title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=401 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Conservation spillover effect of UNESCO World Heritage Sites into surrounding landscapes link: https://peerj.com/articles/15858 last-modified: 2023-10-10 description: Protected areas (PA) are one of the primary tools for conserving and protecting biodiversity, but their goals have evolved overtime beyond nature conservation to include supporting human communities within and adjacent to the PA. UNESCO World Heritage Sites (WHS) offer a unique perspective on the success of PAs as they fall under three categories, cultural, natural, and mixed heritage sites. The nature of these categories encapsulates the inclusion of human communities in the goals of the WHS. To understand the impact and relationship the WHS has with its surrounding landscape, we assessed changes in three indicators, land use and land cover (LULC), human footprint (HF), and forest landscape integrity index (FLII), across three spatial scales, 1, 10, 100 km from the WHS boundary. We found that there is a conservation spillover effect at least within 1 km of the WHS boundary. In this buffer zone, HF was low and FLII was high. FLII was lower and HF was higher at larger spatial scales. The relationship between the WHS and its surrounding landscape is one reason to support the WHS network, however, management of PAs should be more explicit about this relationship as well as relationships between individual PAs. creator: Emilia B. Hyland creator: John E. Quinn uri: https://doi.org/10.7717/peerj.15858 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hyland and Quinn title: Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps link: https://peerj.com/articles/16022 last-modified: 2023-10-10 description: BackgroundBroad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method.MethodsWe quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O–MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH–MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies.ResultsOf the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH–MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H2O–MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera. creator: Lucas Sire creator: Paul Schmidt Yáñez creator: Annie Bézier creator: Béatrice Courtial creator: Susan Mbedi creator: Sarah Sparmann creator: Laurent Larrieu creator: Rodolphe Rougerie creator: Christophe Bouget creator: Michael T. Monaghan creator: Elisabeth A. Herniou creator: Carlos Lopez-Vaamonde uri: https://doi.org/10.7717/peerj.16022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sire et al. title: Molecular and phenotypic distinctions of macrophages in tolerant and susceptible to hypoxia rats link: https://peerj.com/articles/16052 last-modified: 2023-10-10 description: Individual hypoxia tolerance is a major influence on the course and outcome of infectious and inflammatory diseases. Macrophages, which play central roles in systemic inflammatory response and other immunity reactions, are subject to functional activation orchestrated by several transcription factors including hypoxia inducible factors (HIFs). HIF-1 expression levels and the lipopolysaccharide (LPS)-induced systemic inflammatory response severity have been shown to correlate with hypoxia tolerance. Molecular and functional features of macrophages, depending on the organisms resistance to hypoxia, can determine the severity of the course of infectious and inflammatory diseases, including the systemic inflammatory response. The purpose is the comparative molecular and functional characterization of non-activated and LPS-activated bone marrow-derived macrophages under normoxia in rats with different tolerance to oxygen deprivation. Hypoxia resistance was assessed by gasping time measurement in an 11,500 m altitude-equivalent hypobaric decompression chamber. Based on the outcome, the animals were assigned to three groups termed ‘tolerant to hypoxia’ (n = 12), ‘normal’, and ‘susceptible to hypoxia’ (n = 13). The ‘normal’ group was excluded from subsequent experiments. One month after hypoxia resistance test, the blood was collected from the tail vein to isolate monocytes. Non-activated and LPS-activated macrophage cultures were investigated by PCR, flow cytometry and Western blot methods. Gene expression patterns of non-activated cultured macrophages from tolerant and susceptible to hypoxia animals differed. We observed higher expression of VEGF and CD11b and lower expression of Tnfa, Il1b and Epas1 in non-activated cultures obtained from tolerant to hypoxia animals, whereas HIF-1α mRNA and protein expression levels were similar. LPS-activated