Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

Background: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. Methods: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. Findings: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96–1·28). Interpretation: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. Funding: National Institute for Health Research Health Services and Delivery Research Programme

Effectiveness of a national quality improvement programme to improve survival after emergency abdominal surgery (EPOCH): a stepped-wedge cluster-randomised trial

BACKGROUND: Emergency abdominal surgery is associated with poor patient outcomes. We studied the effectiveness of a national quality improvement (QI) programme to implement a care pathway to improve survival for these patients. METHODS: We did a stepped-wedge cluster-randomised trial of patients aged 40 years or older undergoing emergency open major abdominal surgery. Eligible UK National Health Service (NHS) hospitals (those that had an emergency general surgical service, a substantial volume of emergency abdominal surgery cases, and contributed data to the National Emergency Laparotomy Audit) were organised into 15 geographical clusters and commenced the QI programme in a random order, based on a computer-generated random sequence, over an 85-week period with one geographical cluster commencing the intervention every 5 weeks from the second to the 16th time period. Patients were masked to the study group, but it was not possible to mask hospital staff or investigators. The primary outcome measure was mortality within 90 days of surgery. Analyses were done on an intention-to-treat basis. This study is registered with the ISRCTN registry, number ISRCTN80682973. FINDINGS: Treatment took place between March 3, 2014, and Oct 19, 2015. 22 754 patients were assessed for elegibility. Of 15 873 eligible patients from 93 NHS hospitals, primary outcome data were analysed for 8482 patients in the usual care group and 7374 in the QI group. Eight patients in the usual care group and nine patients in the QI group were not included in the analysis because of missing primary outcome data. The primary outcome of 90-day mortality occurred in 1210 (16%) patients in the QI group compared with 1393 (16%) patients in the usual care group (HR 1·11, 0·96-1·28). INTERPRETATION: No survival benefit was observed from this QI programme to implement a care pathway for patients undergoing emergency abdominal surgery. Future QI programmes should ensure that teams have both the time and resources needed to improve patient care. FUNDING: National Institute for Health Research Health Services and Delivery Research Programme

Maintenance and development of Symbiota2, a platform for data sharing and visualization

Symbiota is a database management system for aggregating and displaying record-based biodiversity information from collections of widely varying sizes and integrating them with images of living organisms and image-based records. It is currently used by over 230 collections that collectively provide access to records of over 20 million specimens. Its popularity is attributable to the low financial and learning barriers to participation in a Symbiota network and the wide array of tools it offers for creating resources needed by different user groups. It has been developed through grants, contracts, and pro bono contributions but it suffers from a limited pool of developers (for a project of its size), lack of a coordinated training program, and absence of a structure creating and expanded funding base for maintenance of the program and the networks that adopt it. Symbiota2 is designed to address these issues but development of a business plan is in its preliminary stages. It requires articulation of an overall vision for development of the program, knowledge of its current and potential user base, critical funding needs, and identification of those it benefits, particularly those capable of providing financial support. This presentation was developed in response to an invitation to speak at the Symposium. It outlines our preliminary thoughts on the subject. One of the first needs is to establish an entity, provisionally the Symbiota2 Foundation (S2F), to speak for Symbiota2. Its primary task would be fundraising. S2F would have an advisory board comprising individuals willing to help support Symbiota2 development, both personally and by promoting it to their contacts, plus representatives of Symbiota2’s developers, networks, and network users. The first goal of the Foundation would be raise the funds required to ensure that any established networks remain active and secure by maintaining the currency of network installations, responding to bug reports, informing network managers of changes to the program, and making minor enhancements as requested by users. Grant funding will still be needed to add significant new features. Enhancements requiring major changes in the underlying program or development of completely new apps would still require grant or contract support. Before launching S2F, we need to build more effective communication with network and collection managers; create flyers, booklets, and presentations explaining the power of the program and its benefits to many different user groups; develop case studies illustrating benefits derived from using the program; and create at least one monetized app. These resources will make clearer the benefits that the biodiversity sciences, particularly Symbiota2, provide for the public because, ultimately, it is public support that is needed. We must use all the tools at our disposal to encourage people’s interest in the organisms around them if we are to maintain support for biodiversity science and the collections on which it is based. Symbiota2 can play an important role in this regard. It is, however, unrealistic to expect that Symbiota2 will be able to develop the basic funds needed solely from monetized apps; it is also unrealistic to think it can be supported by charging data providers because many of them are, at present, unfunded. Consequently, there is no choice. We need to look initiate a fund raising program

