Antibiotic Timing and Progression to Septic Shock Among Patients in the ED With Suspected Infection.

BACKGROUND: Recent medical society opinions have questioned the use of early antimicrobials in patients with sepsis, but without septic shock. RESEARCH QUESTION: Is time from ED presentation to administration of antibiotics associated with progression to septic shock among patients with suspected infection? STUDY DESIGN AND METHODS: This was a retrospective cohort study from March 2007 through March 2020. All adults with suspected infection and first antimicrobial administered within 24 h of triage were included. Patients with shock on presentation were excluded. We performed univariate and multivariate logistic regression analyses predicting progression to septic shock. RESULTS: Seventy-four thousand one hundred fourteen patient encounters were included in the study. Five thousand five hundred ten patients (7.4%) progressed to septic shock. Of the patients who progressed to septic shock, 88% had received antimicrobials within the first 5 h from triage. In the multivariate logistic model, time (in hours) to first antimicrobial administration showed an OR of 1.03 (95% CI, 1.02-1.04; P < .001) for progression to septic shock and 1.02 (95% CI, 0.99-1.04; P = .121) for in-hospital mortality. When adjusted for severity of illness, each hour delayed until initial antimicrobial administration was associated with a 4.0% increase in progression to septic shock for every 1 h up to 24 h from triage. Patients with positive quick Sequential Organ Failure Assessment (qSOFA) results were given antibiotics at an earlier time point than patients with positive systemic inflammatory response syndrome (SIRS) score (0.82 h vs 1.2 h; P < .05). However, median time to septic shock was significantly shorter (P < .05) for patients with positive qSOFA results at triage (11.2 h) compared with patients with positive SIRS score at triage (26 h). INTERPRETATION: Delays in first antimicrobial administration in patients with suspected infection are associated with rapid increases in likelihood of progression to septic shock. Additionally, qSOFA score has higher specificity than SIRS score for predicting septic shock, but is associated with a worse outcome, even when patients receive early antibiotics.

Chord Bunch Walks for Recognizing Naturally Self-Overlapped and Compound Leaves.

Effectively describing and recognizing leaf shapes under arbitrary variations, particularly from a large database, remains an unsolved problem. In this research, we attempted a new strategy of describing leaf shapes by walking and measuring along a bunch of chords that pass through the shape. A novel chord bunch walks (CBW) descriptor is developed through the chord walking behavior that effectively integrates the shape image function over the walked chord to reflect both the contour features and the inner properties of the shape. For each contour point, the chord bunch groups multiple pairs of chords to build a hierarchical framework for a coarse-to-fine description that can effectively characterize not only the subtle differences among leaf margin patterns but also the interior part of the shape contour formed inside a self-overlapped or compound leaf. Instead of using optimal correspondence based matching, a Log-Min distance that encourages one-to-one correspondences is proposed for efficient and effective CBW matching. The proposed CBW shape analysis method is invariant to rotation, scaling, translation, and mirror transforms. Five experiments, including image retrieval of compound leaves, image retrieval of naturally self-overlapped leaves, and retrieval of mixed leaves on three large scale datasets, are conducted. The proposed method achieved large accuracy increases with low computational costs over the state-of-the-art benchmarks, which indicates the research potential along this direction.

Chinese species of Pediobius Walker (Hymenoptera: Eulophidae).

The Chinese species of Pediobius Walker, 1846 are treated in this paper, resulting in 34 species, of which 5 are newly described: P. bisulcatus Cao & Zhu sp. n., P. elongatus Cao & Zhu sp. n., P.petiolapilus Cao & Zhu sp. n., P. prominentis Cao & Zhu, sp. n., and P. tortricida Cao & Zhu, sp. n. Nine species are also newly recorded from China: P. anomalus (Gahan, 1920), P. bethylicidus Kerrich, 1973, P. bruchicida (Rondani, 1872), P. cassidae Erdös, 1958, P. claviger (Thomson, 1878), P. erionotae Kerrich, 1973, P. phragmitis Boucek, 1965, P. saulius (Walker, 1839), and P. tetratomus (Thomson, 1878). Four new synonyms are proposed: P. illiberidis Liao, 1987 under P. pyrgo (Walker, 1839) syn. n., P. planiceps Sheng & Kamijo, 1992 under P. inexpectatus Kerrich, 1973 syn. n., P. sinensis Sheng & Wang, 1994 under P. facialis (Giraud, 1863) syn. n., and P. songshaominus Liao, 1987 under P. yunanensis Liao, 1987 syn. n. The species-group concept is used to compare similar species, of which eight are recognized in China including two newly recognized groups: the cassidae-group and the crassicornis-group. One species complex, the P. eubius complex, is also recognized. An updated checklist of the Chinese species of Pediobius is provided, with species-group placement. New host records for Pediobius species from China are summarized in a table and valid species possibly present in China but not included in this study in another table. A key to all known females and males of Chinese Pediobius is also provided.

