Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol
Background Frequently, the women affected by the genitourinary syndrome of menopause experience genitourinary dysfunctions that profoundly influence their overall health. Even though the symptoms do not jeopardize the women’s lives, the urinary and sexual dysfunctions significantly impact their quality of life. Isolated treatments focused on the main causes of the dysfunctions, such as pelvic floor muscle training (PFMT) and photobiomodulation have shown significant improvements in genitourinary dysfunctions. So, the association of PFMT with photobiomodulation may generate additional effects in the genitourinary area. This study aims to create a PFMT protocol isolated and associated with photobiomodulation therapy in women affected by the genitourinary syndrome of menopause. Methods It is a randomized, controlled, double-blind clinical trial protocol study that will include women experiencing genitourinary symptoms related to menopause, sexually active, never practiced pelvic floor muscle exercise or photobiomodulation treatment, and do not use hormone replacement therapy for at least 3 months. The randomization will allocate the women to three groups: PFMT group, PFMT associated with active intracavitary photobiomodulation group, and PFMT associated with sham intracavitary photobiomodulation group. A total of 16 sessions will be conducted twice a week. The assessments will occur before interventions, after the sixteenth session, and 1 month after the sixteenth session (follow-up). The evaluation will include the pelvic floor muscle vaginal manometry as the primary outcome. Also, the international consultation on incontinence questionnaire—short form, the female sexual function index, the Utian Quality of Life scale, the patient global impression of improvement, the modified Oxford scale, and the vaginal health index will be the secondary outcomes. Discussion Despite there are gold standard treatments such as PFMT, to alleviate genitourinary symptoms, interventions mirroring clinical practice are needed. This study protocol might show a groundbreaking and viable method to potentiate the effects of a gold-standard treatment associated with photobiomodulation. Conclusion We expect this protocol to demonstrate that the use of PFMT and photobiomodulation strategies is feasible and able to potentiate the recovery of women affected by the genitourinary syndrome of menopause. The Ethics Committee of the Federal University of Rio Grande do Norte approved the study (n° 6.038.283), and the clinical trials platform registered the protocol (n° RBR-5r7zrs2).
Maria Thereza Albuquerque Barbosa Cabral Micussi
Oliveira Bezerra et al. (2024) Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol. PeerJ 12:e17848 https://doi.org/10.7717/peerj.17848
Maria Thereza Albuquerque Barbosa Cabral
Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)
The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is a serious insect pest of cotton crop. The studies to evaluate the impact of abiotic factors on cotton pests’ biology are limited. The current study was undertaken to determine the impact of abiotic factors (temperature, humidity, photoperiod) and an insecticide (lambda-cyhalothrin) on the biological aspects of P. gossypiella. The results revealed that all the treatments showed a significant impact on different life parameters of P. gossypiella. The temperature exposure at 27 °C revealed a total life span of about 33 days. Maximum mortality for larvae (51.11%), pupae (59.04%) and adults (61.92%) were recorded at 33 °C exposure. Both low and high humidity levels caused negative impacts on life parameters of P. gossypiella. The life span was completed in about 30 days at 60% relative humidity (RH). Maximum mortality for larvae (75.00%) and pupae (49.59%) were recorded at 80% RH level exposure, while adult mortality was maximum (63.09%) at 40% RH level followed by 80% RH level (55.52%). The P. gossypiella exhibited a life span of about 32 days at 14:10 light-dark period. The larval mortality was maximum (14.83%) at 12:12 light-dark period while pupal (47.36%) and adult (48.84%) mortality was maximum at 16:08 light-dark period. Lambdacyhalothrin (LC) showed dose dependent negative impacts on biological aspects of P. gossypiella. The P. gossypiella exhibited a life span of about 26 days at 0.5 ppm LC concentration. The P. gossypiella exposure to highest concentration (LC) revealed maximum mortality of larval (80.22%), pupal (64.63%) and adult (70.74%) stages. Conclusively, the best suited abiotic factor ranges were 27 °C (temperature), 60% (RH) and 14:10 (light-dark) which can be used for successful rearing and bioassay activities of P. gossypiella.
Arif et al. (2024) Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae). PeerJ 12:e18399 https://doi.org/10.7717/peerj.18399
A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents
Ecological niche modeling (ENM) is a valuable tool for inferring suitable environmental conditions and estimating species’ geographic distributions. ENM is widely used to assess the potential effects of climate change on species distributions; however, the choice of modeling algorithm introduces substantial uncertainty, especially since future projections cannot be properly validated. In this study, we evaluated the performance of seven popular modeling algorithms—Bioclim, generalized additive models (GAM), generalized linear models (GLM), boosted regression trees (BRT), Maxent, random forest (RF), and support vector machine (SVM)—in transferring ENM across time, using Mexican endemic rodents as a model system. We used a retrospective approach, transferring models from the near past (1950–1979) to more recent conditions (1980–2009) and vice versa, to evaluate their performance in both forecasting and hindcasting. Consistent with previous studies, our results highlight that input data quality and algorithm choice significantly impact model accuracy, but most importantly, we found that algorithm performance varied between forecasting and hindcasting. While no single algorithm outperformed the others in both temporal directions, RF generally showed better performance for forecasting, while Maxent performed better in hindcasting, though it was more sensitive to small sample sizes. Bioclim consistently showed the lowest performance. These findings underscore that not all species or algorithms are suited for temporal projections. Therefore, we strongly recommend conducting a thorough evaluation of the data quality—in terms of quantity and potential biases—of the species of interest. Based on this assessment, appropriate algorithm(s) should be carefully selected and rigorously tested before proceeding with temporal transfers.
Moreno-Arzate et al. (2024) A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents. PeerJ 12:e18414 https://doi.org/10.7717/peerj.18414
Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress
Cinnamyl alcohol dehydrogenase (CAD) is a crucial enzyme in the final stage of lignin monomer biosynthesis. This study focuses on the CAD gene family within Gossypium hirsutum. Through comprehensive genomic analysis, we identified 29 GhiCAD genes within the Gossypium hirsutum genome using a bioinformatics approach. Phylogenetic analysis revealed that the GhiCAD family can be categorized into four subgroups, which are closest to the evolutionary relationship with Arabidopsis thaliana. There are multiple cis-acting elements on the promoters of GhiCAD genes associated with abiotic stress responses. Some GhiCAD genes demonstrated high expression in various tissues like root, leaf, and sepal, as well as in fiber and ovule at different developmental stages (10 days post anthesis (DPA), 15 DPA, 20 DPA, 25 DPA). The transcript levels of GhiCAD23 were notably elevated when exposed to PEG treatment and drought stress (DS). GhiCAD23 is also co-expressed with many known drought response genes, suggesting its involvement in the plant’s reaction to DS. Employing virus-induced gene silencing (VIGS) technology to silence the GhiCAD23 gene, it was found that silencing GhiCAD23 reduced the tolerance of cotton to DS. Under DS, the relative leaf water content, superoxide dismutase (SOD), and catalase (CAT) enzyme activities of the GhiCAD23-silenced cotton plants were decreased by 31.84%, 30.22% and 14.19%, respectively, while malondialdehyde (MDA) was increased by 72.16% compared with the control cohort. Drought promotes the accumulation of lignin, and it was found that silencing the GhiCAD23 reduces lignin accumulation in cotton under DS. The analysis of phenotypic and physiological indicators indicates that GhiCAD23 is vital in cotton’s resistance to DS. This investigation provides an important reference for future comprehensive exploration of the GhiCAD23 gene’s function in cotton’s DS response mechanism.
Zhang et al. (2024) Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress. PeerJ 12:e18439 https://doi.org/10.7717/peerj.18439
Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress
The C2H2 type zinc finger proteins (C2H2-ZFPs) are prevalent motifs found widely across the eukaryotic kingdom, playing crucial roles in various biological processes, including stress responses and plant growth and development. To date, C2H2-ZFPs have been identified in many plant systems, but there have been no reports in Chinese jujube (Ziziphus jujuba Mill.). In this study, a total of 77 ZjC2H2-ZFPs were identified in Chinese jujube and classified into three groups, with set A containing 29 genes, set B containing two genes, and set C containing 46 genes. The set A group genes were further divided into three groups: A1, A2, and A4 (with no member of the A3 subgroup found in jujube). The set C C2H2-ZFPs genes were also further divided into three groups: C1 containing 24 genes, C2 with two genes, and C3 with three genes. These ZjC2H2-ZFPs were distributed on 12 chromosomes and one tandem duplicated pair of ZjC2H2-ZFPs was found on chromosome 4 (ZjC2H2-21 with ZjC2H2-22). Notably, the 77 ZjC2H2-ZFPs identified in this study lacked finger clusters comprising 10 or more repeats. The structure and protein motif analysis of ZjC2H2-ZFPs showed that most C1 subgroup members were enriched with ‘QALGGH’ motif zinc finger helices and the A1a ZjC2H2-ZFPs contained highly conserved ‘SATALLQKAAQMGS’ residues in jujube. A unique finding was the discovery of a conserved non-finger domain (PCYCC motif) in A1 group members, absent in other ZjC2H2-ZFPs and unreported in other species. The enzyme activity of jujube leaves under different water stress treatments were measured, and the results showed that as the degree of water stress increased, the activity of SOD enzymes and H2O2 content also increased. The POD enzyme activity levels of different treatment groups were CK>MS>SS>LS. The levels of malondialdehyde (MDA) content observed under various treatments were notably higher and the proline content was lower in comparison to the control group (CK). Differential expression of ZjC2H2-ZFPs and specific responses were analyzed under water stress and different fruit development stages of jujube using RNA-Seq data. The correlation between expression patterns and protective enzyme activities under water stress was also examined. The results indicated that the expression levels of different ZjC2H2-ZFPs varied. A further protein interaction analysis indicated that ZjC2H2-ZFPs serve as pivotal transcriptional regulators with diverse functions, encompassing DNA or RNA binding and participation in protein interactions, with ZjC2H2-20, ZjC2H2-36, and ZjC2H2-57 being potential key players in these regulatory processes. Their roles appear particularly crucial in responding to abiotic stresses like water stress and regulating plant hormones. This study provides valuable insights into understanding stress responses and enhancing the quality of Chinese jujube during breeding.
Zhengwan et al. (2024) Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress. PeerJ 12:e18455 https://doi.org/10.7717/peerj.18455
PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation
Background Presenilin enhancer gamma-secretase subunit (PSENEN), the straight target of metformin, is highly expressed in several cancers. The role of PSENEN in kidney renal clear cell carcinoma (KIRC) has not been reported. Methods PSENEN expression in KIRC specimens was investigated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, as well as by immunohistochemical analysis and qPCR assay. The relationship between PSENEN expression and patient survival was discussed. The biological function of PSENEN in KIRC and its correlation with immune infiltration of KIRC were then investigated, and possible cellular mechanisms were again analyzed. The effects of metformin on KIRC cell proliferation, migration and invasion were discussed in cellular experiments. Results PSENEN was found to be highly expressed in KIRC. The high PSENEN expression was an adverse factor in KIRC. Several immune-related pathways were enriched including immune response, complement and coagulation cascade reactions, and neutrophil extracellular trap formation, as evidenced by enrichment analyses. Immune infiltration analysis revealed that PSENEN expression correlated positively with regulatory T cells. Gene set variation analysis suggested that PSENEN expression correlated positively with oxidative phosphorylation. In addition, a certain concentration of metformin was found to inhibit the proliferation, migration and invasion of KIRC cells, in which PSENEN down-regulation, AMPK up-regulation and mTOR down-regulation were also observed. Conclusions PSENEN may be involved in regulating the immune microenvironment of KIRC, and oxidative phosphorylation may also be a pathway for its involvement in cancer development. PSENEN is a novel prognostic marker for KIRC.
Huang et al. (2024) PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation. PeerJ 12:e18457 https://doi.org/10.7717/peerj.18457
The effect of carbonic anhydrase on foraminiferal Mg/Ca
Marine biogenic calcium carbonate production plays a role in the exchange of CO2 between ocean and atmosphere. The effect of increased CO2 on calcification and on the resulting chemistry of shells and skeletons, however, is only partly understood. Foraminifera are among the main marine CaCO3 producers and the controls on element partitioning and isotope fractionation is the subject of many recent investigations. The enzyme carbonic anhydrase (CA) was, for example, shown to be vital for CaCO3 deposition in benthic foraminifera and indicates their ability to manipulate their intracellular inorganic carbon chemistry. Here, we tested whether CA affects the partitioning of Na, Mg and Sr in the perforate, large benthic, symbiont-bearing foraminifer Amphistegina lessonii by addition of the inhibitor acetazolamide (AZ). The effect of dissolved CO2 on the effect of CA on element partitioning was also determined using a culturing setup with controlled atmospheric carbon dioxide levels (400–1,600 ppm). Results show that inhibition by AZ reduces calcification greatly and that CO2 has a small, but positive effect on the amount of calcite formed during the incubations. Furthermore, the inhibition of CA activity has a positive effect on element partitioning, most notably Mg. This may be explained by a (n indirect) coupling of inorganic carbon uptake and inward calcium ion pumping.
De Goeyse et al. (2024) The effect of carbonic anhydrase on foraminiferal Mg/Ca. PeerJ 12:e18458 https://doi.org/10.7717/peerj.18458
Assessing knowledge anxiety in researchers: a comprehensive measurement scale
Background The rapid pace of knowledge production has introduced a phenomenon termed “knowledge anxiety”, a psychological state where researchers feel inadequate in keeping up with emerging information. This state can negatively affect productivity and mental well-being, yet there is no comprehensive tool to measure knowledge anxiety across different research domains. Methods We employed a mixed-methods approach to develop a multidimensional scale for assessing knowledge anxiety. Initial items were generated through a literature review and qualitative interviews with 313 researchers. After pilot testing, the main study involved 26 participants. The scale was refined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to ensure its structural validity and reliability. Results EFA resulted in a 16-item scale with four distinct factors: cognitive, emotional, behavioral, and capability-related anxieties. CFA confirmed a strong model fit, with standardized factor loadings between 0.549 and 0.887. The scale demonstrated high reliability, with a composite Cronbach’s alpha of 0.883. Conclusions This newly developed scale offers a reliable and valid measure of knowledge anxiety, providing researchers with a valuable tool to assess the psychological impacts of knowledge overload.
Zhenlei et al. (2024) Assessing knowledge anxiety in researchers: a comprehensive measurement scale. PeerJ 12:e18478 https://doi.org/10.7717/peerj.18478
Phenotypic diversity and provenance variation of Cupressus funebris: a case study in the Sichuan Basin, China
Background The species Cupressus funebris holds substantial ecological value and economic potential, particularly in the realms of rehabilitating barren mountain landscapes and advancing urban greening endeavors. However, inadequate attention has been given to research endeavors exploring the genetic diversity and morphological characteristics of Cupressus funebris, a deficiency that could potentially hinder its development, utilization, and conservation of genetic resources. Methods To rectify the shortage of existing basic morphological data, a morphological analysis was conducted in this study on 180 Cupressus funebris germplasm resources sourced from five provenances. Key traits explored included growth characteristics, overall morphology, branch/leaf features, and seed traits. This will facilitate the evaluation of genetic diversity in Cupressus funebris. Results The findings reveal a considerable level of phenotypic variation (PVC of 16.9%) and genetic diversity (1.97 index) in Cupressus funebris germplasm resources. The phenotypic differentiation is observed to be 48% between provenances and 52% within provenances, primarily attributed to variation originating from individual provenances. Based on these morphological characteristics, the germplasm resources have been categorized into four distinct groups: Ecological Restoration Planting, Secondary Reserve Forest, Urban Greening, and Timber Forest. Interestingly, the pattern of variation observed within these groups is irregular, exhibiting no significant correlation with their respective provenances. Furthermore, conifer trees sharing similar growth characteristics tend to display comparable patterns of random variation, suggesting potential underlying genetic mechanisms. This study significantly enriches the phenotypic dataset within the genetic variation research of Cupressus funebris, facilitating development and utilization for ecological construction, timber breeding, and horticultural greening.
Yan et al. (2024) Phenotypic diversity and provenance variation of Cupressus funebris: a case study in the Sichuan Basin, China. PeerJ 12:e18494 https://doi.org/10.7717/peerj.18494
Prognosis and immune landscape of bladder cancer can be predicted using a novel miRNA signature associated with cuproptosis
Background Bladder cancer is characterized by a high recurrence rate and mortality, posing a significant challenge to clinical management. Recently, cuproptosis, a novel form of regulated cell death, has been identified as a potential target for therapeutic intervention in various diseases. The contribution of cuproptosis-related microRNAs (miRNAs) in bladder cancer pathogenesis, however, remains largely unexplored. Therefore, the current study aims to construct a miRNA signature related to cuproptosis for predicting the prognosis and facilitating personalized therapeutic strategies in bladder cancer patients. Methods In this study, we retrieved transcriptomic data and clinical information pertaining to bladder cancer from publicly available databases, including the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). We identified a set of 19 cuproptosis-related genes through a comprehensive review of relevant literature. Using multivariate Cox regression and LASSO analysis, we constructed a cuproptosis-related miRNA prognostic signature. The Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were used to validate the accuracy of prediction. Additionally, we developed a nomogram incorporating clinical characteristics and the miRNA signature to further assess its prognostic value. We evaluated the tumor microenvironment (TME) of every patient using immune ESTIMATE, CIBERSORT, and ssGSEA algorithms. We also investigated the differences in tumor mutation burden (TMB) and drug sensitivity between two groups. Finally, we validated the prognostic value of this miRNA signature using the OncomiR dataset. Results We developed a panel of eight cuproptosis-associated miRNAs to serve as a prognostic signature. The predictive validity of this signature was determined using Kaplan-Meier and ROC curves, and was found to be acceptable in both the TCGA training, test and total dataset. The prognostic value of this signature was confirmed by univariate and multivariate Cox regression analysis, indicating its applicability as a prognostic factor. The immune cell infiltration was significantly associated with an immunosuppressive phenotype of TME in the high-risk group of patients; meanwhile, patients in the high-risk group had a lower TMB resulted in shorter survival. Notably, higher estimate scores and IC50 value for chemotherapy drugs were observed in the high-risk group, indicating poor response to immune therapy and chemotherapy.
