title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=495 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)—insights from comparative analysis of complete chloroplast genome link: https://peerj.com/articles/15527 last-modified: 2023-06-26 description: The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species.The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels. creator: Fengxiao Tan creator: Weixi Li creator: Hui Feng creator: Yelin Huang creator: Achyut Kumar Banerjee uri: https://doi.org/10.7717/peerj.15527 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Tan et al. title: The relation between human papillomavirus (HPV) and oropharyngeal cancer: a review link: https://peerj.com/articles/15568 last-modified: 2023-06-26 description: Oropharyngeal squamous cell carcinomas (OPSCC) represent a major public health challenge. In 2020, the international agency for research on cancer (IARC) recorded 98,421 cases of OPSCC worldwide. Over the past decade, the epidemiological profile of patients with OPSCC has shifted, mainly due to a change in etiological factors. Previously, alcohol and tobacco were considered the primary contributors, but the human papillomavirus (HPV) is now recognized as the leading cause of these tumors. This study aimed to conduct a literature review on the relationship between OPSCC and HPV for the general practitioner. The review examined the primary clinical differences between HPV+ and HPV− OPSCC, their prognosis and treatment. In addition, the various HPV diagnostic methods were analyzed. Although there is a vast amount of literature on HPV, this review is unique in its ability to present the key information in an organized and accessible way and enables healthcare professionals to gain a better understanding of the relationship between HPV and oropharyngeal cancer. This, in turn, can contribute to the prevention of various cancers caused by the HPV virus, including oropharyngeal cancer. creator: Chrystiano Campos Ferreira uri: https://doi.org/10.7717/peerj.15568 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ferreira title: Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings link: https://peerj.com/articles/15573 last-modified: 2023-06-26 description: Aerial imagery and video recordings of animals are used for many areas of research such as animal behaviour, behavioural neuroscience and field biology. Many automated methods are being developed to extract data from such high-resolution videos. Most of the available tools are developed for videos taken under idealised laboratory conditions. Therefore, the task of animal detection and tracking for videos taken in natural settings remains challenging due to heterogeneous environments. Methods that are useful for field conditions are often difficult to implement and thus remain inaccessible to empirical researchers. To address this gap, we present an open-source package called Multi-Object Tracking in Heterogeneous environments (MOTHe), a Python-based application that uses a basic convolutional neural network for object detection. MOTHe offers a graphical interface to automate the various steps related to animal tracking such as training data generation, animal detection in complex backgrounds and visually tracking animals in the videos. Users can also generate training data and train a new model which can be used for object detection tasks for a completely new dataset. MOTHe doesn’t require any sophisticated infrastructure and can be run on basic desktop computing units. We demonstrate MOTHe on six video clips in varying background conditions. These videos are from two species in their natural habitat—wasp colonies on their nests (up to 12 individuals per colony) and antelope herds in four different habitats (up to 156 individuals in a herd). Using MOTHe, we are able to detect and track individuals in all these videos. MOTHe is available as an open-source GitHub repository with a detailed user guide and demonstrations at: https://github.com/tee-lab/MOTHe-GUI. creator: Akanksha Rathore creator: Ananth Sharma creator: Shaan Shah creator: Nitika Sharma creator: Colin Torney creator: Vishwesha Guttal uri: https://doi.org/10.7717/peerj.15573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rathore et al. title: Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile link: https://peerj.com/articles/15583 last-modified: 2023-06-26 description: Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater’s initial disposal may have helped the native soil microbial community recover. creator: Abdurrahman S. Masrahi uri: https://doi.org/10.7717/peerj.15583 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Masrahi title: Saccharibacteria (TM7), but not other bacterial taxa, are