title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=653 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Benchmark datasets for SARS-CoV-2 surveillance bioinformatics link: https://peerj.com/articles/13821 last-modified: 2022-09-05 description: BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset.MethodsWe identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.ResultsThe benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2.DiscussionThe datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines. creator: Lingzi Xiaoli creator: Jill V. Hagey creator: Daniel J. Park creator: Christopher A. Gulvik creator: Erin L. Young creator: Nabil-Fareed Alikhan creator: Adrian Lawsin creator: Norman Hassell creator: Kristen Knipe creator: Kelly F. Oakeson creator: Adam C. Retchless creator: Migun Shakya creator: Chien-Chi Lo creator: Patrick Chain creator: Andrew J. Page creator: Benjamin J. Metcalf creator: Michelle Su creator: Jessica Rowell creator: Eshaw Vidyaprakash creator: Clinton R. Paden creator: Andrew D. Huang creator: Dawn Roellig creator: Ketan Patel creator: Kathryn Winglee creator: Michael R. Weigand creator: Lee S. Katz uri: https://doi.org/10.7717/peerj.13821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xiaoli et al. title: Practical guidance for firefighter applicants preparing for cardiorespiratory fitness testing: a secondary analysis of self-reported physical activity levels link: https://peerj.com/articles/13832 last-modified: 2022-09-05 description: Adequate cardiorespiratory fitness is critical for firefighters since an insufficient level of fitness threatens the integrity of their operations and could be dangerous for their lives. In fact, the leading cause of mortality for on-duty firefighters is not injury but sudden cardiac death. Therefore, to mitigate these risks, potential firefighter recruits are often required to perform a graded exercise test to determine their cardiorespiratory fitness as part of the recruitment process. However, there are currently limited data available to prospective firefighters on the amounts and types of exercises needed to be successful in the graded exercise test, commonly known as a V̇O2max test. Physiological parameters for the current secondary analysis were collected on firefighter applicants who performed the graded exercise test where 72% were successful and 28% were unsuccessful to meet the minimum standard set at 42.5 ml kg−1 min−1. Prior to their test, applicants were asked to describe their exercise training routine by indicating the number of minutes per week spent exercising. Activities were then divided into one of two categories: endurance exercise or strength and power exercise training. The total exercise training describes the sum of all activities performed each week. The sum of endurance exercise activities and the sum of strength and power exercise activities were compared between the successful and the unsuccessful groups and results showed that successful applicants had a higher training volume and performed more endurance exercise training as compared to unsuccessful applicants. Therefore, practical recommendations related to exercise training regime are presented for firefighter applicants to embrace as guidance to prepare for their graded exercise test as part of their recruitment process. creator: Sylvie Fortier creator: Liam P. Kelly creator: Fabien A. Basset uri: https://doi.org/10.7717/peerj.13832 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fortier et al. title: Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers link: https://peerj.com/articles/13952 last-modified: 2022-09-05 description: Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities. creator: Jan-Niklas Macher creator: Dimitra Maria Bloska creator: Maria Holzmann creator: Elsa B. Girard creator: Jan Pawlowski creator: Willem Renema uri: https://doi.org/10.7717/peerj.13952 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Macher et al. title: Bone mesenchymal stem cell-derived exosomes prevent hyperoxia-induced apoptosis of primary type II alveolar epithelial cells in vitro link: https://peerj.com/articles/13692 last-modified: 2022-09-02 description: BackgroundThe presence of alveolar epithelial type II cells (AECIIs) is one of the most important causes of bronchopulmonary dysplasia (BPD). Exosomes from bone mesenchymal stem cells (BMSCs) can reduce hyperoxia-induced damage and provide better results in terms of alveolar and pulmonary vascularization parameters than BMSCs. Currently, intervention studies using BMSC-derived exosomes on the signaling pathways regulating proliferation and apoptosis of alveolar epithelial cells under the condition of BPD have not been reported. This study investigated the effects of rat BMSC-derived exosomes on the proliferation and apoptosis of hyperoxia-induced primary AECIIs in vitro.MethodsThe isolated AECIIs were grouped as follows: normal control (21% oxygen), hyperoxia (85% oxygen), hyperoxia+exosome (20 µg/mL), hyperoxia+exosome+LY294002 (PI3K/Akt inhibitor, 20 µM), and hyperoxia+exosome+rapamycin (mTOR inhibitor, 5 nM). We used the PI3K/Akt inhibitor LY294002 and the mTOR inhibitor rapamycin to determine the roles of the PI3K/Akt and mTOR signaling pathways. The effects of BMSC-derived exosomes on AECII proliferation and apoptosis were assessed, respectively.ResultsDecreased levels of the antiapoptotic protein Bcl-2, the cell proliferation