title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=978 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: modelBuildR: an R package for model building and feature selection with erroneous classifications link: https://peerj.com/articles/10849 last-modified: 2021-02-09 description: BackgroundModel building is a crucial part of omics based biomedical research to transfer classifications and obtain insights into underlying mechanisms. Feature selection is often based on minimizing error between model predictions and given classification (maximizing accuracy). Human ratings/classifications, however, might be error prone, with discordance rates between experts of 5–15%. We therefore evaluate if a feature pre-filtering step might improve identification of features associated with true underlying groups.MethodsData was simulated for up to 100 samples and up to 10,000 features, 10% of which were associated with the ground truth comprising 2–10 normally distributed populations. Binary and semi-quantitative ratings with varying error probabilities were used as classification. For feature preselection standard cross-validation (V2) was compared to a novel heuristic (V1) applying univariate testing, multiplicity adjustment and cross-validation on switched dependent (classification) and independent (features) variables. Preselected features were used to train logistic regression/linear models (backward selection, AIC). Predictions were compared against the ground truth (ROC, multiclass-ROC). As use case, multiple feature selection/classification methods were benchmarked against the novel heuristic to identify prognostically different G-CIMP negative glioblastoma tumors from the TCGA-GBM 450 k methylation array data cohort, starting from a fuzzy umap based rough and erroneous separation.ResultsV1 yielded higher median AUC ranks for two true groups (ground truth), with smaller differences for true graduated differences (3–10 groups). Lower fractions of models were successfully fit with V1. Median AUCs for binary classification and two true groups were 0.91 (range: 0.54–1.00) for V1 (Benjamini-Hochberg) and 0.70 (0.28–1.00) for V2, 13% (n = 616) of V2 models showed AUCs < = 50% for 25 samples and 100 features. For larger numbers of features and samples, median AUCs were 0.75 (range 0.59–1.00) for V1 and 0.54 (range 0.32–0.75) for V2. In the TCGA-GBM data, modelBuildR allowed best prognostic separation of patients with highest median overall survival difference (7.51 months) followed a difference of 6.04 months for a random forest based method.ConclusionsThe proposed heuristic is beneficial for the retrieval of features associated with two true groups classified with errors. We provide the R package modelBuildR to simplify (comparative) evaluation/application of the proposed heuristic (http://github.com/mknoll/modelBuildR). creator: Maximilian Knoll creator: Jennifer Furkel creator: Juergen Debus creator: Amir Abdollahi uri: https://doi.org/10.7717/peerj.10849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Knoll et al. title: Detection and monitoring of insect traces in bioaerosols link: https://peerj.com/articles/10862 last-modified: 2021-02-09 description: Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results. creator: Panyapon Pumkaeo creator: Junko Takahashi creator: Hitoshi Iwahashi uri: https://doi.org/10.7717/peerj.10862 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Pumkaeo et al. title: Osmotic stress in banana is relieved by exogenous nitric oxide link: https://peerj.com/articles/10879 last-modified: 2021-02-09 description: Drought is one of the severe environmental stresses threatening agriculture around the globe. Nitric oxide plays diverse roles in plant growth and defensive responses. Despite a few studies supporting the role of nitric oxide in plants under drought responses, little is known about its pivotal molecular amendment in the regulation of stress signaling. In this study, a label-free nano-liquid chromatography-mass spectrometry approach was used to determine the effects of sodium nitroprusside (SNP) on polyethylene glycol (PEG)-induced osmotic stress in banana roots. Plant treatment with SNP improved plant growth and reduced the percentage of yellow leaves. A total of 30 and 90 proteins were differentially identified in PEG+SNP against PEG and PEG+SNP against the control, respectively. The majority of proteins differing between them were related to carbohydrate and energy metabolisms. Antioxidant enzyme activities, such as superoxide dismutase and ascorbate peroxidase, decreased in SNP-treated banana roots compared to PEG-treated banana. These results suggest that the nitric oxide-induced osmotic stress tolerance could be associated with improved carbohydrate and energy metabolism capability in higher plants. creator: Muhammad Asyraf Mohd Amnan creator: Teen-Lee Pua creator: Su-Ee Lau creator: Boon Chin Tan creator: Hisateru Yamaguchi creator: Keisuke Hitachi creator: Kunihiro Tsuchida creator: Setsuko Komatsu uri: https://doi.org/10.7717/peerj.10879 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mohd Amnan et al. title: Validity of the Polar Vantage M watch when measuring heart rate at different exercise