associated with childhood caries regardless of age in a South China population link: https://peerj.com/articles/15605 last-modified: 2023-06-26 description: BackgroundHuman microbiome dysbiosis is related to various human diseases, and identifying robust and consistent biomarkers that apply in different populations is a key challenge. This challenge arises when identifying key microbial markers of childhood caries.MethodsWe analyzed unstimulated saliva and supragingival plaque samples from children of different ages and sexes, performed 16S rRNA gene sequencing, and sought to identify whether consistent markers exist among subpopulations by using a multivariate linear regression model.ResultsWe found that Acinetobacter and Clostridiales bacterial taxa were associated with caries in plaque and saliva, respectively, while Firmicutes and Clostridia were found in plaque isolated from children of different ages in preschool and school. These identified bacterial markers largely differ between different populations, leaving only Saccharibacteria as a significant caries-associated phylum in children. Saccharibacteria is a newly identified phylum, and our taxonomic assignment database could not be used to identify its specific genus.ConclusionOur data indicated that, in a South China population, oral microbial signatures for dental caries show age and sex differences, but Saccharibacteria might be a consistent signal and worth further investigation, considering the lack of research on this microbe. creator: Yang You creator: Meixiang Yin creator: Xiao Zheng creator: Qiuying Liang creator: Hui Zhang creator: Bu-Ling Wu creator: Wenan Xu uri: https://doi.org/10.7717/peerj.15605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 You et al. title: Lp-PLA2 silencing ameliorates inflammation and autophagy in nonalcoholic steatohepatitis through inhibiting the JAK2/STAT3 pathway link: https://peerj.com/articles/15639 last-modified: 2023-06-26 description: BackgroundNonalcoholic steatohepatitis (NASH), a common cause of liver-related morbidity and mortality worldwide, is characterized by inflammation and hepatocellular injury. Our research focuses on lipoprotein-associated phospholipase A2 (Lp-PLA2), an inflammation-related biomarker that has recently garnered interest in the context of NASH due to its potential roles in disease pathogenesis and progression.MethodsWe established a NASH mouse model using a high-fat diet (HFD) and treated it with sh-Lp-PLA2 and/or rapamycin (an mTOR inhibitor). Lp-PLA2 expression in NASH mice was detected by qRT-PCR. Serum levels of liver function parameters and inflammatory cytokines were detected using corresponding assay kits. We examined pathological changes in liver using hematoxylin-eosin, oil red O, and Masson staining, and observed autophagy through transmission electron microscopy. The protein levels of Lp-PLA2, mTOR, light chain 3 (LC3) II/I, phosphorylated Janus kinase 2 (p-JAK2)/JAK2, and phosphorylated signal transducer and activator of transcription 3 (p-STAT3)/STAT3 were determined by western blotting. Kupffer cells extracted from C57BL/6J mice were treated to replicate NASH conditions and treated with sh-Lp-PLA2, rapamycin, and/or a JAK2-inhibitor to further verify the roles and mechanisms of Lp-PLA2 in NASH.ResultsOur data indicate an upregulation of Lp-PLA2 expression in HFD-induced NASH mice. Silencing Lp-PLA2 in NASH mice reduced liver damage and inflammation markers (aspartate aminotransferase (AST), alanine aminotransferase (ALT), total cholesterol (TC), triglycerides (TG), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6)), while increasing IL-10 levels, an anti-inflammatory cytokine. Additionally, Lp-PLA2 silencing decreased lipid and collagen accumulation and promoted autophagy. The beneficial effects of sh-Lp-PLA2 on NASH were enhanced by rapamycin. Furthermore, Lp-PLA2 silencing resulted in the downregulation of the expression of p-JAK2/JAK2 and p-STAT3/STAT3 in NASH mice. Similar results were observed in Kupffer cells treated under NASH conditions; Lp-PLA2 silencing promoted autophagy and repressed inflammation, effects which were potentiated by the addition of rapamycin or a JAK2-inhibitor.ConclusionOur findings suggest that silencing Lp-PLA2 promotes autophagy via deactivating the JAK2/STAT3 signaling pathway, thereby restraining NASH progression. This highlights the potential therapeutic value of targeting Lp-PLA2, adding a new dimension to our understanding of NASH pathogenesis and treatment strategies. creator: Jinmei Yao creator: Ying Zhao uri: https://doi.org/10.7717/peerj.15639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yao and Zhao title: A review of the impact of maize-legume intercrops on the diversity