protein Ki67, p-PI3K, p-Akt, and p-mTOR, as well as increased levels of AECII apoptosis and the proapoptotic protein Bax in the hyperoxia group were observed. Notably, Sprague Dawley rat BMSC-derived exosomes could reverse the effect of hyperoxia on AECII proliferation. However, the application of LY294002 and rapamycin inhibited the protective effects of BMSC-derived exosomes.ConclusionOur findings revealed that BMSC-derived exosomes could regulate the expression of apoptosis-related proteins likely via the PI3K/Akt/mTOR signaling pathway, thereby preventing hyperoxia-induced AECII apoptosis. creator: Wei Yang creator: Chao Huang creator: Wenjian Wang creator: Baozhu Zhang creator: Yunbin Chen creator: Xinlin Xie uri: https://doi.org/10.7717/peerj.13692 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Examining the ability to track multiple moving targets as a function of postural stability: a comparison between team sports players and sedentary individuals link: https://peerj.com/articles/13964 last-modified: 2022-09-02 description: BackgroundThe ability to track multiple objects plays a key role in team ball sports actions. However, there is a lack of research focused on identifying multiple object tracking (MOT) performance under rapid, dynamic and ecologically valid conditions. Therefore, we aimed to assess the effects of manipulating postural stability on MOT performance.MethodsNineteen team sports players (soccer, basketball, handball) and sixteen sedentary individuals performed the MOT task under three levels of postural stability (high, medium, and low). For the MOT task, participants had to track three out of eight balls for 10 s, and the object speed was adjusted following a staircase procedure. For postural stability manipulation, participants performed three identical protocols (randomized order) of the MOT task while standing on an unstable platform, using the training module of the Biodex Balance System SD at levels 12 (high-stability), eight (medium-stability), and four (low-stability).ResultsWe found that the ability to track moving targets is dependent on the balance stability conditions (F2,66 = 8.7, p < 0.001, η² = 0.09), with the disturbance of postural stability having a negative effect on MOT performance. Moreover, when compared to sedentary individuals, team sports players showed better MOT scores for the high-stability and the medium-stability conditions (corrected p-value = 0.008, Cohen’s d = 0.96 and corrected p-value = 0.009, Cohen’s d = 0.94; respectively) whereas no differences were observed for the more unstable conditions (low-stability) between-groups.ConclusionsThe ability to track moving targets is sensitive to the level of postural stability, with the disturbance of balance having a negative effect on MOT performance. Our results suggest that expertise in team sports training is transferred to non-specific sport domains, as shown by the better performance exhibited by team sports players in comparison to sedentary individuals. This study provides novel insights into the link between individual’s ability to track multiple moving objects and postural control in team sports players and sedentary individuals. creator: Teresa Zwierko creator: Piotr Lesiakowski creator: Beatriz Redondo creator: Jesús Vera uri: https://doi.org/10.7717/peerj.13964 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zwierko et al. title: Satellite remote sensing of environmental variables can predict acoustic activity of an orthopteran assemblage link: https://peerj.com/articles/13969 last-modified: 2022-09-02 description: Passive acoustic monitoring (PAM) is a promising method for biodiversity assessment, which allows for longer and less intrusive sampling when compared to traditional methods (e.g., collecting specimens), by using sound recordings as the primary data source. Insects have great potential as models for the study and monitoring of acoustic assemblages due to their sensitivity to environmental changes. Nevertheless, ecoacoustic studies focused on insects are still scarce when compared to more charismatic groups. Insects’ acoustic activity patterns respond to environmental factors, like temperature, moonlight, and precipitation, but community acoustic perspectives have been barely explored. Here, we provide an example of the usefulness of PAM to track temporal patterns of acoustic activity for a nocturnal assemblage of insects (Orthoptera). We integrate satellite remote sensing and astronomically measured environmental factors at a local scale in an Andean Forest of Colombia and evaluate the acoustic response of orthopterans through automated model detections of their songs for nine weeks (March and April of 2020). We describe the acoustic frequency range and diel period for the calling song of each representative species. Three species overlapped in frequency and diel acoustics but inhabit different strata: canopy, understory, and ground surface level. Based on the acoustic frequency and activity, we identified three trends: (i) both sampled cricket species call at lower frequency for shorter periods of time (dusk); (ii) all sampled katydid species call at higher frequency for longer time periods, including later hours at night; and (iii) the diel acoustic activity span window seems to increase proportionally with dominant acoustic frequency, but further research is required. We also identified a dusk chorus in which all the species