macrophage cultures derived from susceptible to hypoxia animals expressed higher levels of Hif1a and CCR7 than the tolerant group; in addition, the activation was associated with increased content of HIF-1α in cell culture medium. The observed differences indicate a specific propensity toward pro-inflammatory macrophage polarization in susceptible to hypoxia rats. creator: Dzhuliia Dzhalilova creator: Anna Kosyreva creator: Anastasiya Lokhonina creator: Ivan Tsvetkov creator: Polina Vishnyakova creator: Olga Makarova creator: Timur Fatkhudinov uri: https://doi.org/10.7717/peerj.16052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dzhalilova et al. title: Dynamic analysis and control of a rice-pest system under transcritical bifurcations link: https://peerj.com/articles/16083 last-modified: 2023-10-10 description: A decision model is developed by adopting two control techniques, combining cultural methods and pesticides in a hybrid approach. To control the adverse effects in the long term and to be able to evaluate the extensive use of pesticides on the environment and nearby ecosystems, the novel decision model assumes the use of pesticides only in an emergency situation. We, therefore, formulate a rice-pest-control model by rigorously modelling a rice-pest system and including the decision model and control techniques. The model is then extended to become an optimal control system with an objective function that minimizes the annual losses of rice by controlling insect pest infestations and simultaneously reduce the adverse impacts of pesticides on the environment and nearby ecosystems. This rice-pest-control model is verified by analysis, obtains the necessary conditions for optimality, and confirms our main results numerically. The rice-pest system is verified by stability analysis at equilibrium points and shows transcritical bifurcations indicative of acceptable thresholds for insect pests to demonstrate the pest control strategy. creator: Sajib Mandal creator: Sebastian Oberst creator: Md. Haider Ali Biswas creator: Md. Sirajul Islam uri: https://doi.org/10.7717/peerj.16083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mandal et al. title: Validation of the HeLD-14 functional oral health literacy instrument in a general population link: https://peerj.com/articles/16106 last-modified: 2023-10-10 description: BackgroundOral health literacy (OHL) is recognized as an important determinant of oral outcomes. Measuring OHL with a valid and reliable instrument that accurately captures the functional nature of this construct across cultures is needed. The short version of the Health Literacy in Dentistry scale (HeLD-14) shows promise as an appropriate instrument due to its inclusion of comprehensive domains hypothesized to comprise OHL. While studies validating the instrument in several languages have occurred, the number of dimensions in the various analyses range from one to seven. Validation of the HeLD-14 in a general English-speaking population is also lacking. The purpose of this study was to explore and confirm the dimensionality of the HeLD-14 in a general US English-speaking population.MethodsThe psychometric properties of HeLD-14 were evaluated in a sample of 631 participants attending the Minnesota State Fair. Construct validity was assessed using exploratory factor analysis (EFA) followed by confirmatory factor analysis (CFA) on the data set split into two groups. Internal consistency reliability was assessed using the Cronbach’s alpha coefficient. Concurrent validity was established between the HeLD-14 and the Oral Health Inventory Profile (OHIP-5) using Pearson’s correlation.ResultsEFA found, and CFA reinforced, a unidimensional structure of the HeLD-14. Cronbach’s alpha was acceptable at 0.92. Fit assessment also supported a unidimensional structure, comparative fit index = 0.992, Tucker-Lewis index = 0.991, root mean square error of approximation = 0.065, and standardized root mean square residual = 0.074. Concurrent validity analyses showed that the HeLD-14 correlated with the OHIP-5.ConclusionsThe HeLD-14 is a unidimensional reliable and valid instrument for measuring the oral health literacy in the general US English-speaking adult population. creator: Priscilla Flynn creator: Aparna Ingleshwar creator: Xing Chen creator: Leah Feuerstahler creator: Yvette Reibel creator: Mike T. John uri: https://doi.org/10.7717/peerj.16106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Flynn et al. title: Sociodemographic distributions and molecular characterization of colonized Enterococcus faecium isolates from locality hospitals in Khartoum, Sudan link: https://peerj.com/articles/16169 last-modified: 2023-10-10 description: