Stroke-Specific Swimming Critical Speed Testing: Balancing Feasibility and Scientific Rigour.

This study aimed to assess the reliability of a two-distance critical speed protocol in the specialist strokes of national-level swimmers and understand the practical feasibility of extending the protocol to increase its validity. Thirty-two national-level swimmers (butterfly n = 7; backstroke n = 8; breaststroke n = 7; front crawl n = 10) swum three 200-m and three 400-m performance trials over a three-week period. Critical speed and supra-critical speed distance capacity were computed from the linear modelling of the distance-time relationship. Swimmers were subsequently asked whether they felt they could or would want to complete an 800-m trial as part of a three-distance critical speed protocol to enhance validity. Both 200-m and 400-m performances (coefficient of variation of < 2%) and derived critical speed (typical error of ≤ 0.04 m·s-1; coefficient of variation of < 4%) were reliable for all strokes, while supra-critical speed distance capacity (typical error from 4 to 9 m; coefficient of variation from 13 to 45%) was not reliable. Response rates to the follow-up questions were 100%. Few butterfly swimmers said they felt they could complete an 800-m performance trial (39%), with more positive responses for breaststroke (71%), backstroke (100%), and front crawl swimmers (100%). Butterfly swimmers were significantly less likely to say they could or would want to complete an 800-m trial than backstroke and front crawl swimmers (p < 0.05). Including a third distance 800-m trial to increase critical speed validity would not be acceptable to butterfly swimmers, would be challenging to breaststroke swimmers, but would be acceptable to front crawl and backstroke swimmers.

Envisaging a global infrastructure to exploit the potential of digitised collections.

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

Microbial diversity across compartments in an aquaponic system and its connection to the nitrogen cycle.

Aquaponics combines hydroponic crop production with recirculating aquaculture. These systems comprise various compartments (fish tank, biofilter, sump, hydroponic table, radial flow settler and anaerobic digester), each with their own specific environmental pressures, which trigger the formation of unique microbial communities. Triplicated aquaponic systems were used to investigate the microbial community composition during three lettuce growing cycles. The sampling of individual compartments allowed community patterns to be generated using amplicon sequencing of bacterial and archaeal 16S rRNA genes. Nitrifying bacteria were identified in the hydroponic compartments, indicating that these compartments may play a larger role than previously thought in the system's nitrogen cycle. In addition to the observed temporal changes in community compositions within the anaerobic compartment, more archaeal reads were obtained from sludge samples than from the aerobic part of the system. Lower bacterial diversity was observed in fresh fish feces, where a highly discrete gut flora composition was seen. Finally, the most pronounced differences in microbial community compositions were observed between the aerobic and anaerobic loops of the system, with unique bacterial compositions in each individual compartment.

Biodiversity data and new species descriptions of polychaetes from offshore waters of the Falkland Islands, an area undergoing hydrocarbon exploration.

Benthic environmental impact assessments and monitoring programs accompanying offshore hydrocarbon industry activities result in large collections of benthic organisms. Such collections offer great potential for systematics, biodiversity and biogeography research, but these opportunities are only rarely realised. In recent decades, the hydrocarbon industry has started exploration activities in offshore waters off the Falkland Islands. A large collection of ca. 25,000 polychaete (Annelida) specimens, representing some 233 morphological species was processed at the Natural History Museum, London. Taxonomic assessment led to recognition of many polychaete species that are new to science. The existing taxonomic literature for the region is outdated and many species in existing literature are likely misidentifications. Initially, an online taxonomic guide (http://falklands.myspecies.info) was created, to provide a single taxonomic source for 191 polychaete species to standardise identification across different environmental contractors working in Falkland Islands. Here, this effort is continued to make data available for 18,015 specimens through publication of raw biodiversity data, checklist with links to online taxonomic information and formal descriptions of five new species. New species were chosen across different families to highlight the taxonomic novelty of this area: Apistobranchus jasoni Neal & Paterson, sp. nov. (Apistobranchidae), Leitoscoloplos olei Neal & Paterson, sp. nov. (Orbiniidae), Prosphaerosyllis modinouae Neal & Paterson, sp. nov. (Syllidae) and Aphelochaeta falklandica Paterson & Neal, sp. nov., and Dodecaceria saeria Paterson & Neal, sp. nov. (both Cirratulidae). The potential of the Falkland Islands material to provide up to date informationfor known species described in the literature is also highlighted by publishing images and redescription of Harmothoe anderssoni Bergström, 1916 and Aphelochaeta longisetosa (Hartmann-Schröder, 1965). Biodiversity and abundance data are made available through a DarwinCore database, including material collected from 83 stations at Sea Lion developmental oil field in North Falklands Basin and voucher specimens' data collected from exploratory oil wells in East Falklands Basin.

Collaborative response to arsenic-contaminated soil in an Appalachian Kentucky neighborhood.