intensities link: https://peerj.com/articles/10893 last-modified: 2021-02-09 description: BackgroundThe use of wrist worn wearable fitness trackers has been growing rapidly over the last decade. The growing popularity can be partly attributed to the improvements in technology, making activity trackers more affordable, comfortable and convenient for use in different fitness and environmental applications. Fitness trackers typically monitor activity level, track steps, distance, heart rate (HR), sleep, peripheral capillary oxygen saturation and more, as the technology continuously is advancing. In terms of measuring HR, photoplethysmography (PPG) is a relatively new technology utilised in wearables. PPG estimates HR through an optical technique that monitors changes in blood volume beneath the skin. With these new products becoming available it is important that the validity of these devices be evaluated. Therefore, the aim of this study was to assess the validity of the Polar Vantage M (PVM) watch to measure HR compared to medical grade ECG on a healthy population during a range of treadmill exercise intensities.MethodsA total of 30 healthy participants (n = 17 males, n = 13 females) were recruited for this study. The validity of the PVM watch to measure HR was compared against the gold standard 5-lead ECG. The study was conducted on 2 separate testing days with 24–48 h between sessions. Participants completed the Bruce Treadmill Protocol, and HR was measured every 30 s. Validation of the PVM watch in comparison to the ECG was measured with an Intraclass Correlation Coefficient (ICC) and associated 95% confidence intervals (CI) and levels of agreement were identified with Bland–Altman plots with 90% limits of agreement. Linear regression analysis was performed to calculate the value of r2 computing the variation of HR obtained by the PVM watch and ECG.ResultsIn total, 30 participants completed the protocol, with data from 28 participants utilised for statistical analysis (16 males, 14 females, 26.10 ± 3.39 years, height 52.36 m ± 7.40 cm, mass 73.59 ± 11.90 kg). A strong and significant correlation was found between the PVM watch and ECG, demonstrating good criterion validity (p < 0.05, r2 = 0.87). Good validity was seen for day 1 and day 2 for stage 0 (ICC = 0.83; 95% CI [0.63–0.92], ICC = 0.74; 95% CI [0.37–0.88]), stage 1 (ICC = 0.78; 95% CI [0.52–0.90], ICC = 0.88; 95% CI [0.74–0.95]), and stage 2 (ICC = 0.88; 95% CI [0.73–0.94], ICC = 0.80; 95% CI [0.40–0.92]). Poor validity was demonstrated on day 1 and day 2 for stages 3–5 (ICC < 0.50).ConclusionThis study revealed that the PVM watch had a strong correlation with the ECG throughout the entire Bruce Protocol, however the level of agreement (LoA) becomes widely dispersed as exercise intensities increased. Due to the large LoA between the ECG and PVM watch, it is not advisable to use this device in clinical populations in which accurate HR measures are essential for patient safety; however, the watch maybe used in settings where less accurate HR is not critical to an individual’s safety while exercising. creator: Tricia Shumate creator: Magdalen Link creator: James Furness creator: Kevin Kemp-Smith creator: Vini Simas creator: Mike Climstein uri: https://doi.org/10.7717/peerj.10893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Shumate et al. title: Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species link: https://peerj.com/articles/10896 last-modified: 2021-02-09 description: Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex. creator: José Cerca creator: Angel G. Rivera-Colón creator: Mafalda S. Ferreira creator: Mark Ravinet creator: Michael D. Nowak creator: Julian M. Catchen creator: Torsten H. Struck uri: https://doi.org/10.7717/peerj.10896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cerca et al. title: Is there a link between pre-existing antibodies acquired due to childhood vaccinations or past infections and COVID-19? A case control study link: https://peerj.com/articles/10910 last-modified: 2021-02-09 description: BackgroundThere is growing evidence indicating that children are less affected from COVID-19. Some authors speculate that childhood vaccinations may provide some cross-protection against COVID-19. In this study, our aim was to compare the circulating antibody titers for multiple childhood vaccine antigens, as an indicator of the state of immune memory between patients with COVID-19 and healthy controls, with a specific aim to identify the association between disease severity and antibody titrations which may indicate a protective function related to vaccine or disease induced memory.MethodsThis study is a case-control study including 53 patients with COVID-19 and 40 healthy volunteers. COVID-19 severity was divided into three groups: asymptomatic, mild and severe. We measured the same set of antibody titers for vaccine antigens, and a set of biochemical and infection markers, in both the case and control groups.ResultsRubella (p = 0.003), pneumococcus (p = 0.002), and Bordetella pertussis (p < 0.0001) titers were found to be significantly lower in the case group than the control group. There was a significant decline in pneumococcus titers with severity of