Pigs in Rites: Rights in Pigs: Porcine Values in the Papua New Guinea Highlands

This paper discusses the place of pigs in the mountains of Papua New Guinea, particularly in the Was valley of the Southern Highlands Province. After a brief introduction to the pigs of the region and their herding arrangements, it gives an ethnographic account of their use in various rites, notably those that feature curing, sorcery and cult activities. They prompt consideration of the relevance of concepts used to understand these ritual activities, whether they are offerings or sacrifices or something else particular to pigs in rites. The cults also include large pig kill festivals that have notable socio-political implications. These relate to rights in pigs and their ownership, which are complex issues that impinge on all of the foregoing activities

INSTRUMENTS OF POWER Developing and Applying Diplomatic Analysis to Enhance Archival Interpretation and Research Uses of Technical Drawings

This study presents a solution to the difficulties of making historical technical drawings available for research. In archives services, such hard-copy drawings are frequently found to be much less manageable than other forms of archival record. Technical drawings can be very complicated intellectually, while also being large and awkward to handle. Archival effort might thus be directed towards making less difficult forms of record available for research. These problems, which impede access to research resources, have not been attended to in the literature. A new way of understanding technical drawings has been created through an innovative development of diplomatic analysis. Traditionally used for historical text analysis, diplomatic has not been applied previously to graphical records such as technical drawings. With this theoretical lens, and statistical techniques, the research design followed the principles of mixed methods methodology. The core of the study comprised a detailed quantitative survey and analysis of a statistical sample of C20th technical drawings. Language was found to be the key to their better understanding. A model was developed to translate the language of technical drawing concepts and characteristics into archival terms. The survey’s statistically robust and replicable results identified concepts and characteristics that were generic, or nearly so. When interpreted and described, those ubiquitous elements will provide a means to enhance understanding of technical drawings held as archives. The research results therefore provide a sound basis for drafting practical guidance for interpreting and processing such technical drawings. That guidance will help to make technical drawings more accessible to researchers. Diplomatic theory has been extended by this research. The utility of diplomatic’s application to graphical records has been demonstrated. So, too, has diplomatic’s extension to records capable of being reprographically reproduced. Unexpectedly, questions have arisen for technical drawings’ certification and authorisation in their original contexts of use. The robust research design and methodology that has been developed is capable of generalisation in future research

CATH: comprehensive structural and functional annotations for genome sequences.

The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235,000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant improvements to the predictive power of our functional families (FunFams); the release of our 'current' putative domain assignments (CATH-B); a new, strictly non-redundant data set of CATH domains suitable for homology benchmarking experiments (CATH-40) and a number of improvements to the web pages

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

The InterPro protein families database: the classification resource after 15 years

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 201

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

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

The InterPro protein families database: the classification resource after 15 years

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36,766 member database signatures integrated into 26,238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012