Zhang et al. (2024) Prognosis and immune landscape of bladder cancer can be predicted using a novel miRNA signature associated with cuproptosis. PeerJ 12:e18530 https://doi.org/10.7717/peerj.18530
Physiological and molecular response mechanisms of tomato seedlings to cadmium (Cd) and lead (Pb) stress
Heavy metal contamination, particularly from cadmium (Cd) and lead (Pb), poses significant risks to soil and water resources and leads to severe damage in plants. This study investigated the physiological and molecular mechanisms of the responses of tomato (Solanum lycopersicum L.) seedlings to Cd and Pb stress by applying 50 mg/L Cd, 100 mg/L Pb, and a combination of 50 mg/L Cd + 100 mg/L Pb. The goal was to understand how these heavy metals impact the growth, antioxidant systems, and secondary metabolic pathways in tomato seedlings. The results showed that compared with the control, Cd + Pb stress significantly increased the content of soluble sugar by 37.40% and 33.46% on days 5 and 15, respectively, and the content of proline by 77.91% to 93.91% during the entire period in tomato seedlings. It also elevated electrical leakage by 110.52% on day 15, maintained the levels of malondialdehyde close to the control, enhanced the activities of superoxide dismutase by 33.32% on day 10 and 11.22% on day 15, peroxidase by 42.15% on day 10, and catalase by 90.78% on day 10. Additionally, it reduced the contents of hydrogen peroxide by 15.47% to 29.64% and the rate of formation of superoxide anions by 26.34% to 53.47% during the entire period of treatment. The transcriptomic analysis revealed a significant differential expression of the genes involved in pathways, such as phenylalanine, glutathione, arginine and proline, and nitrogen metabolism. These genes included PALs, HDCs, GGCT, ODC1, LAPs, SMS, and SAMDC. Notably, transcription factors, such as ERF109, ARF9, GRF3, GRF4, GRF7, and GRF9, were also significantly regulated. The study concluded that Cd and Pb stress enhanced the osmoregulatory and antioxidant defense systems in tomato seedlings, which may contribute to their tolerance to heavy metal stress. Future research could explore the application of these findings to develop strategies to improve the resistance of plants to contamination with heavy metals.
Zhou et al. (2024) Physiological and molecular response mechanisms of tomato seedlings to cadmium (Cd) and lead (Pb) stress. PeerJ 12:e18533 https://doi.org/10.7717/peerj.18533
Effect of prognostic nutritional index on laboratory parameters and survival in metastatic colorectal cancer patients treated with fruquintinib: a retrospective study
Objective Fruquintinib, a novel anti-angiogenic targeted drug, has gained widespread application in the treatment of metastatic colorectal cancer. This study aims to investigate the impact of the prognostic nutritional index (PNI) on the safety and survival outcomes of patients undergoing fruquintinib treatment for metastatic colorectal cancer. Methods A cohort of 106 patients with metastatic colorectal cancer, treated with fruquintinib at Zhejiang Cancer Hospital between 2019 and 2023, was included in this study. Clinical and laboratory data were subjected to chi-square and t-tests for analysis. PNI values were calculated using a specific formula. The optimal thresholds (cut-off values) for post-treatment PNI were determined through the ROC curve analysis. Kaplan-Meier analysis and the Log-rank test were employed to evaluate progression-free survival (PFS) and overall survival (OS) based on PNI. Multivariate Cox regression model was used to determine independent prognostic factors which influenced survival time. Results The study enrolled 106 colorectal cancer patients treated with fruquintinib. Stratified PNI analysis revealed significant differences in various indicators between high and low PNI groups after treatment with fruquintinib. Notably, after fruquintinib treatment, the high PNI group demonstrated elevated levels in white blood cells, lymphocytes, basophils, red blood cells, hemoglobin, platelets, total protein, and albumin compared to the low PNI group. The median OS for patients with high PNI values was 467 days, significantly longer than the 182 days observed for patients with low PNI values (P < 0.05). Cox regression analysis identified wild-type total RAS and BRAF, partial response (PR) + stable disease (SD), and high PNI values as influencing factors for OS in colorectal cancer patients. Additionally, PR + SD was an independent influencing factor for PFS in colorectal cancer patients (P < 0.05). Conclusions This study suggests that fuquinitinib can improve the survival of patients with metastatic colorectal cancer. Patients with high levels of PNI have a better prognosis and longer survival time, ensuring the nutritional status of patients can be a help to improve the treatment of fuquinitinib.
Wang et al. (2024) Effect of prognostic nutritional index on laboratory parameters and survival in metastatic colorectal cancer patients treated with fruquintinib: a retrospective study. PeerJ 12:e18565 https://doi.org/10.7717/peerj.18565
Resistance characterization and transcriptomic analysis of imipenem-induced drug resistance in Escherichia coli
Background Bacteria can develop resistance to various antibiotics under selective pressure, leading to multifaceted changes in resistance mechanisms. Transcriptomic sequencing allows for the observation of transcriptional level alterations in cells under antibiotic stress. Understanding the bacterial response to such stress is essential for deciphering their strategy against drug-resistant antibiotics and identifying potential targets for antibiotic development. Methods This study using wild-type (WT) Escherichia coli (E. coli) discovered that continuous in vitro induction screening for imipenem-resistant strains resulted in bacteria with enhanced biofilm-forming ability and mutations in antibiotic target sites. Transcriptomic sequencing of the resistant bacteria revealed significant changes in carbon and amino acid metabolism, nutrient assimilation, substance transport, nucleotide metabolism, protein biosynthesis, and cell wall biosynthesis. The up-regulated drug efflux genes were disrupted using gene knockout technology. Drug sensitivity tests indicated that drug efflux has a minimal effect on imipenem resistance. Results This suggests a strategy for E. coli drug resistance involving the reduction of unnecessary substance synthesis and metabolism, coupled with an increase in activities that aid in resisting foreign threats.
Tong et al. (2024) Resistance characterization and transcriptomic analysis of imipenem-induced drug resistance in Escherichia coli. PeerJ 12:e18572 https://doi.org/10.7717/peerj.18572
Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development
Trihelix transcription factors (TF) are photoresponsive proteins featuring a characteristic three-helix structure (helix-loop-helix-loop-helix) and contain the Myb/SANT-LIKE (MSL) domain. They perform crucial functions in the development and stress-response of plants. However, the function of the Trihelix TF in potato (Solanum tuberosum L.) remains unknown. In the present study, forty-three StMSLs were characterized in the potato genome and named StMSL1 to StMSL43. Structural domain analysis revealed that motifs 1 and 2 may play a central role in the implementation of trihelix gene functions, and motifs 4 and 9 may be related to specific functions of StMSL. Phylogenetic analysis divided the StMSLs into six groups (SIP1, GT1, GT2, GTγ, SH4 and GT3). The GT3 group, which is rarely identified in the Trihelix TF family, contained three StMSLs. The 43 StMSLs were unevenly distributed on 12 chromosomes in potato and comprised two pairs of tandem duplication and five pairs of segmental duplication genes. Additionally, RNA-Seq analysis found that 36 out of the 43 StMSLs were expressed in at least one of the 12 tissues, with some exhibiting tissue-specific expression patterns. Trihelix transcriptional regulation network analysis identified 387 genes as potential targets of the 36 StMSL genes, and these genes have a wide variety of functions. Furthermore, RNA-Seq analysis revealed that at least 18 StMSLs were upregulated in response to osmotic stress. The induced pattern of eight StMSLs was subsequently validated using qRT-PCR. This study provides a detailed insight into the StMSLs of the potato and lays the foundation for further analysis of the functions of the Trihelix gene in plant development.
Mei et al. (2024) Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (Solanum tuberosum L.) during development. PeerJ 12:e18578 https://doi.org/10.7717/peerj.18578
Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure
Background Sodium-Glucose Transport Protein 2 (SGLT2) inhibitors, and Angiotensin II Receptor Antagonists (ARBs) also have the effect of reducing serum uric acid but few studies worldwide assessed. Objective Evaluate the effectiveness of serum uric acid lowering treatment of SGLT2 inhibitors, and ARB in heart failure (HF) patients. Methods We conducted a cross-sectional analysis study with 8 weeks of follow-up on 733 heart failure (HF) patients treated at Can Tho Central General Hospital from January 2023 to March 2024. Patients enrolled in the study were examined and received losartan (Group A) or dapagliflozin (Group B) monotherapy or losartan and dapagliflozin combined therapy (Group C). The uric acid concentration group was defined into three subgroups with tertile 1 from smallest to quartile (Q) 1, tertile 2 from Q2 to Q3, and tertile 3 from Q3 to the largest value. Results After 8 weeks of treatment, the uric acid reduction effect between groups A, B, and C showed that the combination group had the optimal reducing effect compared to losartan and dapagliflozin monotherapy with the mean difference being −229.62 ± 76.65 µmol/L, −217.00 ± 146.17 µmol/L, and −284.43 ± 136.32 µmol/L, respectively. In total, combination therapy showed the best reduction outcome in the population of male, female, patients with type 2 diabetes mellitus (T2DM), and dyslipidemia with the mean difference ranging from −226.21 ± 74.65 µmol/L to −231.85 ± 76.28 µmol/L and −209.62 ± 184.94 µmol/L to −225.75 ± 78.53 µmol/L and −273.02 ± 204.54 µmol/L to −308.93 ± 72.97 µmol/L in group A, B, and C, respectively. Conclusion The optimal therapy for reducing uric acid levels in HF patients was the combination of losartan and dapagliflozin, and the effectiveness did not change through sex, T2DM, and dyslipidemia patients.
Huynh et al. (2024) Losartan and dapagliflozin combination therapy in reducing uric acid level compared to monotherapy in patients with heart failure. PeerJ 12:e18595 https://doi.org/10.7717/peerj.18595
Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment
Background Exercise in humid and hot environments (HHEs) may result in decreased perception, motor performance, and memory owing to endogenous heat production and exogenous load. However, whether a single bout of exercise (SBOE) intensity affects the magnitude of changes in the levels of hemocytes remains controversial. In this article, we aimed to investigate the effects of a SBOE of varying intensities on blood cells in HHE. Methods Thirty-two volunteers were randomly divided into a quiet control group (QC), 55% VO2max intensity exercise group (HHE55%), 70% VO2max intensity exercise group (HHE70%), and 85% VO2max intensity exercise group (HHE85%). The participants in the exercise groups were assigned to perform an SBOE on the treadmill under HHE conditions for 30 min, whereas participants in the QC remained still under HHE conditions for 30 min (temperature: 28–32 °C, relative humidity: 85–95%). Results The net body mass (NBM), perfusion index (PI), mean corpuscular volume (MCV), platelet (PLT), and plateletcrit (PCT) values were affected significantly by the exercise intensity (P < 0.01) the hemoglobin (HGB) and neutrophil count (NE) were affected significantly by exercise intensity (P < 0.05). After an SBOE, compared with that before exercise, the sublingual temperature (ST) of all groups, the NBM and MCV of all exercise groups, the PI of the HHE55% and HHE70% groups, the HGB, hematocrit (HCT), and NE of the HHE70% group, the red blood cell count (RBC), PLT, and PCT of the HHE70% and HHE85% groups, and the white blood cell count (WBC) of HHE85% changed very significantly (P < 0.01). The PCT of QC, blood oxygen saturation (SaO2), and soluble transferrin receptor (sTfR) levels in the HHE55% group, the lymphocyte count (LY) in the HHE70% group, and the HGB and HCT in the HHE85% group changed significantly (P < 0.05). Conclusion Low- and moderate-intensity SBOE in HHE could increase the serum EPO and serum sTfR levels and decrease the serum IL-3 levels. Conversely, a high-intensity load could increase the risk of inflammation. Therefore, low-intensity exercise may be more appropriate for an SBOE in HHE.
Lv et al. (2024) Effects of a single bout of exercise on human hemocytes and serum interleukin 3, erythropoietin, and soluble transferrin receptor in a hot and humid environment. PeerJ 12:e18603 https://doi.org/10.7717/peerj.18603
Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots
Background Enhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments. Methods Ten maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods. Results and Discussion Analysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions.
Supriadi et al. (2024) Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots. PeerJ 12:e18624 https://doi.org/10.7717/peerj.18624
Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study
Objective Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, characterized by significant individual variations in treatment response. Predicting treatment response remains a formidable challenge. This study aims to identify predictors within the synovium associated with the response to JAK inhibitor therapy in RA patients, employing a retrospective approach. Methods A retrospective analysis was conducted on 27 RA patients who underwent synovial biopsy and received JAK inhibitor therapy for at least three months at our center, from January to November 2023. These patients had comprehensive clinical records. Based on their response to JAK inhibitor therapy, as measured by the ACR20 criteria, they were categorized into non-responder and responder groups. We compared clinical data (including sex, age, disease duration), laboratory findings (RF, ACPA, ESR, CRP, etc.), DAS28-CRP scores, and synovial pathology features—such as synovial lining hyperplasia, neovascularization, stromal activation, inflammatory infiltration, and the expression of CD3, CD20, CD68, and CD138 markers in the synovium—between the two groups. Results The rate of non-responder to JAKi was found to be 33.3% (nine cases out of a total of 27 patients). Non-responders, when compared to responders, exhibited longer disease duration, more pronounced synovial neovascularization alongside reduced infiltration of labeled CD20+ and CD138+ cells in the synovium. Multivariate regression analysis identified synovial neovascularization and disease duration as independent predictors of a poor response to JAK inhibitor treatment. Conclusions The presence of vascular phenotype with low inflammation within the synovium of RA patients is an indicator of poor response to JAK inhibitor therapy, highlighting its potential as a predictive marker for treatment outcomes.
Liu et al. (2024) Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study. PeerJ 12:e18631 https://doi.org/10.7717/peerj.18631
Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma
Background The incidence of oropharyngeal squamous cell carcinoma (OPSCC) mediated by human papilloma virus (HPV) has been steadily increasing worldwide. The specific pathogenesis of HPV-mediated head and neck squamous cell carcinoma (HNSCC) usually induces carcinogenesis in the oropharynx and the roles of CK7, CK19 and p16 in the carcinogenesis mechanism of HPV-mediated OPSCC still remain uncertain. Methods We collected case data and paraffin samples of 69 cases of OPSCC and 40 cases of OSCC from July 2009 to December 2021. Immunohistochemistry was performed on serial paraffin sections from all cases to analyze the expression patterns of CK7, CK19, and p16. HPV-mediated (p16+) and non-HPV-mediated OPSCC were differentiated based on p16 expression. Three to six fields were selected from each case for observation of the expression intensity, localization, and interrelationship of the three proteins. Results In both cancerous nests and pericancerous normal epithelium of OPSCC, various expression combinations of CK7, CK19 and p16 were observed, including CK7+CK19+p16+, CK7−CK19+p16+, and CK7+CK19+p16−, while no expression of CK7+CK19−p16+ was found. The expression of CK7 with CK19, CK7 with p16, and CK19 with p16 all showed consistency in OPSCC (P < 0.05) while only the expression of CK7 and CK19 demonstrated consistency in OSCC (P < 0.05). The positive rates and H-scores for CK7/CK19 in HPV-mediated (p16+) OPSCC were significantly higher than those in non-HPV-mediated OPSCC and OSCC (P < 0.05). Conclusions These results suggest that CK7, CK19 and p16 may relate to HPV-mediated OPSCC. The interaction of CK7, CK19 and p16 may affect the development of HPV-mediated OPSCC.
Yan et al. (2024) Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma. PeerJ 12:e18286 https://doi.org/10.7717/peerj.18286
Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus
Background Understanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons. Methods Thirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene. Results We found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals. Discussion This is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota.
Rodríguez-Barreras et al. (2024) Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus. PeerJ 12:e18298 https://doi.org/10.7717/peerj.18298
Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics
Introduction Severe early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, nearly 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM) was designed in this study. Methods Eleven fresh S-ECC dental plaque samples were collected and cultivated in both NEMM and SHI medium (reference medium) for 0, 1, 3, 6, 9, 15, 21 and 28 days under aerobic and anaerobic conditions. Thereafter, the cultures were harvested, together with their corresponding clinical S-ECC dental plaque samples, for high through-put 16S rRNA sequencing and culturomics. The single colonies were cultured for further confirmation by sequencing the full length of the 16S rRNA gene after bacterial genomic DNA extraction and PCR amplification. Results Either NEMM or SHI medium showed a significant decrease in bacterial alpha diversity compared to clinical dental plaque samples by high throughput 16S rRNA sequencing analysis, indicating a larger room for the improvement of both media. NEMM displayed more living bacteria, abundant bacteria species, uncultured bacteria and capacities in carbohydrate transport and metabolism than SHI medium. The dynamic changes in bacterial community composition over time indicated that some bacteria tended to be enriched at specific time points. Culturomics and identification of bacterial species results were further confirmed by the high throughput 16S rRNA sequencing results. Conclusion We developed a new medium NEMM that could support S-ECC microbiota growth with a higher yield of living bacteria, higher abundance and capacity, and be suitable for cultivating oral uncultured bacteria via culturomics technology.