Supplementary material for: Phylogenetic biodiversity metrics should account for both accumulation and attrition of evolutionary heritage

<p>Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features and other sources of variety through causes other than extinction. Here we introduce `EvoHeritage', a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.</p><p>R for use of code, otherwise PDF and CSV readers are needed to access the files.</p><p>Funding provided by: Leverhulme Trust<br>Crossref Funder Registry ID: https://ror.org/012mzw131<br>Award Number: RF-2022-497</p><p>Funding provided by: New Zealand Marsden Fund*<br>Crossref Funder Registry ID: <br>Award Number: MFPUOC2005</p><p>Data was reprocessed from published sources as described in the associated manuscript methods section</p> <p>There is no primary data included.</p> <p>Supplementary material and glossary contain mathematical details and proofs rather than any primary data sets.</p&gt

Symbiota2: Enabling greater collaboration and flexibility in mobilizing biodiversity data

Symbiota, the most used biodiversity content management system in the United States, has helped mobilize over 35 million specimen records from over 750 natural history collections via 40+ separate installations. Most Symbiota records come from natural history collections but some Symbiota instances also incorporate records from observations, images, publications, and gardens. Symbiota serves as both a data management system for entering, annotating, and cleaning occurrence data, images and associated specimen data (e.g., genetic sequences, images, publications) and as a primary aggregator/publisher for data stored in any database system that can export to a comma separated value (csv) file. Symbiota integrates and displays data and images from many resources in multiple formats, some of which appeal primarily to researchers, others to land managers, educators, and the general public. After nearly 20 years, Symbiota is going through a major software revision through Symbiota2, a US National Science Foundation-funded project. The broad goals of Symbiota2 are to make it easier for developers to add new functionality, to improve usability, and to help site managers administer a site. Symbiota2 will have a plugin-based architecture that will allow developers to encapsulate functionality in a plugin. Symbiota2 will improve usability by supporting off-line use, enabling Wordpress (content-managment system) integration, and having a customizable user interface.  Symbiota2 will help site managers by simplifying installation and management of a site. The three-year project is on-going, but so far we have created a Symbiota2 GithHub repository and a Docker image with all the necessary components for installing, configuring, and running Symbiota2, an object relational mapping (ORM) of the tables in the database management system (DBMS), and web services to connect to the DBMS via the ORM. We used Doctrine 2 for the ORM and API-Platform for the web services.  By the third quarter of 2019, we anticipate deploying the plugin framework to encourage developers to create new functionality for biodiversity content management.

Supplementary material for: Phylogenetic biodiversity metrics should account for both accumulation and attrition of evolutionary heritage

<p>Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features and other sources of variety through causes other than extinction. Here we introduce `EvoHeritage', a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.</p><p>R for use of code, otherwise PDF and CSV readers are needed to access the files.</p><p>Funding provided by: Leverhulme Trust<br>Crossref Funder Registry ID: https://ror.org/012mzw131<br>Award Number: RF-2022-497</p><p>Funding provided by: New Zealand Marsden Fund*<br>Crossref Funder Registry ID: <br>Award Number: MFPUOC2005</p><p>Data was reprocessed from published sources as described in the associated manuscript methods section</p> <p>There is no primary data included.</p> <p>Supplementary material and glossary contain mathematical details and proofs rather than any primary data sets.</p&gt