and abundance of entomophagous and phytophagous insects link: https://peerj.com/articles/15640 last-modified: 2023-06-26 description: In many parts of the world, chemical pesticides are the primary method of pest control in maize (Zea mays L.) crops. Concerns about the negative consequences of chemical pesticide use on people’s health and the environment, as well as the emergence of insecticide resistance, have accelerated attempts to discover alternatives that are effective, low-risk, and cost-effective. Maize-legume intercropping systems are known to have multiple benefits to agroecosystem functioning, including pest regulation. This review focuses on the influence of maize-legume intercropping systems on insect diversity and abundance as a mechanism for insect pest regulation in maize crops. First, this review combines knowledge of maize-legume intercrops, with a particular emphasis on the mechanism by which this practice attracts beneficial insects (e.g., predators, parasitoids) to reduce pest damage in intercropping systems. In addition, the pairings of specific legume species with the greatest potential to attract more beneficial insects and therefore reduce maize pests are also discussed. Finally, future research needs are also recommended. Findings are reviewed in the context of looking for long-term management strategies that can increase the adoption of integrated pest management programs in maize-based production systems. creator: Jacques Fils Pierre creator: Krista L. Jacobsen creator: Luis Latournerie-Moreno creator: Walther J. Torres-Cab creator: Ricardo Chan-Canché creator: Esau Ruiz-Sánchez uri: https://doi.org/10.7717/peerj.15640 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pierre et al. title: A framework for understanding post-detection deception in predator–prey interactions link: https://peerj.com/articles/15389 last-modified: 2023-06-23 description: Predators and prey exist in persistent conflict that often hinges on deception—the transmission of misleading or manipulative signals—as a means for survival. Deceptive traits are widespread across taxa and sensory systems, representing an evolutionarily successful and common strategy. Moreover, the highly conserved nature of the major sensory systems often extends these traits past single species predator–prey interactions toward a broader set of perceivers. As such, deceptive traits can provide a unique window into the capabilities, constraints and commonalities across divergent and phylogenetically-related perceivers. Researchers have studied deceptive traits for centuries, but a unified framework for categorizing different types of post-detection deception in predator–prey conflict still holds potential to inform future research. We suggest that deceptive traits can be distinguished by their effect on object formation processes. Perceptual objects are composed of physical attributes (what) and spatial (where) information. Deceptive traits that operate after object formation can therefore influence the perception and processing of either or both of these axes. We build upon previous work using a perceiver perspective approach to delineate deceptive traits by whether they closely match the sensory information of another object or create a discrepancy between perception and reality by exploiting the sensory shortcuts and perceptual biases of their perceiver. We then further divide this second category, sensory illusions, into traits that distort object characteristics along either the what or where axes, and those that create the perception of whole novel objects, integrating the what/where axes. Using predator–prey examples, we detail each step in this framework and propose future avenues for research. We suggest that this framework will help organize the many forms of deceptive traits and help generate predictions about selective forces that have driven animal form and behavior across evolutionary time. creator: Juliette J. Rubin creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.15389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rubin and Kawahara title: Paediatric hospitalizations over three waves of COVID-19 (February 2020 to May 2021) in Italy: determinants and rates link: https://peerj.com/articles/15492 last-modified: 2023-06-23 description: BackgroundAfter a pneumonia outbreak in late 2019 in China, a new virus related to the Coronaviridae strain, called Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2), was identified as the pathogen of an emerging disease known as COronaVIrus Disease 19 (COVID-19). Preliminary evidence outlines a higher prevalence in adults and lower susceptibility in children. However, recent epidemiologic research highlighted that transmissibility