sing at the same time. To quantify the acoustic response to environmental factors, we calculated a beta regression with the singing activity as a response variable and moon phase, surface temperature and daily precipitation as explanatory variables. The response to the moon phase was significant for the katydids but not for the crickets, possibly due to differences in diel activity periods. Crickets are active during dusk, thus the effects of moonlight on acoustic activity are negligible. The response to precipitation was significant for the two crickets and not for the katydids, possibly because of higher likelihood of rain interrupting crickets’ shorter diel activity period. Our study shows how the local survey of orthopteran acoustic assemblages, with a species taxonomic resolution coupled with remote-sensing environmental measurements can reveal responses to environmental factors. In addition, we demonstrate how satellite data might prove to be a useful alternative source of environmental data for community studies with geographical, financial, or other constraints. creator: Diego A. Gomez-Morales creator: Orlando Acevedo-Charry uri: https://doi.org/10.7717/peerj.13969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gomez-Morales and Acevedo-Charry title: Variation in genetics, morphology, and recruitment of the invasive barnacle Amphibalanus eburneus (Gould, 1841) in the southern Korean peninsula link: https://peerj.com/articles/14002 last-modified: 2022-09-02 description: The ivory barnacle Amphibalanus eburneus is a marine crustacean, which presents near-cosmopolitan distribution due to extensive introduction and exhibits a wide spectrum of phenotypic variation. To elucidate geographical differentiation among populations through invasion, we investigated variation in genetic structure, shell morphology, and recruitment pattern for A. eburneus, from the southern Korean Peninsula where it has been established since the late 1980s. We selected samples from four populations in corresponding ecologically-relevant regions representing all surrounding South Korean waters. From these we amplified the mitochondrial genetic marker cytochrome oxidase subunit I (COI) from 57 individuals and performed a populational genetic analyses with 11 additional GenBank sequences to evaluate population structure. To examine morphological variation, we applied two-dimensional landmark-based geometric morphometrics to the scutum and tergum for 148 and 151 individuals, respectively. Furthermore, we estimated the density of year-old individuals in the field to compare recruitment responses among localities. We detected 33 haplotypes among the four locations belonging to three distinct clades based on moderate intraspecific pairwise genetic distance (≥3.5%). The haplotypes in these clades were not locality-specific in their distribution. In contrast, we did detect interpopulation variation in opercular shape and morphospace structure, and one population could be separated from the rest based on its distinct tergum morphotype alone. This morphologically distinct population was also differentiated by displaying the lowest mean recruitment density. Our results indicate that although there is no relationship between molecular variation in the COI gene and geographic regions in South Korea, association with locality for operculum morphology, and recruitment response suggest ecological adaptation by this barnacle in a new habitat. creator: Jeongho Kim creator: Michael Ubagan creator: Soyeon Kwon creator: Il-Hoi Kim creator: Sook Shin uri: https://doi.org/10.7717/peerj.14002 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kim et al. title: Effects of plastic film mulching on the spatiotemporal distribution of soil water, temperature, and photosynthetic active radiation in a cotton field link: https://peerj.com/articles/13894 last-modified: 2022-09-01 description: Plastic film mulching (PFM) affects the spatiotemporal distribution of soil moisture and temperature, which in turn affects cotton growth and the spatiotemporal distribution of canopy photosynthetically active radiation (PAR). Due to the spatial heterogeneity of soil moisture, temperature and limited monitoring methods, the issues such as relatively few sampling points and long sampling intervals in most existing studies prevent the accurate quantification of spatiotemporal changes in moisture and temperature along soil profile. To investigate the effects of PFM on spatiotemporal changes in soil moisture, temperature, and canopy PAR in cotton fields, two field trials of plastic film-mulched (M) and nonmulched (NM) cultivations were performed in 2018 and 2019. The grid method was used for the soil information continuous monitoring and multiple-time fixed-site canopy PAR monitoring during the duration of cotton growth. Two-year field trial data showed that, M cultivation increased soil moisture by approximately 13.6%–25% and increased temperature by 2–4 °C in the 0–50 cm soil layer before the first irrigation (June 20) and by 1–2 °C in the 70–110 cm soil layer, compared with NM cultivation. In addition, the temperature difference between the two treatments gradually decreased with the increase in irrigation and air temperature. The M treatment reached the peak PAR interception rate 10 days earlier than the NM treatment. In 2018 and 2019, the PAR peak value under the M treatment was 4.62% and 1.8% higher than that under the NM