disease (p = 0.021) and a significant association with disease severity for Bordetella pertussis titers (p = 0.014) among COVID patients. Levels of AST, procalcitonin, ferritin and D-dimer significantly increased with the disease severity.DiscussionOur study supports the hypothesis that pre-existing immune memory, as monitored using circulating antibodies, acquired from childhood vaccinations, or past infections confer some protection against COVID-19. Randomized controlled studies are needed to support a definitive conclusion. creator: Bilge Sumbul creator: Hilmi Erdem Sumbul creator: Ramazan Azim Okyay creator: Erdinç Gülümsek creator: Ahmet Rıza Şahin creator: Baris Boral creator: Burhan Fatih Koçyiğit creator: Mostafa Alfishawy creator: Jeffrey Gold creator: ALİ Muhittin Tasdogan uri: https://doi.org/10.7717/peerj.10910 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sumbul et al. title: Rapid coral reef assessment using 3D modelling and acoustics: acoustic indices correlate to fish abundance, diversity and environmental indicators in West Papua, Indonesia link: https://peerj.com/articles/10761 last-modified: 2021-02-08 description: BackgroundProviding coral reef systems with the greatest chance of survival requires effective assessment and monitoring to guide management at a range of scales from community to government. The development of rapid monitoring approaches amenable to collection at community level, yet recognised by policymakers, remains a challenge. Technologies can increase the scope of data collection. Two promising visual and audio approaches are (i) 3D habitat models, generated through photogrammetry from video footage, providing assessment of coral cover structural metrics and (ii) audio, from which acoustic indices shown to correlate to vertebrate and invertebrate diversity, can be extracted.MethodsWe collected audio and video imagery using low cost underwater cameras (GoPro Hero7™) from 34 reef samples from West Papua (Indonesia). Using photogrammetry one camera was used to generate 3D models of 4 m2 reef, the other was used to estimate fish abundance and collect audio to generate acoustic indices. We investigated relationships between acoustic metrics, fish abundance/diversity/functional groups, live coral cover and reef structural metrics.ResultsGeneralized linear modelling identified significant but weak correlations between live coral cover and structural metrics extracted from 3D models and stronger relationships between live coral and fish abundance. Acoustic indices correlated to fish abundance, species richness and reef functional metrics associated with overfishing and algal control. Acoustic Evenness (1,200–11,000 Hz) and Root Mean Square RMS (100–1,200 Hz) were the best individual predictors overall suggesting traditional bioacoustic indices, providing information on sound energy and the variability in sound levels in specific frequency bands, can contribute to reef assessment.ConclusionAcoustics and 3D modelling contribute to low-cost, rapid reef assessment tools, amenable to community-level data collection, and generate information for coral reef management. Future work should explore whether 3D models of standardised transects and acoustic indices generated from low cost underwater cameras can replicate or support ‘gold standard’ reef assessment methodologies recognised by policy makers in marine management. creator: Mika Peck creator: Ricardo F. Tapilatu creator: Eveline Kurniati creator: Christopher Rosado uri: https://doi.org/10.7717/peerj.10761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Peck et al. title: Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera link: https://peerj.com/articles/10773 last-modified: 2021-02-08 description: Macro and micro nutrient accumulation affects all stages of plant growth and development. When nutrient deficiencies or excesses occur, normal plant growth is altered resulting in symptoms such as leaf chlorosis, plant stunting or death. In grapes, few genomic regions associated with nutrient accumulation or deficiencies have been identified. Our study evaluated micro and macro nutrient concentrations in Vitis vinifera L. to identify associated SNPs using an association approach with genotype by sequencing data. Nutrient concentrations and foliar symptoms (leaf chlorosis and stunting) were compared among 249 F1Vitis vinifera individuals in 2015 and 2016. Foliar symptoms were consistent (≥90%) between years and correlated with changes in nutrient concentrations of magnesium (r = 0.65 and r = 0.38 in 2015 and 2016, respectively), aluminum (r = 0.24 and r = 0.49), iron (r = 0.21 and r = 0.49), and sodium (r = 0.32 and r = 0.21). Single nucleotide polymorphisms associated with symptoms, sodium, and magnesium were detected on each chromosome with the exception of 5, 7 and 17 depending on the trait and genome used for analyses explaining up to 40% of the observed variation. Symptoms and magnesium concentration were primarily associated with SNPs on chromosome 3, while SNPs associated with increased sodium content were primarily found on chromosomes 11 and 18. Mean concentrations for each nutrient varied between years in the population between symptomatic and asymptomatic