Zhang et al. (2024) Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics. PeerJ 12:e18312 https://doi.org/10.7717/peerj.18312
Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231)
Background Natural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231). Methods The optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways. Results ELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell activation, promoting the apoptosis of triple-negative human breast cancer cells (MDA-MB-231), suggesting the potential use of MEPB leaves as an anti-cancer immunostimulant.
Khalaf et al. (2024) Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231). PeerJ 12:e18420 https://doi.org/10.7717/peerj.18420
Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China
Background As one of the most essential vegetation types, grasslands play a vital role in the global carbon cycle. However, current researches on the spatial variation (SV) of soil respiration (Rs) in grasslands faces great uncertainties. Methods The SV of Rs was analysed by obtaining Rs during the early growing season of three types of grasslands (i.e., alpine meadow, desert steppe, and typical steppe) and related impact factors at 19 sites. Results The results demonstrated that during the early growing season, the Rs of the alpine meadow was the highest, followed by the typical steppe and desert steppe. Moreover, soil temperature was the primary factor affecting the SV of Rs in desert steppe. In contrast, soil water content influenced the SV of Rs in typical steppe. This study increases our understanding of the SV of Rs during the early growing season of different grasslands. It provides an important reference for accurately estimating the SV of Rs in grasslands at various time scales.
Spatial and Geographic Information Science
Liu et al. (2024) Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China. PeerJ 12:e18480 https://doi.org/10.7717/peerj.18480
A comprehensive review of oncogenic Notch signaling in multiple myeloma
Multiple myeloma remains an incurable plasma cell cancer with radical case-by-case heterogeneity. Because of this, personalized and disease-specific biology of multiple myeloma must be understood for the discovery of effective molecular targets. The highly evolutionarily conserved Notch signaling pathway has been extensively described as a multifaceted driver of the multiple myeloma disease process—contributing to both intrinsic effects of malignant cells and to widespread remodeling of the tumor microenvironment that further facilitates disease progression. Namely, Notch signaling amongst malignant cells promotes increased proliferation, tumor-initiating capacity, drug resistance, and invasiveness. Moreover, Notch signaling between malignant cells and cells of the tumor microenvironment leads to increased osteodegenerative disease and angiogenesis. This comprehensive review will discuss both the intrinsic implications of pathological Notch signaling in multiple myeloma and the extrinsic implications of Notch signaling in the multiple myeloma tumor microenvironment. Additionally, the genetic origins of Notch signaling dysregulation in multiple myeloma and current attempts at targeting Notch therapeutically will be reviewed. While the subject has been reviewed previously, recent developments in the intervening years demand a revised synthesis of the literature. The aim of this work is to introduce and thoroughly synthesize the current state of knowledge in this vein of research and to highlight future directions for both new and in-the-field scientists.
Roosma (2024) A comprehensive review of oncogenic Notch signaling in multiple myeloma. PeerJ 12:e18485 https://doi.org/10.7717/peerj.18485
The impact of doctor–patient communication on medication adherence and blood pressure control in patients with hypertension: a systematic review
Background This systematic review aims to present existing evidence concerning the effects of doctor–patient communication on medication adherence and blood pressure control in hypertensive patients. Methods Two researchers independently conducted comprehensive searches of five databases and screened relevant studies published from the inception of these databases up to July 21, 2024. The titles, abstracts, and full texts of all the retrieved articles subsequently underwent rigorous duplicate screening, according to predefined inclusion and exclusion criteria. We then synthesized the findings in a narrative format of the included studies. Finally, two researchers independently assessed study quality. Results Eighteen observational studies encompassing 21,542 patients and seven randomized controlled trials with 2,804 patients were included in the systematic review. Diverse approaches were employed for evaluating doctor–patient communication and medication adherence in these studies, with identified themes including communication content and communication skills. Various facets of doctor–patient communication, including patient satisfaction with doctor–patient communication, the specific content discussed, the style of communication, the comprehensive communication skills of doctors, and the duration of these conversations, were scrutinized. In general, the results suggest a promising link between effective doctor–patient communication and increased medication adherence and blood pressure control. Nonetheless, the presence of nuanced variations and subtle distinctions within the literature underscores the imperative for deeper exploration and consideration in clinical practice. Additionally, effective communication interventions must attain a certain threshold of intensity and endure for an adequate duration. Conclusion This review underscores the pivotal role of robust doctor–patient communication in improving both medication adherence and blood pressure control. Nevertheless, additional research may be warranted to address the disparities and subtleties in the literature and to establish precise implications for clinical practice. Moreover, in clinical practice, strategies to enhance doctor–patient communication should be incorporated, given the potential to improve medication adherence and blood pressure control among hypertensive patients. Trial registration Systematic review registration: PROSPERO with registration number CRD42024503112.
Zeng et al. (2024) The impact of doctor–patient communication on medication adherence and blood pressure control in patients with hypertension: a systematic review. PeerJ 12:e18527 https://doi.org/10.7717/peerj.18527
Understanding the progress of COVID-19 transmission in a rural district: a social network approach
Background Social interactions within and between communities influenced the spread of COVID-19. By using social network analysis (SNA), we aimed to understand the effect of social interaction on the spread of disease in a rural district. Method A retrospective record review study using positive COVID-19 cases and contact-tracing data from an area in Malaysia was performed and analysed using the SNA method through R software and visualised by Gephi software. The justification for utilizing SNA is its capability to pinpoint the individuals with the highest impact and accountability for the transmission of COVID-19 within the area, as determined through SNA. Result Analysis revealed 76 (4.5%) people tested positive for COVID-19 from 1,683 people, with 51 (67.1%) of the positive ones being male. Outdegrees for 38 positive people were between 1 and 12, while 41 people had 1–13 indegree. Older males have a higher outdegree, while younger females have a higher outdegree than other age groups among same-sex groups. Betweenness was between 0.09 and 34.5 for 15 people. We identified 15 people as super-spreaders from the 42 communities detected. Conclusion Women play a major role in bridging COVID-19 transmission, while older men may transmit COVID-19 through direct connections. Thus, health education on face mask usage and hand hygiene is important for both groups. Working women should be given priority for the work-from-home policy compared to others. A large gathering should not be allowed to operate, or if needed, with strict adherence to specific standard operating procedures, as it contributes to the spread of COVID-19 in the district. The SNA allows the identification of key personnel within the network. Therefore, SNA can help healthcare authorities recognise evolving clusters and identify potential super-spreaders; hence, precise and timely action can be taken to prevent further spread of the disease.
Mansor et al. (2024) Understanding the progress of COVID-19 transmission in a rural district: a social network approach. PeerJ 12:e18571 https://doi.org/10.7717/peerj.18571
Comprehensive evaluation of physiological response and cold tolerance of domesticated Cinnamomum camphora (L.) Presl under low temperature stress
Improving cold tolerance is one of the key techniques for introducing southern tree species to northern China. To provide a theoretical basis for the introduction and cold-tolerance cultivation of Cinnamomum camphora (L.) Presl, the physiological response and cold tolerance of acclimated Cinnamomum camphora (L.) Presl trees were studied. In this experiment, the cold tolerance physiological indexes of Cinnamomum camphora (L.) Presl were measured in an indoor artificial simulation of low temperature stress. The results showed that under low temperature stress, the Cinnamomum camphora (L.) Presl are cultivated for 1 year, 5 years, 10 years and 15 years, respectively, at 4 °C, 0 °C, −5 °C, −10 °C, −15 °C and −20 °C. The relative electrical conductivity change ranges were 26.26%–13.98%, 30.71%–19.24%, 37.36%–27.18%, 44.16%–32.24%, 63.21%–52.05%, and 86.43%–76.24%; the MDA content ranges were 12.10 mmol/g–3.25 mmol/g, 15.90 mmol/g–4.08 mmol/g, 10.53 mmol/g–2.05 mmol/g, 23.20 mmol/g–5.35 mmol/g, 31.30 mmol/g–5.89 mmol/g, and 36.47 mmol/g–8.13 mmol/g, respectively. The relative water content change ranges were 95.35%–65.92%, 71.36%–49.67%, 54.67%–34.89%, 43.12%–23.12%, 26.03%–11.21%, and 23.03%–8.15%, respectively. At the same stress temperature, these indices decreased with increasing cultivation time, and the degree of membrane damage was reduced accordingly. The osmoprotectants were soluble protein, soluble sugar, and free proline which were increased gradually with cultivation time. at 4 °C, 0 °C, −5 °C, −10 °C, −15 °C and −20 °C, the soluble protein content change ranges were 3.51–6.18 mg/g, 6.24–9.95 mg/g, 9.44–19.59 mg/g, 14.23–28.36 mg/g, 17.34–33.19 mg/g, and 25.15–32.23 mg/g. the soluble sugar content change ranges were 9.64-26.97 mg/g, 15.37–39.86 mg/g, 26.63–53.97 mg/g, 45.49–76.75 mg/g, 52.74–81.24 mg/g, and 55.61–85.34 mg/g. the free proline content change ranges were 55.83–85.23 µg/g, 68.95-89.87 µg/g, 95.38-214.38 µg/g, 219.19-389.89 µg/g, 321.28-453.65 µg/g, and 381.23-478.96 µg/g, respectively. The osmoprotectants increased the cell stability and enhanced the cold tolerance of Cinnamomum camphora (L.) Presl. Protective enzyme activity were catalase, superoxide dismutase, peroxidase which were increased gradually with cultivation time, catalase reached a maximum at about −15 °C SOD reached a maximum at about −5 °C and POD reached a maximum at about −10 °C. These results indicated that the leaves of Cinnamomum camphora (L.) Presl could reduce stress damage by increasing the activity of antioxidant enzymes to clear the active oxygen in the body. A principal component analysis showed that the relative water content, soluble protein content, soluble sugar content, and superoxide dismutase activity could be used as important indexes for cold hardiness in Cinnamomum camphora (L.) Presl. The comprehensive evaluation showed that with the increase of domestication cultivation years, Cinnamomum camphora (L.) Presl. cold tolerance gradually improved.
Ding et al. (2024) Comprehensive evaluation of physiological response and cold tolerance of domesticated Cinnamomum camphora (L.) Presl under low temperature stress. PeerJ 12:e18590 https://doi.org/10.7717/peerj.18590
The applications of anterior segment optical coherence tomography in glaucoma: a 20-year bibliometric analysis
Objective In the past 20 years, the research application of anterior segment optical coherence tomography (AS-OCT) in the field of glaucoma has become a hot topic, but there is still a lack of bibliometric reports on this scientific field. The aim of this study is to explore the research hotspots and trends in the field using bibliometric methods. Method Analyzing literature from 2004 to 2023 on AS-OCT in glaucoma within the SCI database, this study utilized Bibliometric, VOS viewer, and Cite Space for a comprehensive bibliometric analysis covering document counts, countries, institutions, journals, authors, references, and keywords. Results A total of 931 eligible articles were collected, showing a continuous increase in annual research output over the past 20 years. The United States, China, and Singapore were the top three countries in terms of publication volume, with 288, 231, and 124 articles, respectively, and there was close cooperation among these countries. The NATIONAL UNIVERSITY OF SINGAPORE, SUN YAT SEN UNIVERSITY, and SINGAPORE NATIONAL EYE CENTRE were the most productive institutions with 93, 92, and 87 articles, respectively. JOURNAL OF GLAUCOMA, INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, and OPHTHALMOLOGY were the journals with the highest number of publications, with 86, 69, and 46 articles, respectively. PROGRESS IN RETINAL AND EYE RESEARCH, published in the United States, was the top-cited journal. Researchers Aung Tin, He Mingguang, and David S. Friedman were highlighted for their contributions. The reference clustering was divided into 12 categories, among which “deep learning, anterior segment” were the most cited categories. The keywords of research frontiers include deep learning, classification, progression, and management. Conclusion This article analyses the academic publications on AS-OCT in the diagnosis and treatment of glaucoma over the last 20 years. Among them, the United States contributed the largest number of publications in this field, with the highest number of literature citations and mediated centrality. Among the prolific authors, aung, tin topped the list with 77 publications and 3,428 citations. Since the beginning of 2018, advances in artificial intelligence have shifted the focus of research in this field from manual measurements to automated detection and identification of relevant indicators.
Huang et al. (2024) The applications of anterior segment optical coherence tomography in glaucoma: a 20-year bibliometric analysis. PeerJ 12:e18611 https://doi.org/10.7717/peerj.18611
Prevalence, patterns, and determinants of drug-resistant tuberculosis in Gulf Cooperation Council countries: an updated systematic review
Drug resistance (DR) to antituberculosis drugs is a growing global problem that threatens the successful control of tuberculosis (TB) globally and within the Gulf Cooperation Council (GCC). In the GCC, TB remains a major public health issue. Understanding the prevalence and patterns of drug resistance to antituberculosis drugs is crucial for developing effective prevention and treatment strategies. Hence, the present systematic review is aimed at assessing the prevalence, pattern, and risk factors of drug-resistant TB (DR-TB) in GCC countries. We conducted this systematic review adhering to the guidelines outlined in the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) 2020 Statement. Using the relevant keywords in the major databases, we included peer-reviewed articles that were published from 01 January 2014 and onwards in English language journals. The prevalence and patterns of DR-TB levels in different countries were different. Isoniazid monoresistance was the most commonly found type of resistance, with varying degrees of prevalence of multidrug-resistant tuberculosis (MDR-TB). Risk factors for DR-TB included diabetes mellitus, past TB treatment, younger age, female gender, and renal failure. There was a positive correlation between expatriate status and DR-TB. Collaborative actions by relevant stakeholders are essential to implement evidence-based interventions that reduce the DR-TB burden and improve overall community health. Ongoing research and surveillance activities are necessary for monitoring patterns, identifying new risk factors, and providing focused interventions to lessen the threat of DR-TB on public health in GCC countries.
Alibrahim et al. (2024) Prevalence, patterns, and determinants of drug-resistant tuberculosis in Gulf Cooperation Council countries: an updated systematic review. PeerJ 12:e18628 https://doi.org/10.7717/peerj.18628
The fight against malaria in Edo-North, Edo State, Nigeria: identifying risk factors for effective control
Background This study investigated malaria epidemiology in Edo-North, Nigeria; a region within the equatorial rainforest belt that has lacked prior research on malaria prevalence. This research sought to investigate the prevalence of malaria and identify potential risk factors in Edo-North, Nigeria. Additionally, the study aimed to analyze trends in malaria cases to inform the development of effective malaria control measures. Methodology A cross-sectional study was conducted in six local government areas of Edo-North, Nigeria, between June and August 2023. Using systematic sampling, study zones, local governments, towns, villages, and households were selected. Data on sociodemographics and environmental risk factors were collected from 605 participants through questionnaires and blood samples. Blood smears were microscopically examined, binary and multivariate logistic regression was used for data analysis. Malaria disease rate trends were also analyzed from health records. Statistical analyses were performed using R software, with p-values less than 0.05 considered statistically significant. Results The overall malaria prevalence in the study area was 15.54%, with males more likely to be infected than females. Prevalence varied across localities, with Akoko-Edo having the highest rate. Children had the highest prevalence. Rural residents were more likely to have malaria than urban residents. Binary logistic regression identified several risk factors, including age, location, local government area, education, occupation, marital status, housing type, household size, water source, sanitation, surrounding environment, window net use, ceiling type, water storage, and parasite density. The multivariate logistic regression analysis identified several significant risk factors for malaria in the study population. Children, residents of Owan-East, individuals using pit latrines, and those not sleeping under LLINs were at significantly increased risk. Environmental factors such as proximity to bushes, streams/rivers, and storing water in open containers were also associated with higher malaria prevalence. History of malaria treatment at pharmacies and use of Chloroquine/Quinine medication were linked to recurrent infections. The study found a high average parasite density (5,146 parasites/μL) and low consistent LLIN use despite widespread ownership. Trend analysis from malaria records revealed a decline in malaria prevalence from 2020 to 2023. Conclusions The study identified several demographic, environmental and behavioural factors associated with malaria risk in Edo North. Males, children, urban dwellers, those living in mud houses and those in large households, proximity to natural features such as bushes, rivers and streams and low LLIN were more likely to contract malaria. These findings highlight the importance of implementing targeted interventions to address these risk factors and reduce the burden of malaria.