The aim of this study was to identify factors associated with an increased exposure to arsenic-contaminated soil in a Kentucky neighborhood as part of collaborative public health response. An exposure assessment survey was administered to residents and toenail clippings and soil samples analyzed for arsenic concentration. The associations between exposure variables and arsenic concentrations were evaluated using a multivariate-generalized estimating equation. An ecological assessment of cancer incidence in the community was also conducted using standardized incidence ratio maps. Median toenail arsenic was 0.48 micrograms/gram (µg/g), twice the expected regional level of 0.2 µg/g. Mean residence surface soil arsenic level was 64.8 ppm. An increase of 1 ppm of residence concentration was significantly associated with a 0.003 µg/g rise in toenail levels. Concentrations for respondents who engaged in digging were 0.68 µg/g significantly higher compared to individuals who did not. No significantly elevated rates of lung or bladder cancer were observed in the affected ZIP codes. Living in areas with high soil arsenic contamination might lead to (1) increased exposure; (2) elevated residence soil arsenic concentrations and (3) the action of digging in the soil was associated with elevated toenail arsenic levels. Based upon elevated soil levels identified, residents were recommended to move from the contaminated environment until remediation was complete. Additional recommendations included regular health-care follow-up.

The Natural History Museum Data Portal.

The Natural History Museum, London (NHM), generates and holds some of the largest global data sets relating to the biological and geological diversity of the natural world. A majority of these data were, until 2015, not widely accessible, and, even when published, were typically hard to find, poorly documented and in formats that impede discovery and integration. To better serve the bespoke needs of user communities outside and within the NHM, a dedicated data portal was developed to surface these data sets and provide a sustainable platform to encourage their citation and reuse. This paper describes the technical development of the data portal, from its inception to beta launch in December 2015, its first 2 years of operation, and future plans for the project. It outlines the development principles adopted for this prototypical project, which subsequently informed new digital project management methodologies at the NHM. The process of developing the data portal acted as a driver to implement policies necessary to encourage a culture of data sharing at the NHM.

Comparison of Heart-Rate-Variability Recording With Smartphone Photoplethysmography, Polar H7 Chest Strap, and Electrocardiography.

PURPOSE: To establish the validity of smartphone photoplethysmography (PPG) and heart-rate sensor in the measurement of heart-rate variability (HRV). METHODS: 29 healthy subjects were measured at rest during 5 min of guided breathing and normal breathing using smartphone PPG, a heart-rate chest strap, and electrocardiography (ECG). The root mean sum of the squared differences between R-R intervals (rMSSD) was determined from each device. RESULTS: Compared to ECG, the technical error of estimate (TEE) was acceptable for all conditions (average TEE CV% [90% CI] = 6.35 [5.13; 8.5]). When assessed as a standardized difference, all differences were deemed "trivial" (average standard difference [90% CI] = 0.10 [0.08; 0.13]). Both PPG- and heart-rate-sensor-derived measures had almost perfect correlations with ECG (R = 1.00 [0.99; 1.00]). CONCLUSION: Both PPG and heart-rate sensors provide an acceptable agreement for the measurement of rMSSD when compared with ECG. Smartphone PPG technology may be a preferred method of HRV data collection for athletes due to its practicality and ease of use in the field.

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science.

The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project's operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.

Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool.

GeoCAT is an open source, browser based tool that performs rapid geospatial analysis to ease the process of Red Listing taxa. Developed to utilise spatially referenced primary occurrence data, the analysis focuses on two aspects of the geographic range of a taxon: the extent of occurrence (EOO) and the area of occupancy (AOO). These metrics form part of the IUCN Red List categories and criteria and have often proved challenging to obtain in an accurate, consistent and repeatable way. Within a familiar Google Maps environment, GeoCAT users can quickly and easily combine data from multiple sources such as GBIF, Flickr and Scratchpads as well as user generated occurrence data. Analysis is done with the click of a button and is visualised instantly, providing an indication of the Red List threat rating, subject to meeting the full requirements of the criteria. Outputs including the results, data and parameters used for analysis are stored in a GeoCAT file that can be easily reloaded or shared with collaborators. GeoCAT is a first step toward automating the data handling process of Red List assessing and provides a valuable hub from which further developments and enhancements can be spawned.

Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys.

We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue.

Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.

The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author's database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life.

BACKGROUND: Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite series of smaller studies. The discipline's failure to meaningfully connect these small studies with natural history's goal has made it hard to demonstrate the value of natural history to a wider scientific community. Digital technologies provide the means to bridge this gap. RESULTS: We describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science. Scratchpads cater to the particular needs of individual research communities through a common database and system architecture. This is flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and constituent data. Our data model supports web services on standardised data elements that might be used by related initiatives such as GBIF and the Encyclopedia of Life. A Scratchpad allows users to organise data around user-defined or imported ontologies, including biological classifications. Automated semantic annotation and indexing is applied to all content, allowing users to navigate intuitively and curate diverse biological data, including content drawn from third party resources. A system of archiving citable pages allows stable referencing with unique identifiers and provides credit to contributors through normal citation processes. CONCLUSION: Our framework http://scratchpads.eu/ currently serves more than 1,100 registered users across 100 sites, spanning academic, amateur and citizen-science audiences. These users have generated more than 130,000 nodes of content in the first two years of use. The template of our architecture may serve as a model to other research communities developing data publishing frameworks outside biodiversity research.