plants, but relative relationships were mostly consistent. These data suggest a complex relationship among foliar symptoms and micro and macro nutrients accumulating in grapevines. creator: Rachel P. Naegele creator: Jason P. Londo creator: Cheng Zou creator: Peter Cousins uri: https://doi.org/10.7717/peerj.10773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Naegele et al. title: Abnormal expression of HOXD11 promotes the malignant behavior of glioma cells and leads to poor prognosis of glioma patients link: https://peerj.com/articles/10820 last-modified: 2021-02-08 description: BackgroundHomeobox D11 (HOXD11) plays an important role in a variety of cancers, but its precise role in gliomas remains unclear. This study aimed to explore the relationship between HOXD11 and gliomas by combining bioinformatics methods with basic experimental validation.Materials and methodsObtain gene expression information and clinical information of glioma and non-tumor brain tissue samples from multiple public databases such as TCGA (666 glioma samples), CGGA (749 glioma samples), GEPIA(163 glioblastoma samples and 207 normal control samples), GEO (GSE4290 and GSE15824). Nine cases of glioma tissue and five cases of normal control brain tissue were collected from the clinical department of Henan Provincial People’s Hospital for further verification. A series of bioinformatic analysis methods were used to confirm the relationship between HOXD11 expression and overall survival and clinical molecular characteristics of patients with glioma. RT-qPCR was used to verify the change of expression level of HOXD11 in glioma cells and tissues. MTT assay, colony formation assay, wound-healing assay, immunofluorescence staining, flow cytometry and western blotting were used to detect the effect of HOXD11 on the biological behavior of glioma cell line U251.ResultsThe high expression of HOXD11 was significantly related to age, World Health Organization (WHO) grade, chemotherapy status, histological type, and even 1p19q codeletion data and isocitrate dehydrogenase (IDH) mutation. HOXD11, as an independent risk factor, reduces the overall survival of glioma patients and has diagnostic value for the prognosis of glioma. Gene Set Enrichment Analysis (GSEA) showed that HOXD11 was significantly enriched in cell signaling pathway such as cell cycle, DNA replication and so on. Finally, we confirmed that the knockout of HOXD11 can inhibit the proliferation and invasion of U251 glioma cells, and change the biological behavior of tumor cells by preventing the progression of cell cycle.ConclusionsHOXD11 may be used as a candidate biomarker for the clinical application of targeted drug and prognostic assessment treatment of glioma. In addition, This study will help to explore the pathological mechanism of glioma. creator: Jialin Wang creator: Zhendong Liu creator: Cheng Zhang creator: Hongbo Wang creator: Ang Li creator: Binfeng Liu creator: Xiaoyu Lian creator: Zhishuai Ren creator: Wang Zhang creator: Yanbiao Wang creator: Bo Zhang creator: Bo Pang creator: Yanzheng Gao uri: https://doi.org/10.7717/peerj.10820 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Identification of a metabolic-related gene signature predicting the overall survival for patients with stomach adenocarcinoma link: https://peerj.com/articles/10908 last-modified: 2021-02-08 description: BackgroundThe reprogramming of energy metabolism and consistently altered metabolic genes are new features of cancer, and their prognostic roles remain to be further studied in stomach adenocarcinoma (STAD).MethodsMessenger RNA (mRNA) expression profiles and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA) and the GSE84437 databases from the Gene Expression Omnibus (GEO) database. A univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) Cox regression model established a novel metabolic signature based on TCGA. The area under the receiver operating characteristic (ROC) curve (AUROC) and a nomogram were calculated to assess the predictive accuracy.ResultsA novel metabolic-related signature (including acylphosphatase 1, RNA polymerase I subunit A, retinol dehydrogenase 12, 5-oxoprolinase, ATP-hydrolyzing, malic enzyme 1, nicotinamide N-methyltransferase, gamma-glutamyl transferase 5, deoxycytidine kinase, galactosidase alpha, DNA polymerase delta 3, glutathione S-transferase alpha 2, N-acyl sphingosine amidohydrolase 1, and N-acyl sphingosine amidohydrolase 1) was identified. In both TCGA and GSE84437, patients in the high-risk group showed significantly poorersurvival than the patients in the low-risk group. A good predictive value was shown by the AUROC and nomogram. Furthermore, gene set enrichment analyses (GSEAs) revealed several significantly enriched pathways, which may help in explaining the underlying mechanisms.ConclusionsA novel robust metabolic-related signature for STAD prognosis prediction was conducted. The signature may reflect the dysregulated metabolic microenvironment and can provided potential biomarkers for metabolic therapy in STAD. creator: Yuan Nie creator: Linxiang Liu creator: Qi Liu creator: Xuan Zhu uri: https://doi.org/10.7717/peerj.10908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Nie et al.