Braimah et al. (2024) The fight against malaria in Edo-North, Edo State, Nigeria: identifying risk factors for effective control. PeerJ 12:e18301 https://doi.org/10.7717/peerj.18301
Effects of irrigation type and fertilizer application rate on growth, yield, and water and fertilizer use efficiency of silage corn in the North China Plain
Background There is an urgent need to save water and decrease fertilizer application rates in agricultural areas of the North China Plain (NCP) and similar regions. Methods Field experiments were conducted in 2017 and 2018 in the NCP to investigate the effects of border and furrow irrigation under different fertilizer application rates on the growth, yield, and water and fertilizer use efficiencies of silage corn. The experiment applied two irrigation methods, i.e., border and furrow irrigation, each with four compound fertilizer application rates: 750, 600, 450, and 300 kg/ha. Results While the two experiment years were normal hydrological years, variation in precipitation resulted in no irrigation being applied in 2017 and 70 mm of irrigation being applied after sowing in 2018. Plants appeared to grow slightly taller and thicker with larger leaf areas, but with a 9.7% lower fresh weight yield in 2017 relative to 2018. The actual evapotranspiration (ETa) in 2017 was 37.22 mm more than that in 2018, and the higher fresh weight yield and lower ETa caused higher water use efficiency (WUE) in 2018, which was 32% higher than that in 2017. Furrow irrigation promoted growth compared with border irrigation under the same irrigation amount, but without significant effects on fresh weight yield, ETa, or WUE of silage corn. The fertilizer application amount had a significant effect on fresh weight yield and the partial fertilizer productivity of N, P and K of silage corn, but did not affect ETa or WUE of silage corn. Additionally, the fertilizer rate of 600 kg/ha induced slightly higher growth indexes and fresh weight yields compared with the fertilizer rates of 750, 450, and 300 kg/ha. Discussion In the NCP, lower irrigation amounts at the crop development period of silage corn appeared to promote higher yield, WUE, and fertilizer use efficiency, under the condition that there was sufficient water to ensure the emergence of seedlings. The current fertilizer application model, compound fertilizer applied with a seeder at planting, does not match the fertilizer needs of silage corn, and more efficient water and fertilizer application techniques should thus be adopted.
Liu et al. (2024) Effects of irrigation type and fertilizer application rate on growth, yield, and water and fertilizer use efficiency of silage corn in the North China Plain. PeerJ 12:e18315 https://doi.org/10.7717/peerj.18315
The effect of ecological characteristics on the domestication of sand rice (Agriophyllum squarrosum)
Sand rice (Agriophyllum squarrosum) is a pioneer species of annual plant found on mobile dunes in arid and semi-arid areas of China. Its establishment within the community could play a crucial role in the restoration of vegetation in desert environments because the ecological characteristics of sand rice make it well-suited to cope with desertification. Sand rice germinates rapidly when there is sufficient precipitation, and sand burial is beneficial for its germination. After germination, the root system rapidly extends downwards. It has short life cycles, completing the life span in 90 days at drought years. Additionally, sand rice has aerial and soil seed banks, which are suitable for arid ecosystems. Its seeds have high nutrient value of high protein quality and low carbohydrates. These ecological characteristics make sand rice a potentially environmentally friendly crop for addressing future climate change and maintaining food security, especially in desert areas. However it is unknown how ecological advantages affect the de novo domestication of sand rice. In this article, we summarize its ecological characteristics and determine optimal growth conditions for domestication and more applications in future.
Chen et al. (2024) The effect of ecological characteristics on the domestication of sand rice (Agriophyllum squarrosum). PeerJ 12:e18320 https://doi.org/10.7717/peerj.18320
Trends and challenges in organoid modeling and expansion with pluripotent stem cells and somatic tissue
The increasing demand for disease modeling, preclinical drug testing, and long waiting lists for alternative organ substitutes has posed significant challenges to current limitations in organoid technology. Consequently, organoid technology has emerged as a cutting-edge tool capable of accurately recapitulating the complexity of actual organs in physiology and functionality. To bridge the gaps between basic research and pharmaceutical as well as clinical applications, efforts have been made to develop organoids from tissue-derived stem cells or pluripotent stem cells. These developments include optimizing starting cells, refining culture systems, and introducing genetic modifications. With the rapid development of organoid technology, organoid composition has evolved from single-cell to multi-cell types, enhancing their level of biomimicry. Tissue structure has become more refined, and core challenges like vascularization are being addressed actively. These improvements are expected to pave the way for the construction of organoid atlases, automated large-scale cultivation, and universally compatible organoid biobanks. However, major obstacles remain to be overcome before urgently proof-of-concept organoids can be readily converted to practical applications. These obstacles include achieving structural and functional summarily to native tissue, remodeling the microenvironment, and scaling up production. This review aims to summarize the status of organoid development and applications, highlight recent progress, acknowledge existing limitations and challenges, and provide insights into future advancements. It is expected that this will contribute to the establishment of a reliable, scalable, and practical platform for organoid production and translation, further promoting their use in the pharmaceutical industry and regenerative medicine.
Ge et al. (2024) Trends and challenges in organoid modeling and expansion with pluripotent stem cells and somatic tissue. PeerJ 12:e18422 https://doi.org/10.7717/peerj.18422
Clinical efficacy and safety of organ-sparing cystectomy: a systematic review and meta-analysis
Background The clinical safety and efficacy of organ-sparing cystectomy (OSC) are subjects of ongoing debate, particularly concerning the potential increased risk of recurrence when retaining additional organs and its effectiveness in preserving sexual and urinary functions. Methods Adhering to the PRISMA 2020 statement and AMSTAR Guidelines, we conducted a systematic literature search up to February 2024 using PubMed, Embase, and Web of Science. The comparison focused on the clinical safety and effectiveness of OSC and standard radical cystectomy (SRC) in the treatment of bladder tumors. Our assessment covered several dimensions: Surgical safety outcomes (operation time, length of stay (LOS), estimated blood loss (EBL), and complications), oncological safety outcomes (recurrence rate, positive surgical margin rate, overall survival, and cancer-specific survival), and functional efficacy outcomes (daytime and nighttime urinary incontinence at 6 and 12 months, clean intermittent catheterization (CIC) rate, and erectile function within and after 1 year). Results The analysis included 19 eligible studies, encompassing 2,057 patients (1,189 OSC patients and 768 SRC patients). OSC demonstrated significant benefits in terms of erectile function and urinary continence without impacting CIC rates. No significant differences were observed in recurrence rate, positive surgical margin rate, overall survival, and cancer-specific survival. Furthermore, OSC and SRC were comparable in surgical safety outcomes, including operating time, LOS, EBL, and complications. Conclusions OSC offers notable advantages in erectile function and urinary continence. Despite limited clinical practice and potential selection bias, urologists may still consider OSC more based on their experience and specific patient factors.
Zhang et al. (2024) Clinical efficacy and safety of organ-sparing cystectomy: a systematic review and meta-analysis. PeerJ 12:e18427 https://doi.org/10.7717/peerj.18427
The evolution of resource management in Taiwanese fisheries: coastal and offshore perspectives
This study investigates the historical changes in resource development of offshore and coastal fisheries around Taiwan from 1970 to 2021 using the mean trophic level (MTL) and Fishing-in-Balance (FiB) indices. Utilizing data from the Fisheries Statistical Yearbook, three scenarios were employed to assess the effects of highly migratory, oceanic migratory, and seasonal migratory fish species on the MTL and FiB indices. The analysis revealed a continuous increase in MTL for offshore and coastal fisheries, suggesting shifts in the trophic structure and potential over-exploitation of higher trophic level species. The FiB index for offshore fisheries exhibited a declining pattern after 1990, reflecting the depletion of indigenous fish stocks, while the FiB for coastal fisheries showed an increasing trend from 1970 until the 2000s, followed by a decrease, highlighting unsustainable fishing practices. Moreover, the study identified Scomber australasicus, targeted by Taiwanese Purse Seine, as an influential species affecting the resource dynamics of offshore fisheries. The trawling fisheries would also be a crucial issue affecting the indigenous resource dynamics of offshore fisheries in Taiwan. This study identified a fishing-down mechanism within indigenous fishery dynamics. The potential over-exploitation of fish stocks could result in long-term unsustainable practices if left unaddressed. This study advocates for enhanced fisheries management through stricter regulations on fishing gear, continuous monitoring, and adaptive management strategies. These measures are essential for achieving sustainable development goals and conserving marine biodiversity in Taiwan’s waters. By addressing these critical issues, Taiwan can better manage its fisheries resources and promote ecological balance.
Wu et al. (2024) The evolution of resource management in Taiwanese fisheries: coastal and offshore perspectives. PeerJ 12:e18434 https://doi.org/10.7717/peerj.18434
Transiently elevated expression of different forms of brain-derived neurotrophic factor in the neonatal medial prefrontal cortex affected anxiety and depressive-like behaviors in adolescence
Brain-derived neurotrophic factor (BDNF) is a secreted molecule that plays an important role in the survival and growth of nerve cells. BDNF undergoes complex post-translational processing with cellular proteases. Pro- and mature BDNF forms bind to different receptor types in the brain. BDNF is prominent in the neonatal cerebral cortex. The neonatal period is critical for the proper development of the brain and nervous system. Disruptions in these critical periods can have long-lasting effects on behavior and mental health. Individuals who experience adverse effects in the neonatal period have demonstrated a predisposition to depression and other neurobehavioral disorders. In this work we studied the influence of transient expression (P3–P8) elevation of pro-, mature and mutant forms of BDNF that could not be processed with cellular convertases in the neonatal medial prefrontal cortex (mPFC) on anxiety and depressive-like behavior in adolescents. Elevated expression of mature BDNF (LV-BDNF) increased anxiety and depressive-like behavior at P30. Only immobility in the tail suspension test was increased after expression of mutant BDNF (LV-pBDNF mut). Using our RNA-seq data and available online sn-RNAseq results, we investigated transcriptomic changes in the neonatal mPFC at P8 that underlie subsequent behavioral changes. Mature BDNF expression caused an increased transcriptional response in perivascular stromal cells (PSC) with such genes: Ptgds, Slc6a13, Slc22a6, Bnc2, Slc13a4, Aldh1a2. Based on GWAS data, Ptgds is a candidate gene associated with ADHD and bipolar disorder Pujol-Gualdo et al. (2021); Marín-Méndez et al. (2012); Munkholm et al. (2015). LV-pBDNF mut caused a complete opposite set of transcriptional changes in the PSC compared to LV-BDNF. The observed similar behavioral phenotype after expression of mature and mutant forms of BDNF together with the detected genes related to bipolar disorder underpinned that Bdnf could play a substantial role in the pathogenesis of this neurobehavioral disorder.
Lanshakov et al. (2024) Transiently elevated expression of different forms of brain-derived neurotrophic factor in the neonatal medial prefrontal cortex affected anxiety and depressive-like behaviors in adolescence. PeerJ 12:e18465 https://doi.org/10.7717/peerj.18465
Binge drinking among adolescents: the role of stress, problematic internet use, and emotional regulation
Background Adolescence is a period marked by significant physical, psychological, and emotional changes as youngsters transition into adulthood. During this time, many adolescents consume alcohol, and in some cases, this leads to binge drinking, a behavior associated with various health risks and other problematic behaviors. However, knowledge about binge drinking in this population remains limited. Additionally, many adolescents engage in intensive technology use, which has been linked to mental health issues and substance abuse. Stress is often considered a precursor to both alcohol consumption and problematic internet use. In this context, emotional regulation could serve as a protective factor. Therefore, the present study aimed to examine the relationship between stress, problematic internet use, emotional regulation, and binge drinking among adolescents using structural equation modeling. Methods A cross-sectional survey was completed by a sample of 876 high school adolescents (63.57% female, mean age 16.86 years). Data were collected using an online survey, which included sociodemographic information and measures of perceived stress, emotional regulation, excessive alcohol consumption, and problematic internet use. Problematic alcohol use was assessed using several questions adapted from the ‘Survey on Drug Use in Secondary Education in Spain’. Results Problematic internet use emerged as a mediator between stress and binge drinking, suggesting that stress contributes to the development of problematic internet use, which in turn increases the likelihood of binge drinking. Furthermore, stress was negatively correlated with emotional regulation, indicating that inadequate emotional management may predispose adolescents to problematic internet use and binge drinking. The complex interplay between stress, emotional regulation, problematic internet use, and binge drinking underscores the need for comprehensive interventions targeting these factors among adolescents. Conclusions The results provide insights into potential pathways linking stress and binge drinking via problematic internet use and highlight the importance of emotional regulation as a protective mechanism against maladaptive behaviors.
Diaz-Moreno et al. (2024) Binge drinking among adolescents: the role of stress, problematic internet use, and emotional regulation. PeerJ 12:e18479 https://doi.org/10.7717/peerj.18479
Comparison of the performances of six empirical mass transfer-based reference evapotranspiration estimation models in semi-arid conditions
Background Accurately measured or estimated reference evapotranspiration (ETo) data are needed to properly manage water resources and prioritise their future uses. ETo can be most accurately measured using lysimeter systems. However, high installation and operating costs, as well as difficult and time-consuming measurement processes limit the use of these systems. Therefore, the approach of estimating ETo by empirical models is more preferred and widely used. However, since those models are well in accordance with the climatic and environmental traits of the region in which they were developed, their reliability must be examined if they are utilised in distinctive regions. This study aims to test the usability of mass transfer-based Dalton, Rohwer, Penman, Romanenko, WMO and Mahringer models in Van Lake microclimate conditions and to calibrate them in compatible with local conditions. Methods Firstly, the original equations of these models were tested using 9 years of daily climate data measured between 2012 and 2020. Then, the models were calibrated using the same data and their modified equations were created. The original and modified equations of the models were also tested with the 2021 and 2022 current climate data. Modified equations have been created using the Microsoft Excel program solver add-on, which is based on linear regression. The daily average ETo values estimated using the six mass transfer-based models were compared with the daily average ETo values calculated using the standard FAO-56 PM equation. The statistical approaches of the mean absolute error (MAE), mean absolute percentage error (MAPE), root mean square error (RMSE), Nash–Sutcliffe Efficiency (NSE), and determination coefficient (R2) were used as comparison criterion. Results The best and worst performing models in the original equations were Mahringer (MAE = 0.70 mm day−1, MAPE = 15.86%, RMSE = 0.87 mm day−1, NSE = 0.81, R2 = 0.94) and Penman (MAE = 1.84 mm day−1, MAPE = 33.68%, RMSE = 2.39 mm day−1, NSE = −0.49, R2 = 0.91), respectively, whereas in the modified equations Dalton (MAE = 0.29 mm day−1, MAPE = 7.51%, RMSE = 0.33 mm day−1, NSE = 0.97, R2 = 0.97) and WMO (MAE = 0.36 mm day−1, MAPE = 8.89%, RMSE = 0.43 mm day−1, NSE = 0.95, R2 = 0.97). The RMSE errors of the daily average ETo values estimated using the modified equations were generally below the acceptable error limit (RMSE < 0.50 mm day−1). It has been concluded that the modified equations of the six mass transfer-based models can be used as alternatives to the FAO-56 PM equation under the Van Lake microclimate conditions (NSE > 0.75), while the original equations—except for those of Mahringer (NSE = 0.81), WMO (NSE = 0.79), and Romanenko (NSE = 0.76)—cannot be used.
Usta (2024) Comparison of the performances of six empirical mass transfer-based reference evapotranspiration estimation models in semi-arid conditions. PeerJ 12:e18549 https://doi.org/10.7717/peerj.18549
Effect of cigarette smoking on the optical properties of contemporary dental ceramics: an in-vitro analysis
Background Cigarette smoking is the most common form of tobacco use worldwide. With the frequent introduction of new dental materials, the effect of smoking on their optical properties such as long term color stability, should to be thoroughly investigated. Objective This in-vitro study aims to investigate the effect of smoking on the optical properties of contemporary dental ceramics used currently for restoration of teeth. Methods Five different materials in two shades (B1 and C1) were used with 15 samples from each pressable lithium disilicate (Emax), layered lithium disilicate (Lmax), porcelain fused to metal (PFM), monolithic zirconia (MZr) and layered zirconia (LZr) were used (n = 75). The samples were exposed to conventional cigarette smoke and color stability was assessed at four different time intervals i.e., baseline, 1 week, 1 month and 6 months. CIELAB color space (CIE L*a*b*) values were used to evaluate the color difference (ΔE). A one-way analysis of variance (Anova) was used for statistical analysis of ΔE. Significant P-value was kept as <0.05, followed by Tukey post-hoc test. Results All test materials demonstrated significant color differences (ΔE) after exposure to cigarette smoke (p < 0.05). For shade B1, the highest change in shade ΔE 17.02 was exhibited by Lmax, whereas the least change in shade was exhibited by Emax followed by PFM at values of ΔE 10.11 and 11.2 respectively. For shade C1, the highest change (11.47) in shade at 6 months was demonstrated by MZr, whereas lowest values of ΔE were exhibited by Emax (7.52). Conclusions Traditional smoking causes significant change in shade of dental ceramics which can affect the esthetics of the patients. All material samples tested showed the values of ΔE > 3.3 which is higher than the acceptable range. Lowest color change was observed in Emax and PFM.
Alqahtani et al. (2024) Effect of cigarette smoking on the optical properties of contemporary dental ceramics: an in-vitro analysis. PeerJ 12:e18564 https://doi.org/10.7717/peerj.18564
Effects of plastic ingestion on blood chemistry, gene expression and body condition in wedge-tailed shearwaters (Ardenna pacifica)
Plastic pollution is a global threat and occurs in almost every marine ecosystem. The amount of plastic in the ocean has increased substantially over the past decade, posing a mounting threat to biodiversity. Seabirds, typically top predators in marine food chains, have been negatively affected by plastic pollution. Here we explored the sublethal effects of plastic ingested by wedge-tailed shearwaters (Ardenna pacifica) on the island of Maui, Hawai‘ i. Using analyses of blood chemistry, gene expression, morphometrics and regurgitated stomach contents, we investigated the effects of plastic ingestion on adult wedge-tailed shearwaters from three established colonies. We detected plastic in 12 out of 28 birds; however, we did not find significant relationships between ingested plastic, body condition, gene expression and blood analytes. We found a negative relationship between weight, blood urea nitrogen (BUN), hematocrit and potassium, that could reflect body condition in this population. Genes associated with metabolic, biosynthetic pathways, inflammatory responses, and ribosome function were also upregulated in birds placed in a ‘light weight’ category. We suggest that upregulated metabolic activity and elevated levels of hematocrit, BUN and potassium in light weight birds might imply dehydration and a response to increased energetic demand from stressors. Repetitive sampling could better inform whether body condition improves throughout the breeding season. We urge researchers to continue using multiple proxies to study effect of plastic ingestion in free-living populations.
