title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=504 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Stress mitigation by riparian flora in industrial contaminated area of River Chenab Punjab, Pakistan link: https://peerj.com/articles/15565 last-modified: 2023-06-28 description: Faisalabad is a major industrial area in Pakistan’s Punjab province that discharges wastewater into the Chenab River. Industrial effluents in Faisalabad are predicted to pose a significant threat to the riparian vegetation of the Chenab River and nearby vegetation. Heavy metal pollution of plants, water, and soils is one of the biggest problems worldwide that needs to be addressed because heavy metals above normal levels are extremely dangerous to both riparian vegetation and wildlife. The results indicated high levels of pollution in the industrial effluents as well as in the river in terms of salinity, metal toxicity, TSS, TDS, SAR, the acidic and alkaline nature of the industrial effluents, and the spread of industrial effluents up to 15 square kilometres in the Chenab River. Despite the higher pollution, four plants were found at all sites: Calotropis procera, Phyla nodiflora, Eclipta alba and Ranunculus sceleratus. It was found that most of the selected plants were phytoaccumulators, making them best suited to survive in harsh environments such as those with industrial pollution. The Fe concentration in the plant constituents was the highest, along with Zn, Pb, Cd, and Cu, all of which were above the permissible limits of the WHO. The metal transfer factor (MTF) was higher in most of the plants studied, and even exceeded 10 at some severely affected sites. Calotropis procera proved to be the most suitable plant for growth on drainage systems and also at river sites, as it had the highest importance value across all sites and seasons. creator: Toqeer Abbas creator: Iftikhar Ahmad creator: Zafar Iqbal Khan creator: Anis Ali Shah creator: Ryan Casini creator: Hosam O. Elansary uri: https://doi.org/10.7717/peerj.15565 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abbas et al. title: Hydroxyapatite/calcium alginate composite particles for hemostasis and alveolar bone regeneration in tooth extraction wounds link: https://peerj.com/articles/15606 last-modified: 2023-06-28 description: Tooth extractions can lead to complications such as post-extraction bleeding and bone resorption, which may result in unfavorable outcomes for implant restoration afterwards. To strive for an optimal condition for further restoration procedures, appropriate strategies, such as hemostasis or bone regeneration, are encouraged to be employed. However, the existing products are failed to meet both needs. As a widely employed tissue engineering materials, hydroxyapatite and calcium alginate both have demonstrated excellent performance in osteogenesis. However, their inferior mechanical strength poses a major limitation to their use in supporting the contracted extraction socket, which can easily lead to alveolar crest atrophy and barely achieve satisfying results. Calcium alginate improves the mechanical strength of hydroxyapatite, enabling the formation of new bone tissue and degradable in vivo. In this study, we demonstrated the biocompatibility and haemostatic ability of nCA particles on a rat tooth extraction model. In addition, long-term observation has revealed minimal inflammation and bone tissue regeneration. Our findings suggest a promising insight for clinical applications in hemostasis and bone regeneration after tooth extraction. creator: Gang He creator: Zhihui Chen creator: Luyuan Chen creator: Huajun Lin creator: Chengcheng Yu creator: Tingting Zhao creator: Zhengwen Luo creator: Yuan Zhou creator: Siyang Chen creator: Tianjiao Yang creator: Guixian He creator: Wen Sui creator: Yonglong Hong creator: Jianjiang Zhao uri: https://doi.org/10.7717/peerj.15606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 He et al. title: Comparative study of leaf nutrient reabsorption by two different ecotypes of wild soybean under low-nitrogen stress link: https://peerj.com/articles/15486 last-modified: 2023-06-27 description: Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (PN) of GS1 decreased significantly 0.64-fold (p < 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO2 concentrations increased significantly 0.07-fold (p < 0.05), 0.09-fold (p < 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p < 0.05) and 0.07-fold (p < 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a and b decreased significantly 0.45-fold (p < 0.05), 0.13-fold (p > 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p < 0.01) and 0.60-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p < 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn2+ significantly increased by 1.06- and 1.35-fold (p < 0.01) in the young and old leaves of GS2 (p < 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p < 0.05) in the young leaves of GS1 but increased 0.21-fold (p < 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p < 0.01) and 2.85-fold (p < 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources. creator: Yuan Liu creator: Shujuan Gao creator: Yunan Hu creator: Tao Zhang creator: Jixun Guo creator: Lianxuan Shi creator: Mingxia Li uri: https://doi.org/10.7717/peerj.15486 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis link: https://peerj.com/articles/15510 last-modified: 2023-06-27 description: BackgroundThe homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking.Methods and ResultsIn this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type.ConclusionsThis study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza. creator: Yanhong Bai creator: Ying Zhou creator: Qiaoqi Lei creator: Yu Wang creator: Gaobin Pu creator: Zhenhua Liu creator: Xue Chen creator: Qian Liu uri: https://doi.org/10.7717/peerj.15510 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Bai et al. title: Disclosing the native blueberry