Singing from the Grave: DNA from a 180 Year Old Type Specimen Confirms the Identity of Chrysoperla carnea (Stephens)

Copyright: © 2015 Price et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

IMp: The customizable LEGO® Pinned Insect Manipulator

ORCID 0000-0001-8684-8421This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor

Global Cicada Sound Collection I: Recordings from South Africa and Malawi by B. W. Price & M. H. Villet and harvesting of BioAcoustica data by GBIF

The file attached is the published version of the article. © Baker E et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.NHM Repositor

Evaluation of DNA barcode libraries used in the UK and developing an action plan to fill priority gaps

There are approximately 76,000 eukaryote species recognised in the UK, and while we know some of them in great detail, the majority of these species are poorly known, and hundreds of new species are discovered each year. DNA barcoding uses a short, standardised segment of an organism’s genome for identification by comparison to a reference library; however, the UK lags behind several countries in Europe and North America in that we lack trusted, reliable and openly accessible reference sequences for key UK taxa. This report is the first step in rectifying this by engaging diverse stakeholders to facilitate collaboration and coordination; providing robust stakeholder-based and independent assessment of the current state of reference libraries available for all known UK taxa; and prioritising key taxa. A survey was developed and shared with the UK research and end user community, receiving 80 responses from a wide range of stakeholders and covering the focal taxa / assemblages and habitats; the DNA reference libraries in use, their quality assurance and perceived coverage. A formal gap analysis of the public DNA data in major DNA reference libraries highlighted that an estimated 52% of UK species have publicly available DNA data of some sort; however, coverage in gene specific reference libraries varies greatly (eg 2 – 52%), as does the associated quality assurance. Priority taxa highlighted by end users had coverage in reference libraries ranging from almost complete, in the case of known invasive non-native species, to significant coverage (71%) for taxa with conservation designations. However, these data also vary by kingdom and reference library, as does the associated quality assurance. If taking a strict requirement of DNA data provided by UK specimens and held in UK repositories, for robust QC and QA, then the proportion of UK species with public DNA data in reference libraries falls to less than 4% in the largest reference library assessed (BOLD). While standard genes for DNA-based identification have essentially been established, more work is required to establish the priority taxa required for regulatory delivery in contrast to taxa that are surveyed in a non-regulatory framework. Several barriers to the development of barcode libraries were highlighted, the most relevant being sustained large scale funding, expertise, capacity, laboratory skills and equipment, quality control and assurance, collecting logistics (eg permits and access) and communication. Significant opportunities identified include a large network of interested experts, several organisations with significant delivery capabilities, current large-scale projects and funding opportunities, emerging technologies and the economy of scale for DNA sequencing. Following a stakeholder workshop, we have outlined a concise action plan to provide reliable, open access reference sequences, linked to open access vouchers, identified by known experts, to facilitate UK academic and regulatory aims.This report is published by Natural England under the Open Government Licence - OGLv3.0 for public sector information. You are encouraged to use, and reuse, information subject to certain conditions. For details of the licence visit Copyright. Natural England photographs are only available for non-commercial purposes. If any other information such as maps or data cannot be used commercially this will be made clear within the report. ISBN 978-1-78354-671-8 © Natural England and other parties 2020 © Trustees of the Natural History Museum, Londo

The cicadas (Hemiptera: Cicadidae) of India, Bangladesh, Bhutan, Myanmar, Nepal and Sri Lanka: an annotated provisional catalogue, regional checklist and bibliography

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor

Ahead of the curve: three approaches to mass digitisation of vials with a focus on label data capture

There has been little research on novel approaches to digitising liquid-preserved natural history specimens stored in jars or vials. This paper discusses and analyses three different prototypes for high-throughput digitisation using cheap, readily available components. This paper has been written for other digitisation teams or curators who want to trial or improve upon these new digitisation approaches in liquid preserved collections.This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor

Metabarcoding unsorted kick‐samples facilitates macroinvertebrate‐based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA

Pereira‐da‐Conceicoa, L, Elbrecht, V, Hall, A, Briscoe, A, Barber‐James, H, Price, B. Metabarcoding unsorted kick‐samples facilitates macroinvertebrate‐based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA. Environmental DNA. 2020; 00: 1– 19. https://doi.org/10.1002/edn3.116© 2020 The Authors. Environmental DNA published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The attached file is the published pdf