Environmental Contamination and Remediation
Mejia et al. (2024) Effects of plastic ingestion on blood chemistry, gene expression and body condition in wedge-tailed shearwaters (Ardenna pacifica). PeerJ 12:e18566 https://doi.org/10.7717/peerj.18566
Spatiotemporal prediction of alpine wetlands under multi-climate scenarios in the west of Sichuan, China
Background The alpine wetlands in western Sichuan are distributed along the eastern section of the Qinghai-Tibet Plateau (QTP), where the ecological environment is fragile and highly sensitive to global climate change. These wetlands are already experiencing severe ecological and environmental issues, such as drought, retrogressive succession, and desertification. However, due to the limitations of computational models, previous studies have been unable to adequately understand the spatiotemporal change trends of these alpine wetlands. Methods We employed a large sample and composite supervised classification algorithms to classify alpine wetlands and generate wetland maps, based on the Google Earth Engine cloud computing platform. The thematic maps were then grid-sampled for predictive modeling of future wetland changes. Four species distribution models (SDMs), BIOCLIM, DOMAIN, MAXENT, and GARP were innovatively introduced. Using the WorldClim dataset as environmental variables, we predicted the future distribution of wetlands in western Sichuan under multiple climate scenarios. Results The Kappa coefficients for Landsat 8 and Sentinel 2 were 0.89 and 0.91, respectively. Among the four SDMs, MAXENT achieved a higher accuracy (α = 91.6%) for the actual wetland compared to the thematic overlay analysis. The area under the curve (AUC) of the MAXENT model simulations for wetland spatial distribution were all greater than 0.80. This suggests that incorporating the SDM model into land change simulations has high generalizability and significant advantages on a large scale. Furthermore, simulation results reveal that between 2021 and 2100 years, with increasing emission concentrations, highly suitable areas for wetland development exhibit significant spatial differentiation. In particular, wetland areas in high-altitude regions are expected to increase, while low-altitude regions will markedly shrink. The changes in the future spatial distribution of wetlands show a high level of consistency with historical climate changes, with warming being the main driving force behind the spatiotemporal changes in alpine wetlands in western Sichuan, especially evident in the central high-altitude and northern low-altitude areas.
Wang et al. (2024) Spatiotemporal prediction of alpine wetlands under multi-climate scenarios in the west of Sichuan, China. PeerJ 12:e18586 https://doi.org/10.7717/peerj.18586
Assessment of erectile dysfunction prevalence and associated factors in hypertensive men
Background This study aimed to assess the prevalence of erectile dysfunction and identify associated factors among male patients with hypertension. Methods A cross-sectional descriptive study was conducted. Data were gathered from 223 individuals aged 18 and above, solely diagnosed with hypertension. Information was collected through face-to-face questionnaires, personal identification forms, and the 5-question version of the International Sexual Function Index Scale. Results Among the participants, 81.6% exhibited erectile dysfunction, with a mean total score of 18.72 ± 3.60 on the 5-question version of the International Index of Erectile Function Questionnaire, indicating a mild level of dysfunction. Older age, smoking, lower educational attainment, and use of beta blockers were associated with higher levels of erectile dysfunction (p < 0.05). Discussion To mitigate modifiable risk factors influencing erectile dysfunction severity in hypertensive males, promoting healthy lifestyle choices, including diet, exercise, physiotherapy, and psychosocial support, as well as educating patients and their partners, could prove beneficial as non-pharmacological interventions.
Rashidi et al. (2024) Assessment of erectile dysfunction prevalence and associated factors in hypertensive men. PeerJ 12:e18596 https://doi.org/10.7717/peerj.18596
The effects of plasma from patients with active thyroid-associated orbitopathy on the survival and inflammation of melanoma-associated fibroblasts
Background Plasma from patients with active thyroid-associated orbitopathy (TAO-A) could cause inflammation to fibroblasts, and such a mechanism was explored in the context of melanoma. Methods Plasma samples collected from TAO-A patients and healthy control (HC) were primarily co-cultured with the melanoma-associated fibroblasts (MAFs) derived from melanoma patients. The survival and inflammation of the co-cultured MAFs were measured after confirming the levels of pro-inflammatory cytokines. Ki67 and Vimentin (VIM) markers were analyzed by immunofluorescence, and cell survival and migration were assessed using cell counting kit-8 (CCK-8) and Transwell. The THP-1 cells were induced to differentiate into macrophages, which were subsequently co-cultured to assess M1/M2 polarization status. Meanwhile, the levels of inflammatory factor were detected by enzyme-linked immunosorbent assay (ELISA). The gene expression was measured by reverse transcription quantitative PCR (RT-qPCR), and the activation of PI3K/AKT, STAT1, p65, and ERK signaling pathways was detected by Western Blot. Results Plasmas derived from TAO-A patients were characterized by elevated levels of pro-inflammatory cytokines, which enhanced the inflammation status and survival of MAFs, promoted the levels of PI3K and AKT, and downregulated expression of Bax. The co-culture of the plasma with MAFs evidently promoted M1 polarization and the phosphorylation of STAT1, P65 and ERK1/2. Conclusion These findings proved the effects of the plasmas of TAO-A patients on the survival and inflammation of MAFs, providing evidence for future studies to delve into the relevant mechanisms.
Chen et al. (2024) The effects of plasma from patients with active thyroid-associated orbitopathy on the survival and inflammation of melanoma-associated fibroblasts. PeerJ 12:e18612 https://doi.org/10.7717/peerj.18612
Tibetan red deer (Cervus canadensis wallichi) diet composition patterns and associations during lean seasons in Tibet, China
Tibetan red deer (Cervus canadensis wallichi) in the high-altitude environment of the Qinghai-Tibet Plateau could face seasonal challenges from food shortages and nutritional deficiencies but the nutritional requirements are complex. Analyzing diet composition pattern(s) is the first step to disentangle this complexity. From a systematic perspective, we hypothesize that: (A) diet composition pattern or patterns exist within the population and (B) a portion of the diet beyond characterized diet combinations will consist of random combinations. In this study, we investigated diet composition patterns of a Tibetan red deer population distributed in the Sangri Red Deer Reserve, Tibet Autonomous Region, during the harsh lean season. In March 2021 and 2022, we searched for Tibetan red deer in the reserve and collected freshly defecated samples. Diet composition at the individual level was determined using micro-histological analysis, followed by k-means clustering and co-occurrence network analysis to reveal population level diet composition patterns. Diet composition of Tibetan red deer included 14 and 19 plant species (or genera) in 2021 and 2022, respectively. K-means clustering indicated two distinct diet patterns within the population across both sampling periods. In 2021, diet composition of both clusters was dominated by Salix spp. (58.49% and 33.67%). In 2022, R. macrophylla had the highest ranking and occupied 34.83% of diet composition in the first cluster while Salix spp. (39.39%) was the most consumed food in the second cluster. Results of co-occurrence networks showed positively associated food combinations of less dominant food items, with a staple food occurring in all food item pairs in both years. However, randomness accounted for 95.83% and 93% of all food item pairs in 2021 and 2022, respectively, which implies a stable dietary complex system. The 2022 co-occurrence network displayed complex associations, while the 2021 network exhibited limited and simple associations. Our results suggest that Tibetan red deer fulfill their nutritional requirements by consuming high quantities of several food items or a balanced combination of foods with complex co-occurrence associations to overcome potential food shortages, but multilayer networks containing nutritional values and food availabilities are necessary to entangle the complexity of the dietary system.
Liang et al. (2024) Tibetan red deer (Cervus canadensis wallichi) diet composition patterns and associations during lean seasons in Tibet, China. PeerJ 12:e18614 https://doi.org/10.7717/peerj.18614
Comparative efficacy and safety of 180 W XPS vs. 120 W HPS GreenLight laser therapy for benign prostatic hyperplasia: a systematic review and meta-analysis
Objectives To compare the surgical and functional outcomes of the 120 W HPS and 180 W XPS GreenLight laser vaporization systems in the treatment of benign prostatic hyperplasia (BPH). Methods In January 2024, a comprehensive search across PubMed, Cochrane Library, and EMBASE was conducted following PRISMA guidelines, registered under PROSPERO (CRD42024531176). Studies comparing 120 W and 180 W GreenLight lasers in BPH treatment were assessed for clinical outcomes. Results Eight studies were included. The 180 W XPS system improved operation time (MD: 12.70, 95% CI [5.29–20.11], p = 0.0008), lasing duration (MD: 10.09, 95% CI [0.85–19.33], p = 0.03), and catheterization duration (MD: 0.43, 95% CI [0.12–0.74], p = 0.007). No significant differences in energy consumption, energy density, or length of hospital stay were found. Functional outcomes such as International Prostate Symptom Score and maximum urinary flow rate showed no significant differences, except in quality of life (MD: 0.43, 95% CI [0.06–0.80], p = 0.02) and prostate-specific antigen levels (MD: −0.77, 95% CI [−1.28 to −0.25], p = 0.003). The 180 W system exhibited a lower rate of overall (OR: 1.52, 95% CI [1.14–2.04], p = 0.005) and minor complications (OR: 1.84, 95% CI [1.27–2.66], p = 0.001), with no significant differences in major complications or other adverse events. Conclusions The 180 W XPS system demonstrates enhanced efficiency and reduced complication rates, offering a favorable option for BPH treatment, particularly for larger prostates. Future studies should focus on randomized trials to confirm these findings and assess long-term outcomes.
Wang et al. (2024) Comparative efficacy and safety of 180 W XPS vs. 120 W HPS GreenLight laser therapy for benign prostatic hyperplasia: a systematic review and meta-analysis. PeerJ 12:e18615 https://doi.org/10.7717/peerj.18615
Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria)
Background Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality. Methods We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2. Results D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.
Hewson et al. (2024) Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria). PeerJ 12:e18321 https://doi.org/10.7717/peerj.18321
Early-diverging plesiosaurs from the Pliensbachian (Lower Jurassic) of northwestern Germany
The knowledge of Pliensbachian (Early Jurassic, ∼192.9–184.2 Ma) plesiosaurs is notoriously insufficient. Although there have been specimens described from different parts of the world, only three of them have been established as diagnosable taxa. Here, we describe two previously unreported lower Pliensbachian plesiosaur occurrences that originate from two sites located in North Rhine-Westphalia, Germany. One of the new occurrences is represented by three cervical and three indeterminable vertebrae from Werther, the other includes two associated pectoral or anterior dorsal vertebrae from Bielefeld. Although highly incomplete, the Werther individual, which derived from the Uptonia jamesoni Zone, is found to represent the only reliably identified early Pliensbachian pliosaurid known to date. Its material is geographically and stratigraphically proximate to the late Pliensbachian pliosaurid Arminisaurus schuberti, found in a clay-pit located in the Bielefeld district of Jöllenbeck. However, even though the Werther plesiosaur and A. schuberti show a broadly similar morphology of the preserved cervical section, a precise identification of the Werther taxon is currently impossible.
Sachs et al. (2024) Early-diverging plesiosaurs from the Pliensbachian (Lower Jurassic) of northwestern Germany. PeerJ 12:e18408 https://doi.org/10.7717/peerj.18408
Diffuse idiopathic skeletal hyperostosis was the specific risk factors of methicillin-susceptible Staphylococcus aureus spine infection: a retrospective study in a single center
Aim To investigate how risk factors and reduced spinal mobility contribute to spinal infections arising from methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia, known for increased mortality and diagnostic difficulties, especially in patients with septic shock or coma. Methods This retrospective study divided MSSA bacteremia patients into three groups: spinal infections (Group A, n = 14), non-spinal/implant infections (Group B, n = 24), and implant-related infections (Group C, n = 21). Analyses focused on demographics, medical history, laboratory inflammatory markers at antibiotic initiation, and spinal pathologies detected by CT. All results of the statistical analyses were significant at P < 0.05. We employed multinomial univariable logistic regression and contingency table analysis to assess risk factors across three groups. Subsequently, binomial multivariable logistic regression was used to compare Group A against Groups B and C, successfully identifying significant predictors of spinal infection. Results A lower incidence of diabetes (p = 0.029), higher C-reactive protein (CRP) levels at onset (p = 0.014), and the presence of diffuse idiopathic skeletal hyperostosis (diffuse idiopathic skeletal hyperostosis (DISH); p = 0.022) were significantly associated with spinal infections in Group A. Furthermore, binomial analysis revealed DISH (Odds Ratio (OR) = 41.750; 95% Confidence Interval (CI) [1.86–939.0]; p = 0.019), absence of diabetes (OR = 1.20, CI [1.01–1.43], p = 0.038), elevated CRP (OR = 23.34, CI [1.13–483.4], p = 0.042), and a lower day 3/day 1 white blood cell (WBC) ratio (OR = 0.964, CI [0.93–1.00], p = 0.047) as risk factors when compared with other groups. Conclusion Spinal infection patients with MSSA bacteremia are less likely to have diabetes and more likely to have higher initial CRP levels and DISH. Notably, DISH might be emerging as a distinctive risk factor for spinal infection, underscoring its potential as a marker for clinical awareness.
Endo (2024) Diffuse idiopathic skeletal hyperostosis was the specific risk factors of methicillin-susceptible Staphylococcus aureus spine infection: a retrospective study in a single center. PeerJ 12:e18432 https://doi.org/10.7717/peerj.18432
Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma
Canine cutaneous histiocytoma (CCH) is a tumor that originates from dermal Langerhans cells and affects particularly young dogs. The common spontaneous regression of CCH makes it an interesting model in comparative oncology research. Previous studies have indicated that anti-tumor immune responses may be involved, but details remain speculative to date. Here, we asked which specific immuno-oncological dynamics underlie spontaneous regression of CCH on mRNA and protein levels. QuantSeq 3′ mRNA sequencing with functional over-representation analysis and an nCounter RNA hybridization assay were employed on 21 formalin-fixed, paraffin-embedded CCH samples representing three different tumor stages (dataset information: GSE261387—Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma—OmicsDI). Nine additional samples were subjected to matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Surprisingly, only minor stage-specific differences were found. When we investigated expression of B7 family ligands and CD28 family receptors holding co-stimulatory and -inhibitory functions, respectively, we found a higher abundance of CD80, CD86, CTLA4 and CD28, which may trigger a balanced activation of lymphocyte-mediated immune responses. CD80 and CD86 expressing cells were further quantified by in situ hybridization and compared with data from three cases of canine histiocytic sarcoma (HS), a malignant tumor variant originating from antigen-presenting interstitial dendritic cells. A stage-specific increase of CD80 expressing cells was recorded in CCH from the tumor bottom to the top, while CD86 was continuously and homogenously expressed at high levels. Overall expression of CD80 in CCH was similar to that in HS (73.3 ± 37.4% vs 62.1 ± 46.4%), while significantly more CD86 expressing tumor cells were found in CCH (94.7 ± 10.3%) when compared to HS (57.6 ± 11.0%). Our data suggest that major immuno-oncological pathways are not regulated during regression of CCH on the mRNA or protein levels as detectable by the methods used. Instead, our data provide further evidence supporting previous hypotheses towards a role of immune stimulatory B7 family ligands and CD28 family receptors in the regression of CCH.
Loriani Fard et al. (2024) Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma. PeerJ 12:e18444 https://doi.org/10.7717/peerj.18444
LRR1 involved in the abscisic acid signaling pathway to regulate the early growth and development of Arabidopsis thaliana
Background Living organisms possess the remarkable capacity to swiftly adapt to fluctuations in their environment. In the context of cell signal transduction, a significant challenge lies in ensuring the effective perception of external signals and the execution of appropriate responses. To investigate this phenomenon, a recent study utilized Arabidopsis thaliana as a model plant and induced stress by administering abscisic acid (ABA), a plant hormone, to elucidate the involvement of leucine-rich repeat receptor-like kinase1 (LRR1) in ABA signaling pathways. Methods Homozygous T-DNA insertion alleles for LRR1 and KIN7 were isolated. Quantitative real-time PCR (qRT-PCR) was performed to confirm the expression of the LRR1 gene. Subcellular localization and beta-glucuronidase (GUS) tissue labeling techniques were utilized to determine the expression pattern of the LRR1 gene in cells and tissues. Yeast two-hybrid complementation, bimolecular fluorescence complementation assay, and GST pull-down assays were conducted to validate the interaction of LRR1 proteins. Results Phenotypic analyses revealed that lrr1 and kin7 mutants are less sensitive to the inhibitory effects of ABA on germination and cotyledon greening that is seen in WT. Mutants LRR1 and kinase 7 (KIN7) exhibited resistance to ABA and displayed normal growth patterns under control conditions. The double mutant lrr1kin7 showed reduced responsiveness to ABA. Conversely, overexpression lines LRR1ox2 and LRR1ox10 demonstrated heightened sensitivity to ABA, resulting in severe growth reduction. qRT-PCR assay indicated that exogenous application of ABA led to significant down-regulation of ABI3, ABI4, and ABI5 transcription factors in LRR1 material compared to wild-type WT material. An investigation was conducted to determine the expression pattern and transcriptional level of LRR1 in Arabidopsis. The results revealed ubiquitous expression of LRR1 across all developmental stages and tissue tested. Subcellular localization assays confirmed the presence of LRR1 on the plasma membrane of cells. Furthermore, BiFC assay, yeast two-hybrid complementation, and GST pull-down assays demonstrated an interaction between LRR1 and PYL6 in vitro. These findings provide substantial insights into the involvement of LRR1 in the ABA signaling pathway while regulating seed germination and cotyledon greening during early development in Arabidopsis. This study significantly advances our understanding regarding the correlation between LRR1 and ABA signaling pathways with potential applications for enhancing crop stress resistance.