rhizosphere community in Portugal—an integrated metagenomic and isolation approach link: https://peerj.com/articles/15525 last-modified: 2023-06-27 description: BackgorundThe production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop’s resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.MethodsIn this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.ResultsResults showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.DiscussionThis work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops. creator: Anicia Gomes creator: Rodrigo Narciso creator: Laura Regalado creator: Margarida Cardeano Pinheiro creator: Filipa Barros creator: Sara Sario creator: Conceição Santos creator: Rafael J. Mendes uri: https://doi.org/10.7717/peerj.15525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gomes et al. title: A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure link: https://peerj.com/articles/15537 last-modified: 2023-06-27 description: BackgroundThe microbial community structure in saliva differs at different altitudes. However, the impact of acute high-altitude exposure on the oral microbiota is unclear. This study explored the impact of acute high-altitude exposure on the salivary microbiome to establish a foundation for the future prevention of oral diseases. Methods. Unstimulated whole saliva samples were collected from 12 male subjects at the following three time points: one day before entering high altitude (an altitude of 350 m, pre-altitude group), seven days after arrival at high altitude (an altitude of 4,500 m, altitude group) and seven days after returning to low altitude (an altitude of 350 m, post-altitude group). Thus, a total of 36 saliva samples were obtained. 16S rRNA V3-V4 region amplicon sequencing was used to analyze the diversity and structure of the salivary microbial communities, and a network analysis was employed to investigate the relationships among salivary microorganisms. The function of these microorganisms was predicted with a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.ResultsIn total, there were 756 operational taxonomic units (OTUs) identified, with 541, 613, and 615 OTUs identified in the pre-altitude, altitude, and post-altitude groups, respectively. Acute high-altitude exposure decreased the diversity of the salivary microbiome. Prior to acute high-altitude exposure, the microbiome mainly consisted of Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. After altitude exposure, the relative abundance of Streptococcus and Veillonella increased, and the relative abundance of Prevotella, Porphyromonas, and Alloprevotella decreased. The relationship among the salivary microorganisms was also affected by acute high-altitude exposure. The relative abundance of carbohydrate metabolism gene functions was upregulated, while the relative abundance of coenzyme and vitamin metabolism gene functions was downregulated.ConclusionRapid high-altitude exposure decreased the biodiversity of the salivary microbiome, changing the community structure, symbiotic relationships among species, and abundance of functional genes. This suggests that the stress of acute high-altitude exposure influenced the stability of the salivary microbiome. creator: Qian Zhou creator: Yuhui Chen creator: Guozhu Liu creator: Pengyan Qiao creator: Chuhua Tang uri: https://doi.org/10.7717/peerj.15537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al. title: Construction and validation of a novel IGFBP3-related signature to predict prognosis and therapeutic decision making for Hepatocellular Carcinoma link: https://peerj.com/articles/15554 last-modified: 2023-06-27 description: BackgroundIGFBP3 plays a pivotal role in carcinogenesis by being anomalously expressed in some malignancies. However, the clinical value of IGFBP3 and the role of IGFBP3-related signature in HCC remain unclear.MethodsMultiple bioinformatics methods were used to determine the expression and diagnostic values of IGFBP3. The expression level of IGFBP3 was validated by RT-qPCR and IHC. A IGFBP3-related risk score (IGRS) was built via correlation analysis and LASSO Cox regression analysis. Further analyses, including functional enrichment, immune status of risk groups were analyzed, and the role of IGRS in guiding clinical treatment was also evaluated.ResultsIGFBP3 expression was significantly downregulated in HCC. IGFBP3 expression correlated with multiple clinicopathological characteristics and demonstrated a powerful diagnostic capability for HCC. In addition, a novel IGRS signature was developed in TCGA, which exhibited good performance for prognosis prediction and its role was further validated in GSE14520. In TCGA and GSE14520, Cox analysis also confirmed that the IGRS could serve as an independent prognostic factor for HCC. Moreover, a nomogram with good accuracy for predicting the survival of HCC was further formulated. Additionally, enrichment analysis showed that the high-IGRS group was enriched in cancer-related pathways and immune-related pathways. Additionally, patients with high IGRS exhibited an immunosuppressive phenotype. Therefore, patients with low IGRS scores may benefit from immunotherapy.ConclusionsIGFBP3 can act as a new diagnostic factor for HCC. IGRS signature represents a valuable predictive tool in the prognosis prediction and therapeutic decision making for Hepatocellular Carcinoma. creator: Jianlin Chen creator: Wanzhen Zhuang creator: Yu Xia creator: Xiaoqing Yin creator: Mingshu Tu creator: Yi Zhang creator: Liangming Zhang creator: Hengbin Huang creator: Songgao Zhang creator: Lisheng You creator: Yi Huang uri: https://doi.org/10.7717/peerj.15554 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Electrochemical biosensors in healthcare services: bibliometric analysis and recent developments link: https://peerj.com/articles/15566 last-modified: 2023-06-27 description: Biosensors are nowadays being used in various fields including disease diagnosis and clinical analysis. The