treatment, respectively, but the PAR interception rate was decreased rapidly in the late growth stage. Overall, PFM had an effect on soil moisture retention during the whole growth period and greatly increased the soil temperature before budding stage, thus promoted the early growth of cotton. Considering this, we suggest that the irrigation quota and frequency could be appropriately decreased in the case of plastic film mulching cultivation. For nonmulching cultivation, the irrigation quota and frequency should be increased, and it is necessary to take measures to improve the soil temperature before middle July. creator: Beifang Yang creator: Lu Feng creator: Xiaofei Li creator: Guozheng Yang creator: Yunzhen Ma creator: Yabing Li uri: https://doi.org/10.7717/peerj.13894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: CPUE standardization for southern bluefin tuna (Thunnus maccoyii) in the Korean tuna longline fishery, accounting for spatiotemporal variation in targeting through data exploration and clustering link: https://peerj.com/articles/13951 last-modified: 2022-09-01 description: Accounting for spatial and temporal variation in targeting is a concern in many catch per unit effort (CPUE) standardization exercises. In this study we standardized southern bluefin tuna (Thunnus maccoyii, SBT) CPUE from the Korean tuna longline fishery (1996–2018) using generalized linear models (GLMs) with operational set by set data. Data were first explored to investigate the operational characteristics of Korean tuna longline vessels fishing for SBT, such as the spatial and temporal distributions of effort, and changes in the nominal catch rates among major species and species composition. Then we estimated SBT CPUE by area used for the stock assessment in the CCSBT (Commission for the Conservation of Southern Bluefin Tuna) and identified two separate areas in which Korean tuna longline vessels have targeted SBT and albacore tuna (T. alalunga), with targeting patterns varying spatially, seasonally and longer term. We applied two approaches, data selection and cluster analysis of species composition, and compared their ability to address concerns about the changing patterns of targeting through time. Explanatory variables for the GLM analyses were year, month, vessel identifier, fishing location (5° cell), number of hooks, moon phase, and cluster. GLM results for each area suggested that location, year, targeting, and month effects were the principal factors affecting the nominal CPUE. The standardized CPUEs for both areas decreased until the mid-2000s and have shown an increasing trend since that time. creator: Simon D. Hoyle creator: Sung Il Lee creator: Doo Nam Kim uri: https://doi.org/10.7717/peerj.13951 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Hoyle et al. title: Plant traits and environment: floating leaf blade production and turnover of Nymphoides peltata (S.G. Gmel.) O. Kuntze (Menyanthaceae) link: https://peerj.com/articles/13976 last-modified: 2022-09-01 description: BackgroundNymphaeid macrophytes, rooting in the sediment of water bodies and characterized by floating leaves, play an important role in wetland ecosystems. The present research deals with the effects of limited space, limited nutrient availability, water temperature and an unexpected inundation on the production, turnover and plasticity of floating leaves of the globally widespread species Nymphoides peltata (Fringed waterlily).MethodsThe effects of these environmental conditions were studied in two plots in outdoor concrete tanks (CT1, CT2, mesocosms simulating occurrence in small ponds) and in two plots in the floodplain oxbow lake Bemmelse Strang (BS1, BS2). Plot CT1 was situated in a stand coexisting with helophytes, plot CT2 in a monospecific stand, plot BS1 in the center and plot BS2 at the open water border of a monospecific stand. All floating leaf blades within the plots were marked at appearance at the water surface and subsequently length, width and damage of each leaf and maximum and minimum water temperatures were measured bi-weekly. Area and biomass of leaf blades were calculated based on leaf length and width and were used to calculate turnover rates and production.ResultsThe growth period started in May and ended mid-October with continuous production of floating leaves during nearly the whole vegetation period. In the tanks the water level was very stable, but the lake underwent an inundation by river water, causing a sudden loss of existing leaves. Considering environmental conditions and based on the assumed ranking from low to high nutrient availability, the ranking of the plots was CT1, CT2, BS1, BS2. This order was found for maximum leaf life span and maximum leaf length, and the reverse order was found for number of leaves, new leaves per day and duration of the vegetation period. Turnover rates appeared to be relatively similar for plots CT1, CT2 and BS1, but for the deeper border plot BS2 lower ratios were found. These results indicate that increased enclosure with expected nutrient limitation causes (1) the production of high numbers of small leaves with larger totals for leaf area and biomass, (2) a shift towards increased sexual reproduction by the production of more flowering stem leaves. creator: Peter F. Klok creator: Gerard van der Velde uri: https://doi.org/10.7717/peerj.13976 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Klok and van der Velde