The Value of Agricultural Voucher Specimens

Voucher specimens are the ultimate raw data of biodiversity studies because they document the interpretation of the names used in papers and reports resulting from such studies. The value of voucher specimens is increased by making their records web-accessible but they can be further enhanced by linking them to other online resources, particularly if the links are birectional.  In this presentation, we discuss the potential benefits of such links for a group of agricultural significance, the Triticeae, a tribe of grasses that includes wheat, barley and rye among its 300+ species. The late Dr. D.R. Dewey conducted extensive cytogenetic studies in the tribe and deposited voucher specimens in the herbarium of Utah State University. Some of the voucher specimens were collected in the region but the majority were grown from germplasm accessions obtained from GRIN, the United States Department of Agriculture's Germplasm Resources Information Network. The specimen labels of the GRIN vouchers hold minimal information but one item that is present is the “PI Number” or GRIN identifier. Linking the GRIN vouchers to data in the GRIN database gives access to the original collection information, which is often complete enough to permit georeferencing the specimen, thereby enabling it and any derived information to be associated with the environmental parameters at the point of collection. The links could also be used to disseminate changes in identification of the voucher specimen to genebanks with duplicates of the original accession. The PI numbers also link the specimens to trait data deposited in the world’s genebank system and to publications in which the accession was cited, regardless of whether they relate to the original intent of the seed collectors. The impediment is that few collection databases are designed for effective capture of genebank identifiers. Another problem, from a taxonomic perspective, is that such stored trait information is of agricultural but not taxonomic value. Thus, one challenge is to modify specimen database systems so that they can effectively store taxonomically useful data; the other is to persuade those working on a taxonomic group to identify, score, and share data about core taxonomically useful characters for the group. Such “databases” currently exist, if at all, as a spreadsheet on an individual’s computer and may represent hours of labor measuring multiple features of individual specimens. Another potential linkage for many herbarium specimens is the Index of Plant Chromosome Numbers (IPCN). Again, one problem is providing easy access to the linking fields in both IPCN and the collection database; another is the lack of funding for maintaining IPCN. Linking specimens to sequence data is, by comparison, relatively simple but it would be useful for herbarium and genebank managers to know when the specimens/accessions they curate or have duplicates of have been used in a molecular study. Moreover, GenBank needs to have a mechanism for reporting that the identification of a voucher specimen has been changed. Our interest in these questions arises from a decision by The International Triticeae Consortium, a group that shares a common interest in members of the Triticeae, to pursue development of a web site that would provide access to data about the tribe’s members. Because of the economic importance of wheat, barley, and rye, the tribe is studied in almost every country. It is also the subject of significant taxonomic disagreement, an aspect that can present an impediment to those working with its members. Although the presentation will focus on the Triticeae, the approach and principles involved would apply to any taxonomic group.

Determining marine bioregions : A comparison of quantitative approaches

Areas that contain ecologically distinct biological content, called bioregions, are a central component to spatial and ecosystem-based management. We review and describe a variety of commonly used and newly developed statistical approaches for quantitatively determining bioregions. Statistical approaches to bioregionalization can broadly be classified as two-stage approaches that either 'Group First, then Predict' or 'Predict First, then Group', or a newer class of one-stage approaches that simultaneously analyse biological data with reference to environmental data to generate bioregions. We demonstrate these approaches using a selection of methods applied to simulated data and real data on demersal fish. The methods are assessed against their ability to answer several common scientific or management questions. The true number of simulated bioregions was only identified by both of the one-stage methods and one two-stage method. When the number of bioregions was known, many of the methods, but not all, could adequately infer the species, environmental and spatial characteristics of bioregions. One-stage approaches, however, do so directly via a single model without the need for separate post-hoc analyses and additionally provide an appropriate characterization of uncertainty. One-stage approaches provide a comprehensive and consistent method for objectively identifying and characterizing bioregions using both biological and environmental data. Potential avenues of future development in one-stage methods include incorporating presence-only and multiple data types as well as considering functional aspects of bioregions.Peer reviewe