Biodiversity analysis in the digital era.

This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in 'Big Data' biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making.This article is part of the themed issue 'From DNA barcodes to biomes'.

Descriptions of three new species of Dzhanokmenia (Hymenoptera: Eulophidae) from China.

Three new species of Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae: Tetrastichinae), D. muleica Li, Wang & Hu sp. n., D. karamayica Li, Wang & Zhu sp. n. and D. gobica Li, Wang & Zhu sp. n. from Xinjiang Uyghur Autonomous Region of China are described and illustrated. A key to all known species of the genus is provided.

Two new Aprostocetus species (Hymenoptera: Eulophidae: Tetrastichinae), fortuitous parasitoids of invasive eulophid gall inducers (Tetrastichinae) on Eucalyptus and Erythrina.

Two closely related new species of Aprostocetus Westwood (Hymenoptera: Eulophidae: Tetrastichinae) are described as fortuitous parasitoids of invasive gall inducers in two other genera of Tetrastichinae, Leptocybe Fisher & LaSalle and Quadrastichus Girault. Aprostocetus causalis La Salle & Wu is a parasitoid of Leptocybe invasa Fisher & La Salle on Eucalyptus spp. (Myrtaceae) in China and Thailand, and A. felix La Salle, Yang & Lin is a parasitoid of Quadrastichus erythrinae Kim on Erythrina spp. (Fabaceae) in Taiwan. Epitetrastichus nigriventris Girault, 1913 is removed from synonymy from Aprostocetus gala (Walker), and treated as the valid species A. nigriventris (Girault). 

A new species of Zagrammosoma Ashmead (Hymenoptera, Eulophidae) from Qinghai Province, China.

The new species Zagrammosoma dulanense Cao & Zhu, sp. n., from Qinghai Province, China, is described and illustrated. All type specimens were reared from the pupae of Micrurapteryx sophorivora Kuznetzov & Tristan (Lepidoptera: Gracillariidae), a leafmining moth attacking the plant Thermopsis lanceolata R. Br. (Fabaceae). A key to the three known Asian species of Zagrammosoma is provided. All specimens are deposited in the Insect Collection, the Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

Two new species of Selitrichodes (Hymenoptera: Eulophidae: Tetrastichinae) inducing galls on Casuarina (Casuarinaceae).

Two new species of gall-inducing wasps, Selitrichodes casuarinae Fisher & La Salle sp. n. and Selitrichodes utilis Fisher & La Salle sp. n., are described from Micronesia (Guam, Rota and Palau Islands) and Australia respectively. These species induce galls on Casuarina and can cause extensive damage to the trees. Their status as pest or beneficial species is discussed.

Capturing natural-colour 3D models of insects for species discovery and diagnostics.

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity-past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.

Biodiversity into your hands - A call for a virtual global natural history 'metacollection'.

BACKGROUND: Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis. DISCUSSION: Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection.The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general.Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of "gems" of undescribed species hidden in museum accessions. SUMMARY: Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world's natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.

A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.

A specialist's audit of aggregated occurrence records: An 'aggregator's' perspective.

A recent ZooKeys' paper (Mesibov, 2013: http://www.pensoft.net/journal_home_page.php?journal_id=1&page=article&SESID=df7bcb35b02603283dcb83ee0e0af0c9&type=show&article_id=5111) has highlighted data quality issues in aggregated data sets, but did not provide a realistic way to address these issues. This paper provides an aggregator's perspective including ways that the whole community can help to address data quality issues. The establishment of GBIF and national nodes (national aggregators) such as the Atlas of Living Australia (ALA) have integrated and exposed a huge diversity of biological observations along with many associated issues. Much of the admirable work by Mesibov (2013) was enabled by having the data exposed. Data quality, one of the highest priorities for GBIF, the national nodes and other aggregators, depends on both automatic methods and community experts to detect and correct data issues. Not all issues can however be automatically detected or corrected, so community assistance is needed to help improve the quality of exposed biological data. We do need to improve the infrastructure and associated processes to more easily identify data issues and document all changes to ensure a full record is permanently and publicly available.

Whole-drawer imaging for digital management and curation of a large entomological collection.

Whole-drawer imaging is shown to be an effective tool for rapid digitisation of large insect collections. On-line, Whole-drawer images facilitate more effective collection management, virtual curation, and public engagement. The Whole-drawer imaging experience at the Australian National Insect Collection is discussed, with an explanation of workflow and examples of benefits.