BackgroundEnterococcus faecium is an opportunistic pathogen of humans with diverse hosts, encompassing animals as well as human beings. In the past twenty years, there has been a rise in the instances of nosocomial infections that are linked to antibiotic-resistant Enterococcus faecium. The acquisition of diverse antimicrobial resistance factors has driven the global development of robust and convergent adaptive mechanisms within the healthcare environment. The presence of microorganisms in hospitalized and non-hospitalized patient populations has been significantly aided by the facilitation of various perturbations within their respective microbiomes.ObjectiveThis study aimed to determine the antimicrobial profile, demographic and clinical characteristics, along with the detection of virulence encoding genes, and to find out the clonal genetic relationship among colonized E. faecium strains.MethodologyA hospital-based cross-sectional study was carried out between October 2018 and March 2020 at four Khartoum locality hospitals in Sudan. The study comprised a total of 108 strains of E. faecium isolated from patients admitted to four locality hospitals in Khartoum. A self-structured questionnaire was used to gather information on sociodemographic traits. Data were analyzed using chi-square test. In all cases, P value ≤ 0.05 with a corresponding 95% confidence interval was considered statistically significant. Moreover, enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) was utilized to assess the prevalence of clonal relationships, and the gel was analyzed using CLIQS software.ResultsIn this study, the isolation rate of colonized E. faecium strains was 108/170 (63.5%). The colonization of E. faecium and its association with various sociodemographic and clinical features was examined. 73 (67.6%) of patients had multidrug-resistant (MDR), and 22 (20.4%) had extensively drug-resistant (XDR), 73 (67.6%) of patients engaged in self-medication practices. Eighty patients (74.1%) were non-adherence to prescribed antibiotics, while 70 (64.8%) patients reported recent antibiotic usage within the 3 months. The present study suggests that demographic factors may not be significantly associated with the incidence of E. faecium infection except for patients who had a prior history of antibiotic use (P ≤ 0.005). The analysis of virulence genes showed a high prevalence of asa1 gene (22.2%) among strains. In ERIC-PCR the genetic relatedness of E. faecium showed seven identical clusters (A–G) with 100% genetic similarity. This implies clonal propagation in hospitals and communities.ConclusionThis study found that the incidence of E. faecium isolated from locality hospitals in Khartoum was likely due to the spread of E. faecium clones, thereby highlighting the need for intensifying infection control measures to prevent the spreading of nosocomial infection. creator: Loai Abdelati Siddig creator: Magdi Bayoumi creator: Nasreldin Elhadi uri: https://doi.org/10.7717/peerj.16169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Siddig et al. title: Identification of ACHE as the hub gene targeting solasonine associated with non-small cell lung cancer (NSCLC) using integrated bioinformatics analysis link: https://peerj.com/articles/16195 last-modified: 2023-10-10 description: BackgroundSolasonine, as a major biological component of Solanum nigrum L., has demonstrated anticancer effects against several malignancies. However, little is understood regarding its biological target and mechanism in non-small cell lung cancer (NSCLC).MethodsWe conducted an analysis on transcriptomic data to identify differentially expressed genes (DEGs), and employed an artificial intelligence (AI) strategy to predict the target protein for solasonine. Subsequently, genetic dependency analysis and molecular docking were performed, with Acetylcholinesterase (ACHE) selected as a pivotal marker for solasonine. We then employed a range of bioinformatic approaches to explore the relationship between ACHE and solasonine. Furthermore, we investigated the impact of solasonine on A549 cells, a human lung cancer cell line. Cell inhibition of A549 cells following solasonine treatment was analyzed using the CCK8 assay. Additionally, we assessed the protein expression of ACHE, as well as markers associated with apoptosis and inflammation, using western blotting. To investigate their functions, we employed a plasmid-based ACHE overexpression system. Finally, we performed dynamics simulations to simulate the interaction mode between solasonine and ACHE.ResultsThe results of the genetic dependency analysis revealed that ACHE could be identified as the pivotal target with the highest docking