title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=940 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria link: https://peerj.com/articles/11387 last-modified: 2021-05-07 description: The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings. creator: Johnson Adedeji Olusola creator: Adebola Adekunle Shote creator: Abdellah Ouigmane creator: Rima J. Isaifan uri: https://doi.org/10.7717/peerj.11387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Olusola et al. title: Effects of education methods on self-efficacy of smoking cessation counseling among medical students link: https://peerj.com/articles/11408 last-modified: 2021-05-07 description: BackgroundMedical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students.MethodsIn a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools.ResultsAmong 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively).ConclusionThis study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling. creator: Ara Cho creator: Jeonggyu Lee creator: YunJin Kim creator: Byung Mann Cho creator: Sang Yeoup Lee creator: Eunhee Kong creator: Minjeong Kim creator: Jinseung Kim creator: Dong Sik Jung creator: Seongho Han uri: https://doi.org/10.7717/peerj.11408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cho et al. title: Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools link: https://peerj.com/articles/11412 last-modified: 2021-05-07 description: BackgroundIndividual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients.MethodsMultivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model.ResultsThere were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients.ConclusionThe current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Smart Cancer Survival Predictive System could be used at https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_9_LUAD_E1002/. creator: Jinsong Lin creator: Shubiao Lu creator: Zhijian Jiang creator: Chongjing Hu creator: Zhiqiao Zhang uri: https://doi.org/10.7717/peerj.11412 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Lin et al. title: Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications link: https://peerj.com/articles/11179 last-modified: 2021-05-06 description: Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation. creator: Gabriele Bindellini creator: Andrzej S. Wolniewicz creator: Feiko Miedema creator: Torsten M. Scheyer creator: Cristiano Dal Sasso uri: https://doi.org/10.7717/peerj.11179 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bindellini et al. title: Function, structure and quality of striated muscles in the lower extremities in patients with late onset Pompe Disease—an MRI study link: https://peerj.com/articles/10928 last-modified: 2021-05-06 description: BackgroundPompe Disease (PD) is a rare inherited metabolic myopathy, caused by lysosomal-α-glucosidase (GAA) deficiency, which leads to glycogen accumulation within the lysosomes, resulting in cellular and tissue damage. Due to the emergence of a disease modifying treatment with recombinant GAA there has been a large increase in studies of late onset Pompe Disease (LOPD) during the last decade.MethodsThe present study evaluates muscle quality in 10 patients with LOPD receiving treatment with enzyme replacement therapy and in 10 age and gender matched healthy controls applying T1-weighted Dixon MR imaging and isokinetic dynamometry. Muscle quality was determined by muscle strength in relation to muscle size (contractile cross-sectional area, CSA) and to muscle quality (fat fraction). A follow-up evaluation of the patients was performed after 8–12 months. Patient evaluations also included: six-minute walking test (6MWT), forced vital capacity, manual muscle testing and SF-36 questionnaire.ResultsFat fraction of knee flexors (0.15 vs 0.07, p < 0.05) and hip muscles (0.11 vs 0.07, p < 0.05) were higher in patients than controls. In patients, contractile CSA correlated with muscle strength (knee flexors: r = 0.86, knee extensors: r = 0.88, hip extensors: r = 0.83, p < 0.05). No correlation was found between fat fraction and muscle strength. The fat fraction of thigh muscles did not correlate with scores from the clinical tests nor did it correlate with the 6MWT. During follow-up, the contractile CSA of the knee extensors increased by 2%. No other statistically significant change was observed. Quantitative MRI reflects muscle function in patients with LOPD, but larger long-term studies are needed to evaluate its utility in detecting changes over time. creator: Michael Vaeggemose creator: Rosa Andersen Mencagli creator: Julie Schjødtz Hansen creator: Bianca Dräger creator: Steffen Ringgaard creator: John Vissing creator: Henning Andersen uri: https://doi.org/10.7717/peerj.10928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vaeggemose et al. title: Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis link: https://peerj.com/articles/11158 last-modified: 2021-05-06 description: BackgroundEven if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia.MethodsWe recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS.ResultsThe prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class.ConclusionCAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and schools. After controlling for clustering effects at the school and class levels, we found an association between CAS