Performant barcode decoding for herbarium specimen images using vector-assisted region proposals (VARP).

PREMISE: The scale and associated costs of herbarium digitization make process automation appealing. One such process for many workflows is the association of specimen image files with barcode values stored with the specimen. Here, an innovation is presented that improves the speed and accuracy of decoding barcodes from specimen images. METHODS AND RESULTS: Geometric features common in barcodes are used to identify the regions of specimen images that are likely to contain a barcode. The proposed regions are then combined into a significantly reduced composite image that is decoded using traditional barcode reading libraries. Tested against existing solutions, this method demonstrated the highest success rate (96.5%) and the second fastest processing time (617 ms). CONCLUSIONS: This method was developed to support a larger effort to automate specimen image post-processing in real-time, highlighting the importance of execution time. Although initially designed for herbarium digitization, this method may be useful for other high-resolution applications.

Wanted: Standards for FAIR taxonomic concept representations and relationships.

Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption of one-to-one relationships between names and biological entities breaks down (Remsen 2016, Franz and Sterner 2018). Taxonomic treatments and checklists provide authoritative information about the correct usage of names for species, including operational representations of the meanings of those names in the form of range maps, reference genetic sequences, or diagnostic traits. They increasingly provide taxonomic intelligence in the form of precise description of the semantic relationships between different published names in the literature. Making this authoritative information Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al. 2016) would be a transformative advance for biodiversity data sharing and help drive adoption and novel extensions of existing standards such as the Taxonomic Concept Schema and the OpenBiodiv Ontology (Kennedy et al. 2006, Senderov et al. 2018). We call for the greater, global Biodiversity Information Standards (TDWG) and taxonomy community to commit to extending and expanding on how FAIR applies to biodiversity data and include practical targets and criteria for the publication and digitization of taxonomic concept representations and alignments in taxonomic treatments, checklists, and backbones.

Review of Irish patients meeting ST elevation criteria during the COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic has seen the introduction of important public health measures to minimise the spread of the virus. We aim to identify the impact government restrictions and hospital-based infection control procedures on ST elevation myocardial infarction (STEMI) care during the COVID-19 pandemic. METHODS: Patients meeting ST elevation criteria and undergoing primary percutaneous coronary intervention from 27 March 2020, the day initial national lockdown measures were announced in Ireland, were included in the study. Patients presenting after the lockdown period, from 18 May to 31 June 2020, were also examined. Time from symptom onset to first medical contact (FMC), transfer time and time of wire cross was noted. Additionally, patient characteristics, left ventricular ejection fraction, mortality and biochemical parameters were documented. Outcomes and characteristics were compared against a control group of patients meeting ST elevation criteria during the month of January. RESULTS: A total of 42 patients presented with STEMI during the lockdown period. A significant increase in total ischaemic time (TIT) was noted versus controls (8.81 hours (±16.4) vs 2.99 hours (±1.39), p=0.03), with increases driven largely by delays in seeking FMC (7.13 hours (±16.4) vs 1.98 hours (±1.46), p=0.049). TIT remained significantly elevated during the postlockdown period (6.1 hours (±5.3), p=0.05), however, an improvement in patient delays was seen versus the control group (3.99 hours (±4.5), p=0.06). There was no difference seen in transfer times and door to wire cross time during lockdown, however, a significant increase in transfer times was seen postlockdown versus controls (1.81 hours (±1.0) vs 1.1 hours (±0.87), p=0.004). CONCLUSION: A significant increase in TIT was seen during the lockdown period driven mainly by patient factors highlighting the significance of public health messages on public perception. Additionally, a significant delay in transfer times to our centre was seen postlockdown.

Estimating herbarium specimen digitization rates: Accounting for human experience.

PREMISE: Herbaria are invaluable sources for understanding the natural world, and in recent years there has been a concerted effort to digitize these collections. To organize such efforts, a method for estimating the necessary labor is desired. This work analyzes digitization productivity reports of 105 participants from eight herbaria, deriving generalized labor estimates that account for human experience. METHODS AND RESULTS: Individuals' rates of digitization were grouped based on cumulative time performing each task and then used to estimate a series of generalized labor projection models. In most cases, productivity was shown to improve with experience, suggesting longer technician retention can reduce labor requirements by 20%. CONCLUSIONS: Using student labor is a common tactic for digitization efforts, and the resulting outreach exposes future professionals to natural history collections. However, overcoming the learning curve should be considered when estimating the labor necessary to digitize a collection.

Effects of non-invasive respiratory support on gas exchange and outcomes in COVID-19 outside the ICU.

Non-invasive respiratory support (NRS) outside of the ICU has played an important role in the management of COVID-19 pneumonia. There is little data to guide selection of NRS modality. We present outcomes of NRS outside the ICU and discuss the effects of NRS on gas exchange with implications for management.

Enabling automated herbarium sheet image post-processing using neural network models for color reference chart detection.

PREMISE: Large-scale efforts to digitize herbaria have resulted in more than 18 million publicly available Plantae images on sites such as iDigBio. The automation of image post-processing will lead to time savings in the digitization of biological specimens, as well as improvements in data quality. Here, new and modified neural network methodologies were developed to automatically detect color reference charts (CRC), enabling the future automation of various post-processing tasks. METHODS AND RESULTS: We used 1000 herbarium specimen images from 52 herbaria to test our novel neural network model, ColorNet, which was developed to identify CRCs smaller than 4 cm2, resulting in a 30% increase in accuracy over the performance of other state-of-the-art models such as Faster R-CNN. For larger CRCs, we propose modifications to Faster R-CNN to increase inference speed. CONCLUSIONS: Our proposed neural networks detect a range of CRCs, which may enable the automation of post-processing tasks found in herbarium digitization workflows, such as image orientation or white balance correction.

A born-digital field-to-database solution for collections-based research using collNotes and collBook.

PREMISE: The digitization of natural history collections includes transcribing specimen label data into standardized formats. Born-digital specimen data initially gathered in digital formats do not need to be transcribed, enabling their efficient integration into digitized collections. Modernizing field collection methods for born-digital workflows requires the development of new tools and processes. METHODS AND RESULTS: collNotes, a mobile application, was developed for Android and iOS to supplement traditional field journals. Designed for efficiency in the field, collNotes avoids redundant data entries and does not require cellular service. collBook, a companion desktop application, refines field notes into database-ready formats and produces specimen labels. CONCLUSIONS: collNotes and collBook can be used in combination as a field-to-database solution for gathering born-digital voucher specimen data for plants and fungi. Both programs are open source and use common file types simplifying either program's integration into existing workflows.