affinity. The cell experiments yielded significant findings, as evidenced by the negative regulatory effect of solasonine treatment on tumor cells, as demonstrated by the CCK8 assay. Western blotting analysis revealed that solasonine treatment resulted in the downregulation of the Bcl-2/Bax ratio and upregulation of cleaved caspase-3 protein expression levels. Moreover, we observed that ACHE overexpression promoted the expression of the Bcl-2/Bax ratio and decreased cleaved caspase-3 expression in the OE-ACHE group. Notably, solasonine treatment rescued the Bcl-2/Bax ratio and cleaved caspase-3 expression in OE-ACHE cells compared to OE-ACHE cells without solasonine treatment, suggesting that solasonine induces apoptosis. Besides, solasonine exhibited its anti-inflammatory effects by inhibiting P38 MAPK. This was supported by the decline in protein levels of IL-1β and TNF-α, as well as the phosphorylated forms of JNK and P38 MAPK. The results from the molecular docking and dynamics simulations further confirmed the potent binding affinity and effective inhibitory action between solasonine and ACHE.ConclusionsThe findings of the current investigation show that solasonine exerts its pro-apoptosis and anti-inflammatory effects by suppressing the expression of ACHE. creator: Tong Liu creator: Boke Zhang creator: Yating Gao creator: Xingxing Zhang creator: Jiabing Tong creator: Zegeng Li uri: https://doi.org/10.7717/peerj.16195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Predicting the contribution of climate change on North Atlantic underwater sound propagation link: https://peerj.com/articles/16208 last-modified: 2023-10-10 description: Since the industrial revolution, oceans have become substantially noisier. The noise increase is mainly caused by increased shipping, resource exploration, and infrastructure development affecting marine life at multiple levels, including behavior and physiology. Together with increasing anthropogenic noise, climate change is altering the thermal structure of the oceans, which in turn might affect noise propagation. During this century, we are witnessing an increase in seawater temperature and a decrease in ocean pH. Ocean acidification will decrease sound absorption at low frequencies (<10 kHz), enhancing long-range sound propagation. At the same time, temperature changes can modify the sound speed profile, leading to the creation or disappearance of sound ducts in which sound can propagate over large distances. The worldwide effect of climate change was explored for the winter and summer seasons using the (2018 to 2022) and (2094 to 2098, projected) atmospheric and seawater temperature, salinity, pH and wind speed as input. Using numerical modelling, we here explore the impact of climate change on underwater sound propagation. The future climate variables were taken from a Community Earth System Model v2 (CESM2) simulations forced under the concentration-driven SSP2-4.5 and SSP5-8.5 scenarios. The sound modeling results show, for future climate change scenarios, a global increase of sound speed at different depths (5, 125, 300, and 640 m) except for the North Atlantic Ocean and the Norwegian Sea, where in the upper 125 m sound speed will decrease by as much as 40 m s−1. This decrease in sound speed results in a new sub-surface duct in the upper 200 m of the water column allowing ship noise to propagate over large distances (>500 km). In the case of the Northeast Atlantic Ocean, this sub-surface duct will only be present during winter, leading to similar total mean square pressure level (SPLtot) values in the summer for both (2018 to 2022) and (2094 to 2098). We observed a strong and similar correlation for the two climate change scenarios, with an increase of the top 200 m SPLtot and a slowdown of Atlantic Meridional Overturning Circulation (AMOC) leading to an increase of SPLtot at the end of the century by 7 dB. creator: Luca Possenti creator: Gert-Jan Reichart creator: Lennart de Nooijer creator: Frans-Peter Lam creator: Christ de Jong creator: Mathieu Colin creator: Bas Binnerts creator: Amber Boot creator: Anna von der Heydt uri: https://doi.org/10.7717/peerj.16208 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Possenti et al. title: HtrA3: a promising prognostic biomarker and therapeutic target for head and neck squamous cell carcinoma link: https://peerj.com/articles/16237 last-modified: 2023-10-10 description: ObjectiveThe dysregulation of the human high-temperature requirement A (HtrA) family of serine proteases is associated with many malignancies. However, there are few reports on HtrAs in head and neck squamous cell carcinoma (HNSCC). The aim of this study was to investigate the