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Wickham, Hadley; Averick, Mara; Bryan, Jenny; Chang, Winston; McGowan, Lucy D’Agostino; François, Romain; Grolemund, Garrett; Hayes, Alex; Henry, L. Banziiaf; Hester, James; Kühn, Max; Pedersen, Thomas Lin; Miller, Evan; Bache, Stephan Milton; Müller, Kirill; Ooms, Jeroen; Robinson, David M.; Seidel, Dana Paige; Spinu, Vitalie; Takahashi, Kohske; Vaughan, Davis; Wilke, Claus O.; Woo, Kara; Yutani, Hiroaki

doi:10.21105/joss.01686

Cited by 10,623 publications

(6,192 citation statements)

References 4 publications

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“…All community matrix analyses were conducted in R v3.3.4 (R Core Team, 2016). Analyses were aided by the R package tidyverse (Wickham, 2017). Statistical significance was assessed at α = .05.…”

Section: Aquatic Invasive Species Detectionsmentioning

confidence: 99%

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

et al. 2019

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Background: Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community-level analyses due to their use of species-specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon-specific barcodes within an eDNA sample.Aims: Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience. Materials and Methods:In 2016, eight limnologically diverse lakes (surface area range: 13 -1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish-specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.Results: Analysis of species accumulation curves indicated multi-locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 -62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples. | 369SARD et Al.

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Section: Aquatic Invasive Species Detectionsmentioning

confidence: 99%

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

et al. 2019

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“…Coding and analysis were done using ATLAS.ti, version 8.4.24.0 (ATLAS.ti Scientific Software Development GmbH, Berlin, Germany), and R software, 2019 (R Foundation for Statistical Computing, Vienna, Austria). 5,6…”

Section: Methodsmentioning

confidence: 99%

Variability in State Regulations Pertaining to Infection Control and Pandemic Response in US Assisted Living Communities

Bucy¹,

Smith²,

Carder³

et al. 2020

Journal of the American Medical Directors Association

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“…Only COT, HFNC, and NIV were used as respiratory support, for a median duration of 10 (5-14), 0 (0-4), and 0 (0-0) days, respectively. As for PR patients, COT, HFNC, NIV, and IV were used for 18 (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), 0 (0-7), 0 (0-3), and 0 (0-3) days, respectively. Concerning about the NR patients, the median duration for COT, HFNC, NIV and IV were 3 (1-10), 2·5 (0-11), 0 (0-3), and 2 (0-16) days, respectively.…”

Section: (Which Was Not Certified By Peer Review)mentioning

confidence: 99%

Critical Care for Severe COVID-19: A Population-based Study from a Province with Low Case-fatality Rate in China

Liao

Chen

Wang

et al. 2020

Preprint

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Background Data regarding critical care for patients with severe COVID-19 are limited. We aimed to describe the clinical course, multi-strategy management, and respiratory support usage for the severe COVID-19 at the provincial level. Methods Using data from Sichuan Provincial Department of Health and the multicentre cohort study, all microbiologically confirmed COVID-19 patients in Sichuan who met the national severe criteria were included and followed-up from the day of inclusion (D1), until discharge, death, or the end of the study. Findings Out of 539 COVID-19 patients, 81 severe cases (15.0%) were identified. The median (IQR) age was 50 (39-65) years, 37% were female, and 53.1% had chronic comorbidities. All severe cases were identified before requiring mechanical ventilation and treated in the intensive care units (ICUs), among whom 51 (63.0%) were treated in provisional ICUs and 77 patients (95.1%) were admitted by D1. On D1, 76 (93.8%) were administered by respiratory support, including 55 (67.9%) by conventional oxygen therapy (COT), 8 (9.9%) by high-flow nasal cannula (HFNC) and 13 (16.0%) by non-invasive ventilation (NIV). By D28, 53 (65.4%) were discharged, three (3.7%) were deceased, and 25 (30.9%) were still hospitalized. COT, administered to 95.1% of the patients, was the most commonly used respiratory support and met 62.7% of the respiratory support needed, followed by HFNC (19.3%), NIV ventilation (9.4%) and IV 8.5%. Interpretation The multi-strategy management for severe COVID-19 patients including early identification and timely critical care may contribute to the low case-fatailty. Preparation of sufficient conventional oxygen equipment should be prioritized.

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Welcome to the Tidyverse

Cited by 10,623 publications

References 4 publications

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

Variability in State Regulations Pertaining to Infection Control and Pandemic Response in US Assisted Living Communities

Critical Care for Severe COVID-19: A Population-based Study from a Province with Low Case-fatality Rate in China

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