Species‐level image classification with convolutional neural network enables insect identification from habitus images

1. Changes in insect biomass, abundance, and diversity are challenging to track at sufficient spatial, temporal, and taxonomic resolution. Camera traps can capture habitus images of ground-dwelling insects. However, currently sampling involves manually detecting and identifying specimens. Here, we test whether a convolutional neural network (CNN) can classify habitus images of ground beetles to species level, and estimate how correct classification relates to body size, number of species inside genera, and species identity. 2. We created an image database of 65,841 museum specimens comprising 361 carabid beetle species from the British Isles and fine-tuned the parameters of a pretrained CNN from a training dataset. By summing up class confidence values within genus, tribe, and subfamily and setting a confidence threshold, we trade-off between classification accuracy, precision, and recall and taxonomic resolution. 3. The CNN classified 51.9% of 19,164 test images correctly to species level and 74.9% to genus level. Average classification recall on species level was 50.7%. Applying a threshold of 0.5 increased the average classification recall to 74.6% at the expense of taxonomic resolution. Higher top value from the output layer and larger sized species were more often classified correctly, as were images of species in genera with few species. 4. Fine-tuning enabled us to classify images with a high mean recall for the whole test dataset to species or higher taxonomic levels, however, with high variability. This indicates that some species are more difficult to identify because of properties such as their body size or the number of related species. 5. Together, species-level image classification of arthropods from museum collections and ecological monitoring can substantially increase the amount of occurrence data that can feasibly be collected. These tools thus provide new opportunities in understanding and predicting ecological responses to environmental change.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. The attached file is the published pdf

Repeated bedside echocardiography in children with respiratory failure

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to verify the benefits and limitations of repeated bedside echocardiographic examinations in children during mechanical ventilation. For the purposes of this study, we selected the data of over a time period from 2006 to 2010.</p> <p>Methods</p> <p>A total of 235 children, average age 3.21 (SD 1.32) years were included into the study and divided into etiopathogenic groups. High-risk groups comprised: Acute lung injury and acute respiratory distress syndrome (ALI/ARDS), return of spontaneous circulation after cardiopulmonary resuscitation (ROSC), bronchopulmonary dysplasia (BPD), cardiomyopathy (CMP) and cardiopulmonary disease (CPD). Transthoracic echocardiography was carried out during mechanical ventilation. The following data were collated for statistical evaluation: right and left ventricle myocardial performance indices (RV MPI; LV MPI), left ventricle shortening fraction (SF), cardiac output (CO), and the mitral valve ratio of peak velocity of early wave (E) to the peak velocity of active wave (A) as E/A ratio. The data was processed after a period of recovery, i.e. one hour after the introduction of invasive lines (time-1) and after 72 hours of comprehensive treatment (time-2). The overall development of parameters over time was compared within groups and between groups using the distribution-free Wilcoxons and two-way ANOVA tests.</p> <p>Results</p> <p>A total of 870 echocardiographic examinations were performed. At time-1 higher average values of RV MPI (0.34, SD 0.01 vs. 0.21, SD 0.01; p < 0.001) were found in all groups compared with reference values. Left ventricular load in the high-risk groups was expressed by a higher LV MPI (0.39, SD 0.13 vs. 0.29, SD 0.02; p < 0.01) and lower E/A ratio (0.95, SD 0.36 vs. 1.36, SD 0.64; p < 0.001), SF (0.37, SD 0.11 vs. 0.47, SD 0.02; p < 0.01) and CO (1.95, SD 0.37 vs. 2.94, SD 1.03; p < 0.01). At time-2 RV MPI were lower (0.25, SD 0.02 vs. 0.34, SD 0.01; p < 0.001), but remained higher compared with reference values (0.25, SD 0.02 vs. 0.21, SD 0.01; p < 0.05). Other parameters in high-risk groups were improved, but remained insignificantly different compared with reference values.</p> <p>Conclusion</p> <p>Echocardiography complements standard monitoring of valuable information regarding cardiac load in real time. Chest excursion during mechanical ventilation does not reduce the quality of the acquired data.</p