and susceptibility among children and adolescents become higher due to new virus variants. Infections among youth arises with mainly respiratory and gastrointestinal symptoms and malaise. Nevertheless, critical illness affects new-borns and fragile children, requiring hospitalization and possibly intensive care support. Aim of this study was to examine the impact of COVID-19 pandemic on hospital admissions among children and adolescents aged 0 to 17 years over three waves of COVID-19 (from February 2020 to May 2021) in Piedmont, a large Italian region, and to investigate the possible determinants of hospitalizations.MethodsA meta-analysis for risk assessment was performed over three waves of COVID-19 (from February 2020 to May 2021). Data were extracted from the official Italian National Information System and ISTAT.ResultsOverall, 442 paediatric patients were enrolled and admissions concerned mostly the age group 0–4 years (60.2%). Trends of hospitalization showed a slight increase of paediatric admissions already in March 2020 and a rise during second and third waves (November 2020, March 2021). Paediatric age-grouped hospitalizations (0–4; 12–17; 5–11) reproduced an analogous trend. The children and adolescent hospitalization rate appeared lower than overall population with a moderate slope of increase in comparison with population slope. Monthly hospitalization rate (per 100,000) of children and adolescents aged 0–17 years reproduced the increasing trend of hospitalization numbers. This trend was influenced, in particular, by the trend of hospitalization rates for children aged 0–4 years. The meta-analysis for risk assessment showed a decreased likelihood of rescue of hospitalizations in female, 5–11 and 12–17 age groups. Conversely, the meta-analysis showed a positive association between foreign nationality and hospitalizations.ConclusionsOur results show a comparable trend of paediatric hospital admissions for COVID-19 and of the entire population hospitalizations over three waves. COVID-19 hospital admissions increase with a bimodal age distribution and the most admissions are among patients aged ≤4 or 5–11 years. Significant predictive factors of hospitalization are identified. creator: Manuela Martella creator: Alberto Peano creator: Gianfranco Politano creator: Roberta Onorati creator: Maria Michela Gianino uri: https://doi.org/10.7717/peerj.15492 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martella et al. title: CD4+ and CD8+ cell counts are significantly correlated with absolute lymphocyte count in hospitalized COVID-19 patients: a retrospective study link: https://peerj.com/articles/15509 last-modified: 2023-06-23 description: BackgroundCoronavirus disease 2019 (COVID-19) is a contagious respiratory illness that was declared a pandemic in March 2020. Lymphopenia is one of the specific laboratory results disturbance in COVID-19 patients. Such findings are frequently associated with substantial changes in T-cell counts, particularly CD4+ and CD8+ T-cells. This study aimed to examine the correlation between CD4+ and CD8+ cell counts and absolute lymphocyte count (ALC) in COVID-19 patients and analyze its difference based on the COVID-19 patients’ severity.MethodsFrom March 2022 to May 2022, we conducted a retrospective cohort study using medical records and laboratory data from patients diagnosed with COVID-19 at our hospital who met the inclusion and exclusion criteria. The total sampling method was used to recruit study participants. We conducted bivariate analysis, which consisted of correlation and comparative analysis.ResultsThirty-five patients met the inclusion and exclusion criteria and were divided into two severity groups (mild-moderate and severe-critical). The findings of this study revealed a significant correlation between CD4+ cell count and ALC on admission (r = 0.69, p < 0.001) and the tenth day of onset (r = 0.559, p < 0.001). Similarly, there was a correlation between CD8+ and ALC at admission (r = 0.543, p = 0.001) and on the tenth day of onset (r = 0.532, p = 0.001). Individuals with severe-critical illness had lower ALC, CD4+, and CD8+ cell counts than those with mild-moderate illness.ConclusionAccording to the findings of this study, there is a correlation between CD4+ and CD8+ cell counts and ALC in COVID-19 patients. All lymphocyte subsets also showed a lower value in severe forms of the disease. creator: Phey Liana creator: Aprilia Paskah Samosir creator: Nurmalia Purnama Sari creator: Raden Ayu Linda Andriani creator: Verdiansah Verdiansah creator: Hidayatullah Hidayatullah creator: Zen Ahmad creator: Tungki Pratama Umar uri: https://doi.org/10.7717/peerj.15509 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liana et al.