Mimic Men (1967), Alan Sillitoe’s Saturday Night and Sunday Morning (1958), and Anthony Burgess’s The Right to an Answer (1960). In varying ways, these texts depict the durability of centre-periphery relations at local levels through the informal segregation of the colonizer and the colonized. In doing so they point to what Jacques Derrida has outlined, in Of Hospitality (2000), as the power relationship inherent in policies of immigration, whereby the host-nation remains in control of the conditions upon which hospitality rests

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

"Looking all lost towards a Cook's guide for beauty”: the art of literature and the lessons of the guidebook in modernist writing

This article explores the impact of the guidebook, especially the Baedeker series, on modernist literary culture. It argues that the guidebook is a literary phenomenon in its own right and that, as such, it attracts special attention from those engaged in defending and/or extending the category of literature as part of a modernist agenda. In particular, modernist writers are concerned as to whether the guidebook counts as a form of literature and, if so, what this means for the more familiar forms seen in their own essays, fiction and travelogues. What might the invention of the star system to rank scenes and monuments mean for the future of art criticism? How might the guidebook help or hinder the traveller in his/her pursuit of the beautiful or the picturesque? What does recourse to the guidebook reveal about the taste and education of the traveller? And, more pointedly still, what kind and quality of writing is the guidebook itself? This article surveys the extent of modernism's interest in the guidebook, both as a noteworthy new form and as a form modernist writers adapted for use in their own books, before turning in detail to commentary on the guidebook by E.M. Forster, Ernest Hemingway, H.D. and Virginia Woolf. In conclusion, it finds that the guidebook in modernism is very rarely just that. Instead, the guidebook finds unexpected affinities with modernism in its attempt to “modernise” literature – to make it more rational, more totalising and, in the eyes of its critics, less able to discriminate.This is an Accepted Manuscript of an article published by Taylor & Francis in Studies in Travel Writing on 4th March 2015, available online: http://wwww.tandfonline.com/10.1080/13645145.2014.994924

Modernism, class and colonialism in Robert Noonan’s The Ragged Trousered Philanthropists

This essay explores Robert Noonan’s 1914 novel, The Ragged Trousered Philanthropists, as a work of Irish modernist fiction. Reading its fragmented narrative as a reflection of the author’s subaltern position as an Irish republican and socialist, it interprets Noonan’s work as the product of the anticolonial and class struggles in which he was involved. Its critique of capitalist and imperial hegemony and the assertions that suffering, injustice and violence are normal, natural or inevitable phenomena reflects the author’s frustration, anger and desperation. In this way the novel counters and decentres the bourgeois-imperial dynamic that was reflected in the textual stability of Victorian realism. The Ragged Trousered Philanthropists is an uneasy text that is at once ruptured and uncertain of its own aesthetic status and conveys, through its shifting, episodic plot, the precariousness of a working-class existence permanently poised “on the brink of destitution.” © 2018 Informa UK Limited, trading as Taylor & Francis Grou

Class, Youth and Dirty Jobs: The Working-Class and Post-War Britain in Pete Townshend's Quadrophenia

FOS

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p