Xie et al. (2024) LRR1 involved in the abscisic acid signaling pathway to regulate the early growth and development of Arabidopsis thaliana. PeerJ 12:e18460 https://doi.org/10.7717/peerj.18460
A structural equation model for the patient safety competency of clinical nurses
Background Nurses are crucial for enhancing patient safety due to their continuous presence at patients’ bedsides and close interactions with families and other healthcare providers. This study aims to examine the relationships among safety education, perception of patient safety culture, safety control, and patient safety competence in clinical nurses, while also exploring the mediating effect of perceptions on patient safety culture and safety control. Methods The study involved 165 nurses, including 10 males (6.1%) and 155 females (93.9%). Structural equation modeling (SEM) was used to test the hypothesized model, and data were analyzed using SPSS and AMOS programs. Results Significant positive correlations were among the frequency of attending safety education, the perception of patient safety culture, safety control, and patient safety competency. The number of safety education briefings attended did not directly influence patient safety competence; however, safety education for nurses indirectly influenced patient safety competence via the perception of patient safety culture and safety control. These findings suggest that enhancing safety education for nurses can improve patient safety competence by shaping their perceptions of patient safety culture and safety control.
Choi et al. (2024) A structural equation model for the patient safety competency of clinical nurses. PeerJ 12:e18462 https://doi.org/10.7717/peerj.18462
Multi-environment QTL mapping identifies major genetic loci influencing soybean main stem node architecture
Soybean plant architecture has a significant impact on yield potential, but the genetic underpinnings of key architectural traits remain elusive. The primary objective of this study was to explore the genetic foundations underlying main stem node number (MSN) in soybeans. Recombinant inbred lines (RILs) contained a 234 individual derived from crosses between two cultivars Zhonghuang35 (ZH35) and Jindou21 (JD21) was evaluated for seed hardness across 3 years (2013, 2014, and 2015 in Gansu). Markedly, the parent varieties, shown significant differences in MSN. Also, the RIL population exhibited a wide range of genetic variation in MSN. A high-density genetic map composed of 8,078 specific-locus amplified fragment (SLAF) markers, spanning 3,480.98 centimorgans (cM) with an average inter-marker distance of 0.59 cM were used to construct linkage map. Using ICIM analysis identified a total of 23 Quantitative Trait Loci (QTLs) across the 20 chromosome, of which five QTLs were detected in multiple years in Chr.6. Notably, we identified a stable major QTL, qMSN-6-4, explaining up to 24.81% of phenotypic variation. This QTL govern seven candidate genes with potential roles in regulating MSN development in soybean, including Glyma.06G027500 with a domain of unknown function, Glyma.06G027600 involved in proton transport, Glyma.06G027700 linked to proteolysis, Glyma.06G027900 related to transcriptional regulation, and Glyma.06G028000 and Glyma.06G028050 associated with membrane functions. The RT-PCR analysis confirmed that these genes were expressed differently between the parental lines this supports the idea that they may play a role in determining MSN. Glyma.06G027500 and Glyma.06G027600 showing higher expression in JD21 leaves and nodes, while Glyma.06G027700 and Glyma.06G028000 exhibited increased expression in ZH35 stems, highlighting their distinct roles in transcription regulation, membrane activities, and protein degradation that contribute to MSN formation in soybean. This study offers valuable insights into the genetic mechanisms governing soybean MSN, providing a foundation for future research and crop improvement efforts.
Ren et al. (2024) Multi-environment QTL mapping identifies major genetic loci influencing soybean main stem node architecture. PeerJ 12:e18539 https://doi.org/10.7717/peerj.18539
Effect of GR24 on the growth and development of licorice under low phosphorus stress
Background Glycyrrhiza, a perennial herbaceous medicinal plant, is extensively utilized in the pharmaceutical industry. The growth of Glycyrrhiza is frequently constrained by soil phosphorus availability, as a significant portion of arable land in China suffers from phosphorus deficiency. Method This study utilized Ural Glycyrrhiza uralensis Fisch as the subject and examined the application of GR24, a synthetic strigolactone, under three phosphorus conditions: none (P1), low (P2), and high (P3). The research aimed to ascertain the optimal concentration of GR24 for promoting licorice growth and development, thereby providing a theoretical foundation for its agricultural management. Results The optimal GR24 concentration for P3 and P2 conditions was identified as G3 (10 µM), which enhanced growth metrics, chlorophyll a and b levels, while also boosting antioxidant enzyme activities in licorice. Specifically under P3, significant increases in liquiritigenin and glycyrrhizic acid levels were observed. Under P2, increases were noted in isoliquiritigenin, liquiritigenin, and liquiritin levels. Transcriptome analysis revealed differential gene, with 137 and 270 genes up-regulated and 77 and 294 genes down-regulated in the P3 and P2 treatments, respectively. GO functional enrichment identified 132 and 436 differentially expressed genes for P3 and P2 respectively, while KEGG pathways were predominantly enriched in plant-pathogen interactions and phenylpropanoid biosynthesis. Application of GR24 in P1 conditions did not significantly affect growth indices but did enhance glycyrrhetic acid, isoliquiritin, and liquiritin accumulation. Transcriptome profiling in this treatment identified 465 up-regulated and 1,109 down-regulated genes. GO annotation involved 1,108 differentially expressed genes, and KEGG analysis was primarily enriched in the plant-pathogen interaction pathway. Furthermore, transcription factor analysis revealed alterations in the C2H2, NAC, and MYB families, which are associated with phosphorus response.
Jing et al. (2024) Effect of GR24 on the growth and development of licorice under low phosphorus stress. PeerJ 12:e18546 https://doi.org/10.7717/peerj.18546
Divergent effects of short-term and continuous anthropogenic noise exposure on Western Bluebird parental care behavior
Sensory environments are rapidly changing due to increased human activity in urban and non-urban areas alike. For instance, natural and anthropogenic sounds can interfere with parent-offspring communication and mask cues reflective of predation risk, resulting in elevated vigilance at the cost of provisioning. Here we present data from two separate studies involving anthropogenic noise and nestling provisioning behavior in Western Bluebirds (Sialia mexicana): one in response to short-term (1 h) experimental noise playback and a second in the context of nests located along a gradient of exposure to continuous noise. In the short-term playback experiment, nests were sequentially exposed to trials with either traffic noise or a silent audio track. The effect of the playback type interacted with the effect of the order in which trials were presented. The outcome was that provisioning rates during second trials with the silent track playback were higher than provisioning rates during noise playback on first or second trials, but not first trials with the silent track playback. Additionally, failed provisioning attempts only occurred during noise trials. In contrast, provisioning rates increased with the amplitude of noise among nests located in a gradient of continuous noise exposure. For nests along the noise gradient, the latency to resume provisioning behavior following human disturbance from approaching the nest negatively covaried with noise exposure amplitude. Specifically, birds resumed provisioning behavior more quickly with increased noise amplitude. Collectively, both studies demonstrate that noise can influence avian parental care of offspring, but the direction of the effect of noise are opposite. This difference could reflect variation in populations, noise characteristics or latent environmental contexts, or different ages of nestlings. However, it is also possible that the divergent responses reflect important differences in organismal responses to short-term versus long-term noise exposure. The possibility of mismatches in responses to short-term versus long-term noise exposure should be the focus of additional research, especially because short-term noise exposure experiments are often used to understand the consequences of noise pollution for organisms living in noisy environments.
Ozkan et al. (2024) Divergent effects of short-term and continuous anthropogenic noise exposure on Western Bluebird parental care behavior. PeerJ 12:e18558 https://doi.org/10.7717/peerj.18558
Evaluation of nutrient content of different harvest stages in switchgrass (Panicum virgatum L.) cultivars
Panicum virgatum L., also known as switchgrass, is a warm season short-day, C4-perennial crop gaining attention in feedstock production. The harvest stage of the forage crops and the cultivars used directly affect the feed quality as animal feed. In this study, differences were evaluated in various macro element contents of switchgrass (Panicum virgatum L.) cultivars at different harvest stages. Eight different switchgrass cultivars (Alamo, BoMaster, Kanlow, Cave in Rock, Long Island, Shawnee, Shelter, and Trailblazer) were evaluated in the study. According to the results of the study, significant differences were found among the cultivars studied for phosphate (P), potassium (K), calcium (Ca), and magnesium (Mg). The Long Island cultivar had the highest mineral concentration (0.223% P, 1.049% K, 0.581% Ca, and 0.201% Mg). As harvest proceeded, the levels of P and K in the plants decreased while the levels of Ca and Mg increased. The highest P (0.223%) and K (1.030%) values were obtained from plants harvested at the pre-flowering stage, while the highest Ca (0.538%) and Mg (0.183%) values were obtained from plants harvested at the full flowering stage. Switchgrass cultivars were found to be insufficient to meet animal needs for P and Ca content throughout the plant’s harvest stages. Mg was found to be sufficient in all harvest stages, while K was sufficient in the first two harvest stages, pre-flowering and 50% flowering, but insufficient in the full flowering stage. The dry matter’s Ca/P ratio, regardless of cultivar or harvest stage, posed no risk to animal health. The K/(Ca+Mg) ratio varied between 0.807 and 1.235 depending on the cultivar and harvest stage. This ratio does not pose any risk to animal health. Based on these results, it would be appropriate to supplement feed rations with materials containing P and Ca or to use switchgrass in animal feeding together with feeds rich in these minerals when using dry matter obtained from switchgrass cultivars alone as roughage. In general, although Panicum virgatum has an important potential as a feed source in animal nutrition, it needs to be supplemented with nutrient-containing additives. It would also be appropriate to determine the nutrient content of these varieties under different ecological conditions.
Acikbas (2024) Evaluation of nutrient content of different harvest stages in switchgrass (Panicum virgatum L.) cultivars. PeerJ 12:e18570 https://doi.org/10.7717/peerj.18570
Phase angle as a predictor of mortality in elderly patients with multimorbidity: a matched case-control study
Background We aimed to investigate the value of phase angle (PhA) as a prognostic marker for mortality in elderly patients with multimorbidity using a matched case-control study. Methods This study was conducted with patients 70 years of age or older with multimorbidity at Beijing Geriatric Hospital. The body composition parameters including PhA were determined using bioelectrical impedance analysis. Common hematological indices were determined using blood tests. The outcome was mortality 1 year after admission. A multivariate logistic regression analysis was employed to identify independent risk factors for death. A receiver-operating characteristic (ROC) curve analysis was used to evaluate the performance of risk factors in predicting death. Results A total of 30 deceased patients were included in the death group. The living patients were matched 1:1 with the deceased patients in age, gender, and Cumulative Illness Rating Scale-Geriatric score to generate a survival group of 30. The death group exhibited higher levels of blood urea nitrogen and extracellular water to total body water ratio and lower levels of PhA and prealbumin than the survival group. The multivariate logistic regression analysis identified PhA as the only independent risk factor for mortality (OR = 3.296, 95% CI [1.201–9.044], P < 0.05). For the ROC curve analysis, PhA had an area of 0.854 (95% CI [0.755–0.955], P = 000). The Youden index was 0.700, and the optimal cutoff value associated with the Youden index was 2.45°. Conclusion PhA serves as a good prognostic marker for mortality in elderly patients with multimorbidity.
Wang et al. (2024) Phase angle as a predictor of mortality in elderly patients with multimorbidity: a matched case-control study. PeerJ 12:e18592 https://doi.org/10.7717/peerj.18592
Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment
The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.
McCartin et al. (2024) Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment. PeerJ 12:e18607 https://doi.org/10.7717/peerj.18607
Ferroptosis and its implications in bone-related diseases
Ferroptosis, a recently recognized form of regulated cell death (RCD) characterized by iron-dependent lipid peroxide accumulation, has emerged as a noteworthy regulator in various bone-related diseases, including osteoporosis (OP), osteoarthritis (OA), and osteosarcoma (OS). OS primarily afflicts the elderly, rendering them susceptible to fractures due to increased bone fragility. OA represents the most prevalent arthritis in the world, often observed in the aging population. OS predominantly manifests during adolescence, exhibiting an aggressive nature and bearing a significantly unfavorable prognosis. In this review article, we present an overview of the characteristics and mechanism of ferroptosis and its involvement in bone-related diseases, with a particular focus on OP, OA, and OS. Furthermore, we summarize chemical compounds or biological factors that impact bone-related diseases by regulating ferroptosis. Through an in-depth exploration of ferroptosis based on current research findings, this review provides promising insights for potential therapeutic approaches to effectively manage and mitigate the impact of these bone-related pathological conditions.
Wang et al. (2024) Ferroptosis and its implications in bone-related diseases. PeerJ 12:e18626 https://doi.org/10.7717/peerj.18626
Effect of basal luteinizing hormone/follicle-stimulating hormone ratio on clinical outcome of In Vitro fertilization in patients with polycystic ovarian syndrome: a retrospective cohort study
Background The basal luteinizing hormone (LH) and the prior LH to follicle-stimulating hormone (FSH) ratio (LH/FSH) in polycystic ovarian syndrome (PCOS) are generally higher than those in non-PCOS patients and the general population. The potential negative effects of elevated LH on human reproductive function are highly controversial, as are the effects of down-regulation of LH on reproductive function. The purpose of this study was to evaluate the effect of the basal LH/FSH ratio on the live birth rate of PCOS patients undergoing in vitro fertilization (IVF) cycles. Methods A retrospective analysis was conducted on 698 patients with polycystic ovary syndrome undergoing IVF treatments with a mild stimulation protocol (n = 95) and a gonadotropin-releasing hormone (GnRH) agonist protocol (n = 603). The basal LH/FSH ratio of 2 was used as the cut-off value for further subgroup analysis. The demographic properties, controlled ovarian hyperstimulation (COH) processes, and clinical pregnancy outcomes were compared between groups under each ovulation stimulation protocol. Results The live birth rate for patients with a LH/FSH ratio ≥ 2 group (56.38%, n = 149) was not statistically different from that of the ones with a ratio < 2 (53.74%, n = 454) in the GnRH agonist protocol (P = 0.576). Correspondingly, the live birth rate for the LH/FSH ratio ≥ 2 group (43.48%, n = 23) also showed no statistical difference from the ratio < 2 group (48.61%, n = 72) in the mild stimulation protocol (P = 0.668). Additionally, LH/FSH ratios had no significant effect on the live birth rate after adjusting for confounders both in the GnRH agonist protocol (adjusted OR: 1.111; 95% CI [0.467–2.642], P = 0.812) and in the mild stimulation protocol (adjusted OR: 4.057; 95% CI [0.431–38.195], P = 0.221). Furthermore, there was no significant difference in the live birth rate between different ovulation stimulation protocols in PCOS patients with the LH/FSH ratio ≥ 2. Conclusions The live birth rate in IVF outcomes was not affected by an elevated basal LH/FSH ratio in patients with polycystic ovary syndrome. The choice of the GnRH agonist protocol or mild stimulation protocol for ovulation stimulation does not affect the final clinical outcomes either for PCOS patients with a basal LH/FSH ratio ≥ 2.
Shan et al. (2024) Effect of basal luteinizing hormone/follicle-stimulating hormone ratio on clinical outcome of In Vitro fertilization in patients with polycystic ovarian syndrome: a retrospective cohort study. PeerJ 12:e18635 https://doi.org/10.7717/peerj.18635
Method selection affects the estimates of residency and site fidelity in bottlenose dolphins: testing sensitivity and performance of different methods using mark-resight data
Residency (R) and site fidelity (SF) are important parameters in population ecology, yet their quantification poses challenges in marine mammals. Based on a previous review, this study used simulated and empirical mark-resight data to assess the variations and performance of the most used R (n = 8) and SF (n = 11) indices in peer-reviewed literature under different scenarios. We applied the Jolly-Seber model to simulate thousands of bottlenose dolphin populations varying resighting (p) and survival (Phi) probabilities, and performed calibration, sensitivity, and validation analyses. Our results underscore the effects of p and Phi on individual categorization within the diverse simulated conditions, representing the often-overlooked heterogeneity in residency classification for Tursiops populations. All SF indices showed similar and consistent performance (>0.70 Gower’s distance) across the simulated scenarios, even when compared to field study data from wild dolphin populations (i.e., Savannah, USA, and Alvarado, Mexico); thus, SF should be a critical parameter for interstudy comparisons. Conversely, R indices were remarkably different based on their definitions and classification criteria. The different thresholds among definitions largely biased the proportion of residents and transient individuals (or occasional visitors) even leading to counterintuitive outcomes. This emphasizes the importance of considering trade-offs in R index selection aligned with project goals, specific sampling efforts, and population dynamics. For instance, the simplified binomial categorization of R defined by Conway (2017) (https://digitalcommons.coastal.edu/etd/10/) easier to interpret but R indices incorporating temporal components (e.g., monthly, seasonal, and annual) outperformed (>0.70 Gower’s distance) other R indices lacking such criteria. This allowed for a more detailed representation of the temporal structure of the population, and higher consistency and accuracy while classifying individuals. Also, although the residency categories proposed by Möller, Allen & Harcourt (2002) (DOI 10.1071/AM02011) did not perform as well, these seemed to fit better when dealing with data gaps across spatial and temporal scales. Our results contribute to the ongoing discussion on methodological implications for the interpretation of ecological patterns, facilitating a nuanced understanding of population dynamics, aiding scientists, and conservation agencies in making informed decisions for bottlenose dolphin populations worldwide.