and increasing age, not always washing hands with soap after using latrine, walking barefoot, and T. trichiura infection. Using treated water for drinking was found to have a protective effect against CAS. Thus, educating children on personal hygiene and provision of safe drinking water could reduce the CAS burden in schoolchildren in rural areas of southern Ethiopia. creator: Hiwot Hailu Amare creator: Bernt Lindtjorn uri: https://doi.org/10.7717/peerj.11158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Amare and Lindtjorn title: First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics link: https://peerj.com/articles/11294 last-modified: 2021-05-06 description: BackgroundThe mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae.MethodsHere, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out.ResultsMitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae. creator: Chen-Guang Zheng creator: Xiu-Xiu Zhu creator: Li-Ping Yan creator: Yuan Yao creator: Wen-Jun Bu creator: Xin-Hua Wang creator: Xiao-Long Lin uri: https://doi.org/10.7717/peerj.11294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zheng et al. title: Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama link: https://peerj.com/articles/11308 last-modified: 2021-05-06 description: Seagrass meadows are valued coastal habitats that provide ecological and economic benefits around the world. Despite their importance, many meadows are in decline, driven by a variety of anthropogenic impacts. While these declines have been well documented in some regions, other locations (particularly within the tropics) lack long-term monitoring programs needed to resolve seagrass trends over time. Effective and spatially-expansive monitoring within under-represented regions is critical to provide an accurate perspective on seagrass status and trends. We present a comprehensive dataset on seagrass coverage and composition across 24 sites in Bahía Almirante, a lagoon along the Caribbean coast of Panama. Using a single survey, we focus on capturing spatial variation in seagrass physical and elemental characteristics and provide data on key seagrass bio-indicators, such as leaf morphology (length and width), elemental content (% nitrogen and phosphorus) and stable isotopic signatures (δ13C and δ15N). We further explore relationships between these variables and water depth (proxy for light availability) and proximity to shore (proxy for terrestrial inputs). The seagrass assemblage was mostly monospecific (dominated by Thalassia testudinum) and restricted to shallow water (<3 m). Above-ground biomass varied widely, averaging 71.7 g dry mass m−2, yet ranging from 24.8 to 139.6 g dry mass m−2. Leaf nitrogen content averaged 2.2%, ranging from 1.76 to 2.57%, while phosphorus content averaged 0.19% and ranged from 0.15 to 0.23%. These values were high compared to other published reports for T. testudinum, indicating elevated nutrient availability within the lagoon. Seagrass stable isotopic characteristics varied slightly and were comparable with other published values. Leaf carbon signatures (δ13C) ranged from −11.74 to −6.70‰ and were positively correlated to shoreline proximity, suggesting a contribution of terrestrial carbon to seagrass biomass. Leaf nitrogen signatures (δ15N) ranged from −1.75 to 3.15‰ and showed no correlation with shoreline proximity, suggesting that N sources within the bay were not dominated by localized point-source discharge of treated sewage. Correlations between other seagrass bio-indicators and environmental metrics were mixed: seagrass cover declined with depth, while biomass was negatively correlated with N, indicating that light and nutrient availability may jointly regulate seagrass cover and biomass. Our work documents the response of seagrass in Bahía Almirante to light and nutrient availability and highlights the eutrophic status of this bay. Using the broad spatial coverage of our survey as a baseline, we suggest the future implementation of a continuous and spatially expansive seagrass monitoring program within this region to assess the health of these important systems subject to global and local stressors. creator: Julie Gaubert-Boussarie creator: Andrew H. Altieri creator: J. Emmett Duffy creator: Justin E. Campbell uri: https://doi.org/10.7717/peerj.11308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gaubert-Boussarie et al. title: Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines link: https://peerj.com/articles/11344 last-modified: 2021-05-06 description: Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases. creator: Elham Karimi creator: Enora Geslain creator: Arnaud Belcour creator: Clémence Frioux creator: Méziane Aïte creator: Anne Siegel creator: Erwan Corre creator: Simon M. Dittami uri: https://doi.org/10.7717/peerj.11344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Karimi et al. title: Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum link: https://peerj.com/articles/11345 last-modified: 2021-05-06 description: Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum. creator: Li Zhou creator: Xiaoding Yu creator: Donghao Wang creator: Lin Li creator: Wen Zhou creator: Qian Zhang creator: Xinrui Wang creator: Sumin Ye creator: Zhezhi Wang uri: https://doi.org/10.7717/peerj.11345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al.