Large-area imaging in tropical shallow water coral reef monitoring, research and restoration : A practical guide to survey planning, execution, and data extraction

This is a practical guide to the implementation of large-area imaging (LAI) for coral reef scientists. LAI refers to an approach to generate composite 3D (and derived 2D) image products from sequences of field-collected images using structure-from-motion (SfM) photogrammetry. Coral reef scientists conducting coral restoration, environmental monitoring, or research often require time series or high taxonomic resolution data to calculate metrics such as abundance or density, percent cover, species condition, and reef complexity. These data have a history of in situ collection by divers; however, the time-intensive challenge of traditional fieldwork approaches limits the volume and spatial extent of data collection and is therein a fundamental bottleneck for many restoration, monitoring, and research objectives. This is a practical guide to the implementation of large-area imaging (LAI) for coral reef scientists. LAI refers to an approach to generate composite 3D (and derived 2D) image products from sequences of field-collected images using structure-from-motion (SfM) photogrammetry. Coral reef scientists conducting coral restoration, environmental monitoring, or research often require time series or high taxonomic resolution data to calculate metrics such as abundance or density, percent cover, species condition, and reef complexity. These data have a history of in situ collection by divers; however, the time-intensive challenge of traditional fieldwork approaches limits the volume and spatial extent of data collection and is therein a fundamental bottleneck for many restoration, monitoring, and research objectives. LAI is a flexible, computationally reliant approach that emerged from the disciplines of engineering and computer vision. For most scenarios, the tools and software needed to conduct LAI have matured to the degree that little technical expertise is needed to effectively implement the approach. However, applications of LAI for coral reef science are still relatively new, and few comprehensive instructional materials have been designed specifically for a non-technical audience. Existing documentation is often case-specific, limited in scope, or not widely available. To make the LAI process more accessible to the coral reef community, the first part of this document provides a broad overview to LAI and its implementation. The approach is divided into four steps of the "LAI pipeline": 1- image collection, 2- model construction, 3ecological analysis, and 4- data curation. The key technical details of LAI are summarized, focusing on those aspects of the approach where user intervention is required, and a framework is provided to help guide project planning decisions. This guide is intended for a broad group of users, including first-time adopters as well as experienced professionals. The LAI approach described in Part I of this guide is compatible with most existing coral restoration, environmental monitoring, and research programs. While the information provided is relevant to work conducted across a spectrum of spatial scales and levels of resolution, the focus is on concepts related to the creation of LAI that allow for detailed taxonomic descriptions of benthic organisms at high levels of replication. Decisions made during both image collection and model construction can have huge implications for LAI resolution and the quality of the derived metrics. This report also provides best practices intended to ensure comparability of datasets into the future. Part II of the guide provides a series of standard operating procedures (SOPs) currently used by experienced groups for a wide range of objectives. The SOPs are briefly summarized by their respective authors with commentary designed to provide exposure to the different approaches. These SOPs are also available from the individual authors at their respective institutions, with links provided in Part II. The computational aspects of the LAI approach represent a rapidly evolving field. While efforts have been taken to present the state of the art, many of the technical details included here, from the algorithms used to the available computer hardware, will undoubtedly evolve dramatically over the next 2–5 years. Readers are encouraged to stay up to date on the technologies presented here and routinely visit the websites where the individual SOPs are hosted, as updates to these documents will be made as they become available

Experiences with IL-1 blockade in systemic juvenile idiopathic arthritis - data from the German AID-registry