Huesca-Domínguez et al. (2024) Method selection affects the estimates of residency and site fidelity in bottlenose dolphins: testing sensitivity and performance of different methods using mark-resight data. PeerJ 12:e18329 https://doi.org/10.7717/peerj.18329
Testing the ‘parasite-mediated domestication’ hypothesis: a comparative approach to the wild boar and domestic pig as model species
The mechanisms underlying the domestication process have already been well explained. Starting with Belyaev’s pioneering experiment on silver foxes, which showed that selection for tameness (reduced fear response, changes in the ‘hypothalamic-pituitary-adrenal system’—HPA axis) leads to destabilisation of the regulatory systems that control morphological and behavioural development, resulting in the changes characteristic of the domestication syndrome. Later, the thyroid rhythm hypothesis and the neural crest cell (NCC) hypothesis provided additional explanations. Recently, the parasite-mediated domestication hypothesis (PMD) has been proposed, suggesting an important role of endoparasites in the domestication process. Since parasites either directly or indirectly affect all mechanisms underlying the domestication syndrome (HPA, thyroid, NCC), the PMD proposes that they may be an important trigger of domestication. PMD can be tested either experimentally or comparatively. One of the basic assumptions of PMD is that parasite-susceptible, genetically less resistant/more tolerant wild animals were originally domesticated and that the susceptibility to parasites has been passed on to today’s domestic animals. This can be verified primarily by comparing the parasite susceptibility of existing wild and domestic populations of the same species. We, therefore, followed a systematic comparative approach by analysing the parasite load in wild boar (WB) and free-ranging domestic pig (DP) populations from a comparable environment in a geographically close area. Fresh faeces from WB and DP populations, one each from Slovenia (SI) and Croatia (HR), were sampled. A total of 59 individual faecal samples were collected (SI: 12 WB, 20 DP; HR: 14 WB, 13 DP). Parasitological diagnostics were carried out using the sedimentation and floatation method. Five different taxa were found in WB and seven in DP. Three parasite taxa were found exclusively in DP (Cystoisospora suis, Trichuris sp., Balantidium coli), and one (Strongyloides sp.) only in WB. Of the parasites found in both cohorts, strongyles/Oesophagostomum sp. were significantly more abundant in DP, while Eimeria sp. was found in equal amounts in both (but in HR only in WB). According to the preliminary study presented here, there is evidence to support the PMD baselines in the wild boar—domestic pig association. However, we cannot draw a definitive conclusion as there are many aspects that may bias the interpretation based on parasite load alone, which are also discussed here. Therefore, comparative studies should be supported by a more focussed methodology, including an experimental approach.
Oleinic et al. (2024) Testing the ‘parasite-mediated domestication’ hypothesis: a comparative approach to the wild boar and domestic pig as model species. PeerJ 12:e18463 https://doi.org/10.7717/peerj.18463
Effect of kinematics on ground reaction force during single-leg jump landing in children: a causal decomposition approach in jumpers and non-jumpers
Background The interaction between joint kinematics and kinetics is usually assessed by linear correlation analysis, which does not imply causality. Understanding the causal links between these variables may help develop landing interventions to improve technique and create joint-specific strengthening programs to reduce reaction forces and injury risk. Objective Therefore, the aim of this study was to analyze the causal interaction between lower limb sagittal kinematics and vertical ground reaction force (VGRF) during single-leg jump landing in children who are jumpers (volleyball and gymnastics) and non-jumpers, using the causal empirical decomposition method. Our hypothesis is that children who participate in jumping sports, compared to those who do not, employ a different joint strategy to regulate ground reaction forces during landing, particularly at the ankle level. Methods Two groups were compared: the jumpers group (n = 14) and the non-jumpers (control group, n = 11). The causal interaction between sagittal kinematics and VGRF was assessed using ensemble empirical mode decomposition (EEMD) and time series instantaneous phase dependence in bi-directional causality. The relative causal strength (RCS) between the time series was quantified as the relative ratio of absolute cause strength between kinematics and VGRF. Results A significant interaction between joint and group was found for RCS (p = 0.035, η2p = 0.14). The post-hoc analysis showed the jumpers group had higher ankle-to-VGRF RCS than the control group (p = 0.017, d = 1.03), while in the control group the hip-to-VGRF RCS was higher than the ankle-to-VGRF RCS (p = 0.004, d = 0.91). Conclusion Based on the causal decomposition approach, our results indicate that practicing jumping sports increases the causal effect of ankle kinematics on ground reaction forces in children. While non-jumper children rely more on the hip to modulate reaction forces, jumper children differ from non-jumpers by their greater use of the ankle joint. These findings could be used to develop specific training programs to improve landing techniques according to practice level, potentially helping to reduce the risk of injury in both athletes and non-athletes.
Cruz-Montecinos et al. (2024) Effect of kinematics on ground reaction force during single-leg jump landing in children: a causal decomposition approach in jumpers and non-jumpers. PeerJ 12:e18502 https://doi.org/10.7717/peerj.18502
Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes
Background This study provides new information on long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the hair follicles of Hetian sheep via the sequencing and analysis of the transcriptome of skin hair follicles during three periods of periodicity change. This is important for improving the quality of carpet wool, providing a preliminary basis for further research on the targeting relationship of these mRNAs and their target genes, and providing a scientific basis for marker-assisted selection of Hetian sheep. Methods The periodic variation of anagen (P I, May, n = 3), catagen (p II, October, n = 3), and telogen (p III, January, n = 3) of the skin hair follicle tissue of three Hetian sheep ewes were selected. Skin samples were collected from the right mid-side of each sampled sheep at three hair follicle developmental stages. The three sheep were used for each developmental stage as biological and technical replicates for transcriptome sequencing and analysis. Results The statistical power of this experimental design, calculated in RNASeqPower, was 0.92. Differential expression analysis revealed 81 lncRNAs that were differentially expressed (46 up-regulated and 35 down-regulated) and 129 mRNAs that were differentially expressed (46 up-regulated and 83 down-regulated) during the PI and PII periods. Between the PI and PIII periods, a total of 144 differentially expressed lncRNAs and 693 differentially expressed mRNAs were identified. Of these, 73 lncRNAs were significantly up-regulated and 71 were significantly down-regulated, while 474 mRNAs were significantly up-regulated and 219 were down-regulated. Additionally, a total of 87 lncRNAs were found to be differentially expressed, with 40 up-regulated and 47 down-regulated, along with 39 differentially expressed mRNAs (23 up-regulated and 16 down-regulated), between the PII and PIII stages. The functional assessment revealed that the mRNA expressed in the cells is related to the membrane, cell processes, metabolism, extracellular region, and other GO items. It is enriched in thyroid hormone synthesis, choline metabolism, cancer, AMPK, Hedgehog, and other signaling pathways. Conclusion A total of 2,286 lncRNAs (including 965 known and 1,321 novel lncRNAs) and 20,879 mRNAs were identified. These co-expressed differentially expressed genes could be used as candidate genes for studying the periodic changes of the hair follicles in Hetian sheep.
Chen et al. (2024) Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes. PeerJ 12:e18542 https://doi.org/10.7717/peerj.18542
Diversity, antibacterial and phytotoxic activities of actinomycetes associated with Periplaneta fuliginosa
Background Insect-associated actinomycetes represent a potentially rich source for discovering bioactive metabolites. However, the diversity, antibacterial and phytotoxic activities of symbiotic actinomycetes associated with Periplaneta fuliginosa have not yet been conducted. Results A total of 86 strains of actinomycetes were isolated from the cornicles and intestines of both nymphs and adults of P. fuliginosa. Diversity analysis revealed that the isolated strains were preliminarily identified as 17 species from two genera, and the dominant genus was Streptomyces. A total of 36 crude extracts (60%) obtained from the supernatant of the 60 fermented strains exhibited a potent antibacterial activity against at least one tested pathogenic bacterium. Among these active strains, 27 crude extracts (75%) exhibited phytotoxic activity against the radicle of Echinochloa crusgalli. Furthermore, seven known compounds, including methoxynicotine (1), (3Z,6Z)-3-(4-methoxybenzylidene)-6-(2-methylpropyl) piperazine-2,5-dione (2), XR334 (3), 1-hydroxy-4-methoxy-2-naphthoic acid (4), nocapyrone A (5), β-daucosterol (6), and β-sitosterol (7) were isolated from an active rare actinomycete Nocardiopsis sp. ZLC-87 which was isolated from the gut of adult P. fuliginosa. Among them, compound 4 exhibited moderate antibacterial activity against Micrococcus tetragenus, Staphylococcus aureus, Escherichia coli, and Pseudomonas syringae pv. actinidiae with the zone of inhibition (ZOI) of 14.5, 12.0, 12.5, and 13.0 mm at a concentration of 30 μg/disc, respectively, which was weaker than those of gentamicin sulfate (ZOI of 29.5, 19.0, 18.5, and 24.5 mm). In addition, the compound 4 had potent phytotoxic activity against the radicle of E. crusgalli and Abutilon theophrasti with the inhibition rate of 65.25% and 92.68% at the concentration of 100 μg/mL. Conclusion Based on these findings, this study showed that P. fuliginosa-associated actinomycetes held promise for the development of new antibiotic and herbicide resources.
Liu et al. (2024) Diversity, antibacterial and phytotoxic activities of actinomycetes associated with Periplaneta fuliginosa. PeerJ 12:e18575 https://doi.org/10.7717/peerj.18575
Feldspathic sandstone as an emerging soil stabilizer for aeolian sand in the Mu Us Sandy Land: insights into particle size distribution
Stabilization of aeolian sand is essential for achieving desertification control, soil and water conservation, and agricultural development in sandy lands. Feldspathic sandstone is a soft clay rock widely found in the Mu Us Sandy Land. The purpose of this study was to ascertain the mechanism for aeolian sand stabilization with feldspathic sandstone from the perspective of particle size distribution. Feldspathic sandstone was added to aeolian sand at different ratios (mf:ms = 1:0, 1:1, 1:2, 1:5, and 0:1, where mf is the mass of feldspathic sandstone and ms is the mass of aeolian sand). The results showed that the soil texture was modified upon addition of feldspathic sandstone. The content of particles <0.05 mm increased with increasing addition ratio of feldspathic sandstone, in contrast to the downward trend observed for particles >0.05 mm. Consequently, the soil texture changed from sand to sandy loam, then loam, and finally silty loam. The addition of feldspathic sandstone ameliorated aeolian sand, resulting in a broader particle size distribution and lower particle size uniformity. Continuously well-graded soil was obtained at mf:ms = 1:5 (coefficient of uniformity: 54.71; coefficient of curvature: 2.54) or 1:2 (coefficient of uniformity: 76.21; coefficient of curvature: 1.12). While the addition of feldspathic sandstone solved the problem of single particle size distribution in aeolian sand, the presence of aeolian sand prevented soil compaction caused by the high clay content of feldspathic sandstone. Findings of this study indicate that the addition of feldspathic sandstone to aeolian sand leads to the mixing of various sized particles and continuous gradation of the soil. Although a higher addition ratio of feldspathic sandstone is more favorable for soil texture improvement, mf:ms = 1:5 is recommended for practical application in terms of particle gradation and cost effectiveness.
Zhang et al. (2024) Feldspathic sandstone as an emerging soil stabilizer for aeolian sand in the Mu Us Sandy Land: insights into particle size distribution. PeerJ 12:e18577 https://doi.org/10.7717/peerj.18577
Balance training in older adults enhances feedback control after perturbations
Background As we age, avoiding falls becomes increasingly challenging. While balance training can mitigate such challenges, the specific mechanisms through which balance control improves remains unclear. Methods We investigated the impact of balance training in older adults on feedback control after perturbations, focusing on kinematic balance recovery strategies and muscle synergy activation. Twenty older adults aged over 65 underwent short-term (one session) and long-term (3-weeks, 10 sessions) balance training, and their recovery from unpredictable mediolateral perturbations was assessed. Perturbations consisted of 8° rotations of a robot-controlled platform on which participants were balancing on one leg. We measured full-body 3D kinematics and activation of 15 leg and trunk muscles, from which linear and rotational kinematic balance recovery responses and muscle synergies were obtained. Results Our findings revealed improved balance performance after long-term training, characterized by reduced centre of mass acceleration and (rate of change of) angular momentum. Particularly during the later stage of balance recovery the use of angular momentum to correct centre of mass displacement was reduced after training, decreasing the overshoot in body orientation. Instead, more ankle torque was used to correct centre of mass displacement, but only for perturbations in medial direction. These situation and strategy specific changes indicate adaptations in feedback control. Activation of muscle synergies during balance recovery was also affected by training, specifically the synergies responsible for leg stiffness and ankle torques. Training effects on angular momentum and the leg stiffness synergy were already evident after short-term training. Conclusion We conclude that balance training in older adults refines feedback control through the tuning of control strategies, ultimately enhancing the ability to recover balance.
Koster et al. (2024) Balance training in older adults enhances feedback control after perturbations. PeerJ 12:e18588 https://doi.org/10.7717/peerj.18588
Risk factors and prediction models for recurrent acute ischemic stroke: a retrospective analysis
Background Ischemic stroke is one of the leading causes of disability and death worldwide, with a high risk of recurrence that severely impacts the quality of life of patients. Therefore, identifying and analyzing the risk factors for recurrent ischemic stroke is crucial for the prevention and management of this disease. Methods A total of 114 cases of recurrent acute ischemic stroke patients admitted from July 2017 to March 2021 were selected as the observation group, and another 409 cases of initial ischemic stroke patients from the same period as the control group. The clinical data of the observation group and the control group were compared to analyze the risk factors associated with the readmission of ischemic stroke. A single-factor analysis (Model 1), Least Absolute Shrinkage and Selection Operator (LASSO) regression, and machine learning methods (Model 2) were used to screen important variables, and a multi-factor COX Proportional Hazards Model regression stroke recurrence risk prediction model was constructed. The predictive performance of the model was evaluated by the consistency index (C-index). Results Multivariate COX regression analysis revealed that history of hypertension (Hazard Ratio [HR] = 2.549; 95% Confidence Interval (CI) [1.503–4.321]; P = 0.001), history of cerebral infarction (HR = 1.709; 95% CI [1.066–2.738]; P = 0.026), cerebral artery stenosis (HR = 0.534; 95% CI [0.306–0.931]; P = 0.027), carotid arteriosclerosis (HR = 1.823; 95% CI [1.137–2.924]; P = 0.013), systolic blood pressure (HR = 0.981; 95% CI [0.971–0.991]; P < 0.0001), red cell distribution width-coefficient of variation (RDW-CV) (HR = 1.251; 95% CI [1.019–1.536]; P = 0.033), mean platelet volume (MPV) (HR = 1.506; 95% CI [1.148–1.976]; P = 0.003), uric acid (UA) (HR = 0.995; 95% CI [0.991–1.000]; P = 0.049) were found significantly associated with acute ischemic stroke. The C-index of the full COX model was 0.777 (0.732~0.821), showing a good discrimination between Model 1 and Model 2. Conclusions History of hypertension, history of cerebral infarction, cerebral artery stenosis, carotid atherosclerosis, systolic blood pressure, UA, RDW-CV, and MPV were identified as risk factors for acute ischemic stroke recurrence. The model can be used to predict the recurrence of acute ischemic stroke.
Ke et al. (2024) Risk factors and prediction models for recurrent acute ischemic stroke: a retrospective analysis. PeerJ 12:e18605 https://doi.org/10.7717/peerj.18605
Effect of the diet level of whole-plant corn silage on the colonic microflora of Hezuo pigs
Background Whole-plant corn silage (WPCS) is an important roughage source for livestock, and have critical influences on rumen or intestinal microbiota, thus affecting the growth performance and feed efficiency. Our previous studies showed that adding WPCS to the diet of Hezuo pigs could promote the growth and fiber digestibility. While the aim of this study is to understand the effect of dietary WPCS on the colonic microflora in Hezuo pigs, which is essential for improving the roughage exploitation of pigs. Methods Thirty-two Hezuo pigs with similar body weight (7.88 ± 0.81) kg were selected and randomly divided into four groups with eight pigs in each group. Pigs in the control group were fed a basal diet, pigs in the experimental groups (Groups I, II, and III) were fed basal diet supplemented with 5%, 10%, and 15% WPCS, respectively, under 120 d experimental period. Six pigs from each group were picked for collecting colonic contents samples. 16S rRNA sequencing was performed to analyze the colonic microbiota of experimental pigs. Results The results showed that community richness indexes Chao1 and Observed_species in group III of Hezuo pig were significantly lower than that of the other three groups, community diversity indexes Shannon and Simpson were significantly higher in group I and II in comparison to the control group, and significantly lower in group III in comparison to the control group, group I and II. Adding WPCS to the diet of Hezuo pigs has no influence on the colonic dominant phylum, Clostridium sensu stricto 1 and Rikenellaceae RC9 gut group were most prevalent in the colon of Hezuo pig. When compared with the control group, the relative abundance of Streptococcus was significantly decreased in three experimental groups, while p-251-o5, Parabacteroides, Prevotellaceae UCG-003, Prevotellaceae UCG-001, and F082 exhibited significantly higher relative abundances in at least two experimental groups. Fibrobacter, Rikenellaceae RC9 gut group in group I, UCG-010 in group II, Bacteroides in group III exhibited increased relative abundance as compared with the control group. PICRUSt functional annotation indicated that the functions of cellular process and signaling were significantly increased in all WPCS-rationed groups, cancers, nervous system, immune system and environmental adaptation were all differed from groups I and II; three predominant pathways of translation, nucleotide metabolism and signal were only differed from the group II. Conclusions Feeding with 5% and 10% WPCS for Hezuo pigs could improve their colonic microflora diversity, and increase the relative abundance of fiber-digesting bacteria, which may potentially help to improve the fibre digestibility of Hezuo pigs by regulating the microbial function of cellular process and signaling, nucleotide metabolism, translation.