expression, prognostic value, and biological functions of HtrAs in HNSCC.MethodsThe RNA-sequencing data and clinical data of HNSCC were downloaded from The Cancer Genome Atlas (TCGA) database. The GSE30784 and GSE31056 datasets from the Gene Expression Omnibus (GEO) database were used for further verification. This study explored the differential expression of HtrAs and assessed their potential impact on the prognosis of HNSCC patients using a survival module. Correlations between clinical characteristics and HtrA expression levels were then explored using a Wilcoxon rank sum test. A Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed using “clusterProfile” in the R software. A Pearson/Spearman correlation test was applied to analyze the relationship between HtrAs and immune infiltration level/checkpoint genes. Validation of HtrA expression levels were carried out by RT-PCR and western blot in human squamous carcinoma cell lines (Fadu and Cal-27) and human non-tumorigenic bronchial epithelium cells (BEAS-2B). Finally, through cell transfection, CCK-8, Ki-67 immunofluorescence, and flow cytometry assays, the effect of HtrA3 knockdown on the malignant biological behavior of HNSCC cells was explored.ResultsThe gene expression levels of HtrAs were significantly upregulated and associated with patient age, TNM stage, clinical stage, and TP53 mutation status in the TCGA-HNSCC cohort. High expressions of HtrA1/3 were associated with shorter overall survival, shorter progress-free interval, and lower disease-specific survival in HNSCC. A nomogram for HtrAs was constructed and validated. HtrA-related genes were significantly enriched in the immune response and cell apoptosis pathway. In addition, the expression of HtrAs showed significant correlations with B cells, M cells, DC cell infiltration, and immune infiltration checkpoint (CD276, TNFRSF14). Validation of HtrA expression was carried out by RT-PCR and western blot. Results of in vitro experiments indicated that HtrA3 gene knockdown inhibits the proliferation of FaDu and Cal-27 cells while concurrently promoting apoptosis.ConclusionsHtrA3 shows significant potential as both a prognostic marker and a promising therapeutic target for HNSCC, highlighting its relevance and importance in future research and potential clinical applications. creator: Yan Chen creator: Jianfeng Yang creator: Hangbin Jin creator: Weiwei Wen creator: Ying Xu creator: Xiaofeng Zhang creator: Yu Wang uri: https://doi.org/10.7717/peerj.16237 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Identification of a novel intermittent hypoxia-related prognostic lncRNA signature and the ceRNA of lncRNA GSEC/miR-873-3p/EGLN3 regulatory axis in lung adenocarcinoma link: https://peerj.com/articles/16242 last-modified: 2023-10-10 description: BackgroundLung adenocarcinoma (LUAD) is still the most prevalent type of respiratory cancer. Intermittent hypoxia can increase the mortality and morbidity associated with lung cancer. Long non-coding RNAs (lncRNAs) are crucial in lung adenocarcinoma. However, the effects of intermittent hypoxia-related long non-coding RNAs (IHRLs) on lung adenocarcinoma are still unknown.MethodIn the current research, eight IHRLs were selected to create a prognostic model. The risk score of the prognostic model was evaluated using multivariate and univariate analyses, and its accuracy and reliability were validated using a nomogram and ROC. Additionally, we investigated the relationships between IHRLs and the immune microenvironment.ResultOur analysis identified GSEC, AC099850.3, and AL391001.1 as risk lncRNAs, while AC010615.2, AC010654.1, AL513550.1, LINC00996, and LINC01150 were categorized as protective lncRNAs. We observed variances in the expression of seven immune cells and 15 immune-correlated pathways between the two risk groups. Furthermore, our results confirmed the ceRNA network associated with the intermittent hypoxia-related lncRNA GSEC/miR-873-3p/EGLN3 regulatory pathway. GSEC showed pronounced expression in lung adenocarcinoma tissues and specific cell lines, and its inhibition resulted in reduced proliferation and migration in A549 and PC9 cells. Intriguingly, GSEC manifested oncogenic properties by sponging miR-873-3p and demonstrated a tendency to modulate EGLN3 expression favorably.ConclusionGSEC acts as an oncogenic lncRNA by interacting with miR-873-3p, modulating EGLN3 expression. This observation underscores the potential of GSEC as a diagnostic and therapeutic target for LUAD. creator: Peijun Liu creator: Long Zhou creator: Hao Chen creator: Yang He creator: Guangcai Li creator: Ke Hu uri: https://doi.org/10.7717/peerj.16242 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al.