BackgroundSystemic juvenile idiopathic arthritis (sJIA) is a complex disease with dysregulation of the innate immune system driven by cytokines. A major role is ascribed to interleukin-1 beta (IL-1 beta), supporting the autoinflammatory character of the disease and offering an effective blocking mechanism for treatment. Here we present clinical practice data from the German AID-registry for patients treated with IL-1 inhibition (IL-1i).MethodsIn 2009 a clinical and research consortium (AID-Net) was established, including an online AID-registry. Patients with documented sJIA diagnosis were identified. Data for this retrospective IL-1i study were recorded by 17 centers. Response to treatment was evaluated according to Wallace criteria and additionally by an own classifying clinical response system.ResultsIn 6years, 202 patients with confirmed sJIA were recorded in the AID-registry. Out of these, 111 children received therapy with Anakinra (ANA) (n=84, 39 f) and/or Canakinumab (CANA) (n=27, 15 f) at a median age of 8.7 y (range 0.6-19.1). During the first 12months 75/111 (ANA 55, CANA 20) patients were evaluated according to Wallace criteria (achievement of inactive disease 28/55 and 17/20, remission over 6months under medication 13/55 and 7/20 cases). Over the whole period of time, clinical response was preserved in the majority of patients (ANA 54/80, CANA 20/27). Arthritis mostly persisted in polyarticular (PA) courses. During treatment with IL-1i concomitant medication could be tapered in about 15%. IL-1i was discontinued in 59/111 patients. 45 (15) adverse events (AE)s in ANA (CANA) treated patients (19.7 (26.6) AE/100 ANA (CANA) exposure years, 95%CI: 14.4-26.4 (14.9-43.9)) were reported.ConclusionIn a large cohort of sJIA patients from Germany, we can confirm an overall favorable clinical response to both available IL-1 blocking agents. IL-1i was well tolerated with acceptable safety and effectiveness in a real-life clinical setting

Neonatal sepsis definitions from randomised clinical trials

Introduction: Neonatal sepsis is a leading cause of infant mortality worldwide with non-specific and varied presentation. We aimed to catalogue the current definitions of neonatal sepsis in published randomised controlled trials (RCTs). Method: A systematic search of the Embase and Cochrane databases was performed for RCTs which explicitly stated a definition for neonatal sepsis. Definitions were sub-divided into five primary criteria for infection (culture, laboratory findings, clinical signs, radiological evidence and risk factors) and stratified by qualifiers (early/late-onset and likelihood of sepsis). Results: Of 668 papers screened, 80 RCTs were included and 128 individual definitions identified. The single most common definition was neonatal sepsis defined by blood culture alone (n = 35), followed by culture and clinical signs (n = 29), and then laboratory tests/clinical signs (n = 25). Blood culture featured in 83 definitions, laboratory testing featured in 48 definitions while clinical signs and radiology featured in 80 and 8 definitions, respectively. Discussion: A diverse range of definitions of neonatal sepsis are used and based on microbiological culture, laboratory tests and clinical signs in contrast to adult and paediatric sepsis which use organ dysfunction. An international consensus-based definition of neonatal sepsis could allow meta-analysis and translate results to improve outcomes

Neonatal sepsis definitions from randomised clinical trials

IntroductionNeonatal sepsis is a leading cause of infant mortality worldwide with non-specific and varied presentation. We aimed to catalogue the current definitions of neonatal sepsis in published randomised controlled trials (RCTs).MethodA systematic search of the Embase and Cochrane databases was performed for RCTs which explicitly stated a definition for neonatal sepsis. Definitions were sub-divided into five primary criteria for infection (culture, laboratory findings, clinical signs, radiological evidence and risk factors) and stratified by qualifiers (early/late-onset and likelihood of sepsis).ResultsOf 668 papers screened, 80 RCTs were included and 128 individual definitions identified. The single most common definition was neonatal sepsis defined by blood culture alone (n = 35), followed by culture and clinical signs (n = 29), and then laboratory tests/clinical signs (n = 25). Blood culture featured in 83 definitions, laboratory testing featured in 48 definitions while clinical signs and radiology featured in 80 and 8 definitions, respectively.DiscussionA diverse range of definitions of neonatal sepsis are used and based on microbiological culture, laboratory tests and clinical signs in contrast to adult and paediatric sepsis which use organ dysfunction. An international consensus-based definition of neonatal sepsis could allow meta-analysis and translate results to improve outcomes

GNU Radio

GNU Radio is a free & open-source software development toolkit that provides signal processing blocks to implement software radios. It can be used with readily-available, low-cost external RF hardware to create software-defined radios, or without hardware in a simulation-like environment. It is widely used in hobbyist, academic, and commercial environments to support both wireless communications research and real-world radio systems

Coronal Heating as Determined by the Solar Flare Frequency Distribution Obtained by Aggregating Case Studies

Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counter-intuitively heats coronae to temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfv\'en waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, $\alpha=2$ as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed $>$600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: pre-flare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that $\alpha = 1.63 \pm 0.03$. This is below the critical threshold, suggesting that Alfv\'en waves are an important driver of coronal heating.Comment: 1,002 authors, 14 pages, 4 figures, 3 tables, published by The Astrophysical Journal on 2023-05-09, volume 948, page 7