title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=648
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: An optimistic future of C4 crop broomcorn millet (Panicum miliaceum L.) for food security under increasing atmospheric CO2 concentrations
link: https://peerj.com/articles/14024
last-modified: 2022-09-07
description: Broomcorn millet, a C4 cereal, has better tolerance to environmental stresses. Although elevated atmospheric CO2 concentration has led to grain nutrition reduction in most staple crops, studies evaluating its effects on broomcorn millet are still scarce. The yield, nutritional quality and metabolites of broomcorn millet were investigated under ambient CO2 (aCO2, 400 µmol mol–1) and elevated CO2 (eCO2, aCO2+ 200 µmol mol–1) for three years using open-top chambers (OTC). The results showed that the yield of broomcorn millet was markedly increased under eCO2 compared with aCO2. On average, eCO2 significantly increased the concentration of Mg (27.3%), Mn (14.6%), and B (21.2%) over three years, whereas it did not affect the concentration of P, K, Fe, Ca, Cu or Zn. Protein content was significantly decreased, whereas starch and oil concentrations were not changed by eCO2. With the greater increase in grain yield, eCO2 induced increase in the grain accumulations of P (23.87%), K (29.5%), Mn (40.08%), Ca (22.58%), Mg (51.31%), Zn (40.95%), B (48.54%), starch (16.96%) and oil (28.37%) on average for three years. Flavonoids such as kaempferol, apigenin, eriodictyol, luteolin, and chrysoeriol were accumulated under eCO2. The reduction in L-glutamine and L-lysine metabolites, which were the most representative amino acid in grain proteins, led to a reduction of protein concentration under eCO2. Broomcorn millet has more desirable nutritional traits for combating hidden hunger. This may potentially be useful for breeding more nutritious plants in the era of climate change.
creator: Xinrui Shi
creator: Jie Shen
creator: Bingjie Niu
creator: Shu Kee Lam
creator: Yuzheng Zong
creator: Dongsheng Zhang
creator: Xingyu Hao
creator: Ping Li
uri: https://doi.org/10.7717/peerj.14024
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Shi et al.

title: Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation
link: https://peerj.com/articles/13937
last-modified: 2022-09-06
description: BackgroundRotational cropping practices can change the fungal structure and diversity of cropping soil, and these changes can promote crop development. However, only a few studies have explored the effects of rotational cropping of pineapple on soil fungal diversity.MethodsIn this study, we investigated fungal diversity in continuous and rotational cropping soil of pineapple in Xuwen and Leizhou of China in summer and winter through high throughput sequencing of the fungal internal transcribed spacer region.ResultsThe diversity and richness of the fungal community were observed to be significantly increased after rotational cropping in Xuwen and Leizhou in summer, whereas no changes were observed in winter. Furthermore, Ascomycota, Basidiomycota, Zygomcota, and Chytridiomycota were the dominant phyla, and Chaetomium, Penicillium, Fusarium, Trichoderma, and Cryptococcus were the dominant genera in the continuous and rotational cropping soil of pineapple, respectively, in both summer and winter. Chytridiomycota at phylum level and Gibberella at genus level were observed in rotational cropping soil; however, Ascomycota at the phylum level and Chaetomium at the genus level were the most abundant fungi, and their abundance dramatically decreased in continuous cropping soil. Redundancy analysis revealed that rotational cropping reduced the correlation between environmental parameters and the fungal community in winter. In addition, several fungal biomarkers were found in Xuwen in both continuous and rotational cropping soil samples, including Sporobolomyces, Aspergillus, Corynascus sp JHG 2007, and Corynascus at the genus level, Penicillium and fungal sp p1s11 at the species level in rotational cropping soil, and ales family Incertae sedis and Sordariomycetes at the class level in continuous cropping soil. These results revealed the changes in the structure and diversity of fungal community in continuous and rotational cropping practices for pineapple cultivation, which may be associated with crop yield and quality.
creator: Jing Chen
creator: Hui Zeng
uri: https://doi.org/10.7717/peerj.13937
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Chen and Zeng

title: Predictors of tuberculosis disease in smokers: a case-control study in northeastern Malaysia
link: https://peerj.com/articles/13984
last-modified: 2022-09-06
description: ObjectiveTuberculosis (TB) is a leading infectious disease. However, many TB cases remain undetected and only present symptoms at a late stage of the infection. Therefore, targeted TB screening in high-risk populations, including smokers, is crucial. This study aimed to determine the predictors of TB disease among the smoker population in northeast Malaysia from 2019 to 2020.MethodsA case-control study was conducted involving smokers aged 18 years and older from health clinics in Bachok Kelantan, Malaysia. Data were collected via face-to-face interviews or telephone calls from 159 participants, randomly selected from outpatient TB records. Simple and multiple logistic regression, using R software, were used to identify the determinants of TB.ResultsMost participants were male (59.1%) and had a secondary education (56.0%). Active smokers constituted 35.2% of the group, and the mean (SD) duration of exposure to smoking was 23.9 (16.47) and 18.4 (12.84) years for the case and control groups, respectively. Being an ex-smoker (adjusted odds ratio (AOR) 6.17; 95% CI [1.55–28.32]; p = 0.013), weight loss (AOR 13.45; 95% CI [4.58–44.46]; p < 0.005), night sweats (AOR 63.84; 95% CI [8.99–1392.75]; p < 0.005) and duration of symptoms (AOR 1.02; 95% CI [1.01–1.04]; p = 0.022) were shown to be significant predictors for TB disease.ConclusionFour predictors of TB disease in the population of smokers were recognised in this study and should be prioritised for early TB screening and diagnosis. This may help increase TB detection, initiate prompt treatment and reduce complications among the group at risk for TB.
creator: Tengku Noor Farhana Tengku Khalid
creator: Wan Mohd Zahiruddin Wan Mohammad
creator: Razan Ab Samat
creator: Nik Rosmawati Nik Husain
uri: https://doi.org/10.7717/peerj.13984
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Tengku Khalid et al.

title: Antibiotic resistance and genomic features of Clostridioides difficile in southwest China
link: https://peerj.com/articles/14016
last-modified: 2022-09-05
description: BackgroundClostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown.MethodsAntibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates.ResultsForty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found. None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene.ConclusionsMost of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains.
creator: Wenpeng Gu
creator: Wenge Li
creator: Senquan Jia
creator: Yongming Zhou
creator: Jianwen Yin
creator: Yuan Wu
creator: Xiaoqing Fu
uri: https://doi.org/10.7717/peerj.14016
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Gu et al.

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