ability to detect biomolecules associated with disease is vital not only for accurate diagnosis of disease but also for drug discovery and development. Among the different types of biosensors, electrochemical biosensor is most widely used in clinical and health care services especially in multiplex assays due to its high susceptibility, low cost and small in size. This article includes comprehensive review of biosensors in medical field with special emphasis on electrochemical biosensors for multiplex assays and in healthcare services. Also, the publications on electrochemical biosensors are increasing rapidly; therefore, it is crucial to be aware of any latest developments or trends in this field of research. We used bibliometric analyses to summarize the progress of this research area. The study includes global publication counts on electrochemical biosensors for healthcare along with various bibliometric data analyses by VOSviewer software. The study also recognizes the top authors and journals in the related area, and determines proposal for monitoring research. creator: Ghazala Yunus creator: Rachana Singh creator: Sindhu Raveendran creator: Mohammed Kuddus uri: https://doi.org/10.7717/peerj.15566 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yunus et al. title: Assessment of health promotion behavior and associated factors among the northern Saudi adolescent population: a cross-sectional study link: https://peerj.com/articles/15567 last-modified: 2023-06-27 description: Background and AimHealth promotions among the adolescent population have a significant role in achieving the 2030 sustainable development goals of the World Health Organization. The COVID-19 pandemic has led to several devastating impacts on the health, economic, social, and healthcare systems, and adolescents’ health promotions are no exception. We assessed health promotion behaviors and associated factors among the adolescent population of northern Saudi Arabia (KSA).MethodsWe used the Arabic version of the adolescent health promotion scale (AHPS-40) among the 400-adolescent population. The AHPS-40 assessed six domains of adolescent health behavior: nutrition, social support, health responsibility, life appreciation, exercise, and stress management. We applied the Chi-square test to identify the associated factors of adolescent health promotion activities and the logistic regression test to find the predictors for overall health promotion categories.ResultsOf the studied participants, the mean ± SD of the total AHPS-40 was 103.31 ± 18.78. The nutrition domain of the AHPS-40 was significantly associated with the age group (p = 0.002), and the social support domain was significantly related to fathers’ (p = 0.022) and mothers’ education (p = 0.006). The exercise domain of AHPS-40 was significantly associated with age group (p = 0.018) and school level (p = 0.026). Gender was significantly associated with most of the six domains. Furthermore, more than half (52.7%) of them had a low health promotion behavior, which was significantly associated with gender (adjusted odds ratio = 1.59, 95% CI of AOR = 1.04 –2.45, p = 0.032).ConclusionOur study results suggest improving health promotion behaviors by instituting awareness-raising and health promotion intervention programs for adolescent groups. Furthermore, we recommend a focused, exploratory, mixed-method survey among the adolescents of other regions of KSA to identify the region-specific adolescent’s health promotion behaviors. creator: Thamer Alshami M. Alruwaili creator: Saad Abdullah K. Alshehri creator: Ashokkumar Thirunavukkarasu creator: Mohamed Shawky Elfarargy creator: Khalid Tariq Alanazi creator: Khalid Muharib R. Alruwaili creator: Yousef Salman Abdullah Alanezi creator: Abdulelah Abdulhadi Alruwaili uri: https://doi.org/10.7717/peerj.15567 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alruwaili et al. title: The use of wireless sensors in the neonatal intensive care unit: a study protocol link: https://peerj.com/articles/15578 last-modified: 2023-06-27 description: BackgroundContinuous monitoring of vital signs and other biological signals in the Neonatal Intensive Care Unit (NICU) requires sensors connected to the bedside monitors by wires and cables. This monitoring system presents challenges such as risks for skin damage or infection, possibility of tangling around the patient body, or damage of the wires, which may complicate routine care. Furthermore, the presence of cables and wires can act as a barrier for parent-infant interactions and skin to skin contact. This study will investigate the use of a new wireless sensor for routine vital monitoring in the NICU.MethodsForty-eight neonates will be recruited from the Montreal Children’s Hospital NICU. The primary outcome is to evaluate the feasibility, safety, and accuracy of a wireless monitoring technology called ANNE® One (Sibel Health, Niles, MI, USA). The study will be conducted in 2 phases where physiological signals will be acquired from the standard monitoring system and the new wireless monitoring system simultaneously. In phase 1, participants will be monitored for 8 h, on four consecutive days, and the following signals will be obtained: heart rate, respiratory rate, oxygen saturation and skin temperature. In phase 2, the same signals will be recorded, but for a period of 96 consecutive hours. Safety and feasibility of the wireless devices will be assessed. Analyses of device accuracy and performance will be accomplished offline by the biomedical engineering team.ConclusionThis study will evaluate feasibility, safety, and accuracy of a new wireless monitoring technology in neonates treated in the NICU. creator: Eva Senechal creator: Daniel Radeschi creator: Lydia Tao creator: Shasha Lv creator: Emily Jeanne creator: Robert Kearney creator: Wissam Shalish creator: Guilherme Sant Anna uri: https://doi.org/10.7717/peerj.15578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Senechal et al.