Yang et al. (2024) Effect of the diet level of whole-plant corn silage on the colonic microflora of Hezuo pigs. PeerJ 12:e18630 https://doi.org/10.7717/peerj.18630
Climate change effect on the widely distributed Palearctic plant bug species (Insecta: Heteroptera: Miridae)
Insects are poikilothermic organisms and temperature increase usually accelerates their development rates, population and distribution area growth. Therefore, it is assumed that global warming can be beneficial for the pests and other widespread species at least in the relatively cool temperate zones. However, climate change’s effect on the widespread species in the Palearctic remains poorly studied. This work was performed on three plant bug species (Insecta: Heteroptera: Miridae), at present inhabiting Europe and Asia. Liocoris tripustulatus is known from the Western Palearctic, Lygocoris pabulinus occupies the territories from Western Europe to South Asia, Lygus punctatus is distributed from Northern Europe to the Far East. In this paper, it is tested whether temperature rise is positively connected with the area of preferred climatic conditions for those species, and explores the particular climatic variables which can be limiting for the distribution of those species. Maxent software was used for the environmental niche modeling and to find the variables with significant contribution to the climatic models for the studied species. Based on those models, areas with preferred climatic conditions over different periods were calculated in QGIS. Principal component analysis and logistic regression were performed to find the variables highly contributing to the differences between the species. The results contradict the assumption that temperature growth alone can be a predictor for the widespread species and pest distribution range change. All species differ in suitable climatic conditions and their area dynamics in time, and the temperature affects each species differently. Only Liocoris tripustulatus might significantly expand its distribution area by 2070 due to the climate change. The areas in Asia and above the polar circle will be more suitable by that time for all three species than now. However, conditions in Europe might be less suitable for Lygocoris pabulinus and Lygus punctatus in the future. Both, temperature and precipitation variables, can be important for shaping distribution of Liocoris tripustulatus and Lygocoris pabulinus. Mean annual temperature and temperature in winter, most probably, limit the distribution of at least Liocoris tripsutulatus and Lygus punctatus, but changes in this variable affect those two species differently.
Namyatova et al. (2024) Climate change effect on the widely distributed Palearctic plant bug species (Insecta: Heteroptera: Miridae). PeerJ 12:e18377 https://doi.org/10.7717/peerj.18377
Fluctuations of continuous soil moisture evaporation under different rainfall conditions during the growing period of the non-monsoon season, the eastern Loess Plateau
Soil moisture is an important link between material and energy exchange between the land and atmosphere, and its evaporation loss is crucial to sustainable development of agriculture. Based on observations of long-term stable isotopes of soil moisture in the eastern Loess Plateau (ECLP) during the non-rainy season growing period, this study systematically explored soil water evaporation loss at different soil depths using the Craig–Gordon model and revealed the internal relationship between soil evaporation loss and environmental elements. Main findings included: (1) The soil moisture content showed a gradual decreasing trend, with a weak soil moisture δ18O fluctuation appearing in April, whereas a stronger fluctuation was observed in June. (2) A significant vertical spatial heterogeneity was observed in soil moisture δ18O of each soil layer. Enriched soil moisture δ18O values appeared in the 0–20 cm soil layer, and the minimum value appeared in the 40–60 cm soil layer. (3) A significant spatial and temporal heterogeneity was observed in the soil moisture evaporation loss fraction (f) (0–23.35%), with weaker values at the beginning of the study period and larger values between mid-late May and mid-June. The largest soil evaporation loss was observed in the 0–20 cm soil layer (average value of 8.97%), a fluctuating decreasing trend appeared with increasing soil depth. (4) Regional soil moisture evaporation loss was positively correlated with regional air temperature (T) and potential evapotranspiration (ET0) and negatively correlated with soil water content (SWC) and relative humidity (RH). The correlation between soil moisture evaporation loss and environmental elements gradually weakened with increasing soil depth. (5) The environmentally driven model of continuous evaporation of soil moisture was suitable for larger amounts, especially for the surface soil layers. The results of this study have important implications for water resource management, ecosystem stability, and sustainable regional agriculture in the ECLP.
Sun et al. (2024) Fluctuations of continuous soil moisture evaporation under different rainfall conditions during the growing period of the non-monsoon season, the eastern Loess Plateau. PeerJ 12:e18514 https://doi.org/10.7717/peerj.18514
Targeting squalene epoxidase in the treatment of metabolic-related diseases: current research and future directions
Metabolic-related diseases are chronic diseases caused by multiple factors, such as genetics and the environment. These diseases are difficult to cure and seriously affect human health. Squalene epoxidase (SQLE), the second rate-limiting enzyme in cholesterol synthesis, plays an important role in cholesterol synthesis and alters the gut microbiota and tumor immunity. Research has shown that SQLE is expressed in many tissues and organs and is involved in the occurrence and development of various metabolic-related diseases, such as cancer, nonalcoholic fatty liver disease, diabetes mellitus, and obesity. SQLE inhibitors, such as terbinafine, NB598, natural compounds, and their derivatives, can effectively ameliorate fungal infections, nonalcoholic fatty liver disease, and cancer. In this review, we provide an overview of recent research progress on the role of SQLE in metabolic-related diseases. Further research on the regulation of SQLE expression is highly important for developing drugs for the treatment of metabolic-related diseases with good pharmacological activity.
Chen et al. (2024) Targeting squalene epoxidase in the treatment of metabolic-related diseases: current research and future directions. PeerJ 12:e18522 https://doi.org/10.7717/peerj.18522
Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses
Background Autophagy plays a key role in the development of carotid atherosclerosis (CAS). This study aimed to identify key autophagy-related genes (ATGs) related with CAS using bioinformatics analysis, in vivo AS mouse model, and in vitro experiments. Methods The GSE100927 and GSE28829 datasets were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics analyses of differentially expressed ATGs (DE-ATGs) was conducted. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the biological processes and pathways associated with DE-ATGs. Protein-protein interaction (PPI) network was constructed with the DE-ATGs to identify the key CAS-related DE-ATGs. Receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic value of the key CAS-related DE-ATGs. CIBERSORT analysis was performed to determine the infiltration status of 22 immune cell types and their correlation with the expression levels of the key CAS-related DE-ATGs. Hematoxylin and eosin (HE) staining was used to estimate the plaque histology in the AS mouse model. Western blotting, quantitative real-time PCR (qRT-PCR), and immunohistochemistry (IHC) were performed to validate the protein and mRNA expression levels of the key CAS-related DE-ATGs in the in vitro and in vivo models. Results We compared transcriptome profiles of 12 early CAS plaques and 29 advanced CAS plaques in the GSE100927 dataset and identified 41 DE-ATGs (33 up-regulated and eight down-regulated). Functional enrichment analysis showed that the DE-ATGs were closely related with apoptosis, autophagy, and immune activation. ROC curve analysis showed that the area under the curve (AUC) values for the three key CAS-related DE-ATGs (CCL2, LAMP2, and CTSB) were 0.707, 0.977, and 0.951, respectively. CIBERSORT analyses showed close association between the three key CAS-related DE-ATGs and the infiltration of immune cell types in the plaques. Finally, the western blot, qRT-PCR, and IHC staining confirmed that CCL2, LAMP2, and CTSB were highly expressed in the plaques of the AS model mice or ox-LDL-treated human umbilical vein endothelial cells (HUVECs) and human aorta vascular smooth muscle cells (HAoSMCs). Conclusion We identified and validated three key CAS-associated ATGs, namely, CCL2, LAMP2, and CTSB with high diagnostic value. These three key CAS-associated ATGs are promising diagnostic markers and therapeutic targets for patients with CAS.
Huang et al. (2024) Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses. PeerJ 12:e18543 https://doi.org/10.7717/peerj.18543
Different sound exposures causes alterations in stress-related serum indicators, behaviors, and cecal microbiota of green-shell egg-laying chickens under different stocking densities
Sound and stocking density are two common factors which influence the performance and welfare of layers. Accumulated studies have been conducted on the impacts of the two factors on production performance, while knowledge regarding the impacts of the two factors and their interactions on stress-related serum indicators, behaviors, and cecal bacterial communities in laying hens is still limited. A 3 × 3 factorial design with three sound sources (natural sound (NS), instrumental music (IMS), or mixed road noise (MRS)) and three stocking densities (low density (LD), medium density (MD), and high density (HD)) was used in this 24-day experiment, in which 378 30-week-old Xiandao green-shell layers were randomly distributed into nine treatments with six replicates per treatment. At the 3rd, 12th, and 24th experimental day, we evaluated the serum levels of adrenocorticotropic hormone (ACTH) and corticosterone (CORT) and recorded stress-related animal behaviors. At the end of the experiment, 16S rRNA gene amplicon sequencing of the cecal bacterial communities was performed. Our results confirmed that MRS and HD induced significantly elevated serum ACTH and CORT levels, and were correlated with significantly increased feather pecking behavior. IMS and LD were associated with enhanced preening behavior and reduced feather pecking behavior. LD significantly increased the Firmicutes/Bacteriodetes ratio and IMS significantly enriched the beneficial Lactobacillus population. Based on the obtained results we proposed that music exposure and reduced stocking density were helpful in reducing stress and improving cecal bacterial profile, which were beneficial for improving layers’ health status and welfare.
Cao et al. (2024) Different sound exposures causes alterations in stress-related serum indicators, behaviors, and cecal microbiota of green-shell egg-laying chickens under different stocking densities. PeerJ 12:e18544 https://doi.org/10.7717/peerj.18544
Tilianin content and morphological characterization of colchicine-induced autotetraploids in Agastache mexicana
Background Agastache mexicana Linton & Epling subsp. mexicana (Lamiaceae) is an aromatic medicinal plant, characterized by a high concentration of tilianin, a flavonoid with therapeutic potential in cardiovascular diseases. In this study, we have explored the use of colchicine to obtain autotetraploid lines of A. mexicana and analyze their morphological characteristics. In addition, we aimed to identify polyploid plants with a high content of tilianin. Methods In vitro seedlings at the stage of cotyledon emergence were dipped in colchicine solution at 0.0%, 0.1%, 0.3%, and 0.5% (w/v) for 6, 12, and 24 h. Seedlings were cultured on half-strength basal Murashige and Skoog medium supplemented with 20 g/L sucrose. After 2 months, the shoots from surviving seedlings were excised and grown individually in the same medium to obtain plantlets. The ploidy level of all materials was verified through flow cytometry and chromosome counting before acclimatization and transfer to the greenhouse. The investigated characteristics included length, density and stomatal index, leaf area, chlorophyll content, flower size and color, and tilianin content measured by high-performance liquid chromatography. Results The most efficient production of tetraploid in terms of percentage was achieved with 0.1% colchicine for 6 h resulting in no generation of mixoploids. Tetraploid plants had twice the number of chromosomes (2n = 4x = 36) and nearly twice the total DNA content (2.660 ± 0.236 pg) of diploids. Most tetraploid A. mexicana plants showed variations in flower and leaf characteristics compared to the diploid controls. High-performance liquid chromatography analysis showed that tetraploid plants with small leaves produced the greatest amount of tilianin; up to 32.964 ± 0.004 mg/g dry weight (DW), compared to diploid plants with 6.388 ± 0.005 mg/g DW. Conclusion In vitro polyploidization using colchicine demonstrates potential for enhancing bioactive constituents of A. mexicana. This approach has proven effective in generating elite tetraploid lines with increased tilianin production.
Martínez-Aguilar et al. (2024) Tilianin content and morphological characterization of colchicine-induced autotetraploids in Agastache mexicana. PeerJ 12:e18545 https://doi.org/10.7717/peerj.18545
Exploring quadriceps activity variations in women: the role of seated posture during stair climbing
Background Adults in modern society spend most of their time in a sitting position. However, sitting for long periods of time can affect the length and sensation of the quadriceps muscle and negatively affect the performance of functional tasks required in daily life. In addition, it may have different characteristics according to sitting postures. Aim The aim of this study is to investigate the differences in quadriceps muscle activity during stair climbing and descending based on various sitting postures. Methods Thirty healthy adult women were classified into sitting upright (SU), sitting with legs crossed (SLC), and sitting with ankles crossed over knees (SAC). The muscle activities of the vastus medialis (VM), vastus lateral (VL), and rectus femoris (RF) were collected during climbing and descending the stairs three times each. After which a sitting posture was maintained for 15 min, the post-measurement was performed in the same way as the pre-measurement. One-way analysis of variance or Kruskal-Walli’s test was used to check homogeneity between each group, least significant difference (LSD) was used for post-hoc testing. Paired-sample t-test or Wilcoxon signed-rank test was used to check before-and-after differences within the group. Repeated measures analysis of variance was used to determine between-group and within-group interactions. Results VM muscles were significantly decreased after maintaining a sitting posture during descending stairs of SAC group (p = 0.047). In conclusion, this study indicates that maintaining a SAC sitting posture for a certain period causes a temporary decrease in muscle activity of the VM muscle during descending stairs. This provides important implications for early treatment to manage knee pain and strengthen quadriceps muscles in women. Future studies should focus on groups with patellofemoral pain syndrome or knee pain to better understand the impact of sitting posture on quadriceps activity.
Chun et al. (2024) Exploring quadriceps activity variations in women: the role of seated posture during stair climbing. PeerJ 12:e18547 https://doi.org/10.7717/peerj.18547
Tae-miR396b regulates TaGRFs in spikes of three wheat spike mutants
Tillering and spike differentiation are key agronomic traits for wheat (Triticum aestivum L.) production. Numerous studies have shown that miR396 and growth-regulating factor genes (GRFs) are involved in growth and development of different plant organs. Previously, we have reported that wheat miR396b (tae-miR396b) and their targets TaGRFs (T. aestivum GRFs) play important roles in regulating wheat tillering. This study was to investigate the regulatory roles of tae-miR396b and TaGRFs played during wheat spike development. Wheat cultivar Guomai 301 (wild type, WT) and its three sipke mutants dwarf round spike mutant (drs), apical spikelet sterility mutant (ass) and prematurely terminated spike differentiation mutant (ptsd1) were studied. Three homeologous genes of tae-miR396b on the long arms of chromosomes 6A, 6B, and 6D were identified, and they encoded the same mature miRNA. Complementary sequences of mature tae-miR396b were identified in 23 TaGRFs, indicating they were the target genes of tae-miR396b. Tae-miR396b had different regulatory effects on TaGRFs between Guomai 301 and its mutants. TaGRF2-7A was confirmed to be the target gene of tae-miR396b by molecular interaction assay. The expression levels of tae-miR396b and TaGRFs were different between WT and mutants drs, ass and ptsd1 at the floret primordium visible (S1), the two awns/spikelet reaching apical meristem of the spikelet (S2), and the green anther stage (S3). The expression level of tae-miR396b in WT was significantly higher than that in mutants drs and ass. The most TaGRFs were negatively regulated by tae-miR396b. The abnormal expressions of TaGRF1 (6A, 6D), TaGRF2 (7A, 7B, 7D), TaGRF4 (6A, 6B), TaGRF5 (4A, 7A, 7D), and TaGRF10 (6A, 6B, 6D) were important causes for abnormal spike development in the three mutants. This study laid foundation for further elucidating functions of tae-miR396b and TaGRFs underlying wheat spike development. Regulating tae-miR396b and TaGRFs will be a new approach for wheat high yield breeding.
Yao et al. (2024) Tae-miR396b regulates TaGRFs in spikes of three wheat spike mutants. PeerJ 12:e18550 https://doi.org/10.7717/peerj.18550
Multifaceted roles of cGAS-STING pathway in the lung cancer: from mechanisms to translation
Lung cancer (LC) remains one of the most prevalent and lethal malignancies globally, with a 5-year survival rate for advanced cases persistently below 10%. Despite the significant advancements in immunotherapy, a substantial proportion of patients with advanced LC fail to respond effectively to these treatments, highlighting an urgent need for novel immunotherapeutic targets. The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway has gained prominence as a potential target for improving LC immunotherapy due to its pivotal role in enhancing anti-tumor immune responses, augmenting tumor antigen presentation, and promoting T cell infiltration. However, emerging evidence also suggests that the cGAS-STING pathway may have pro-tumorigenic effects in the context of LC. This review aims to provide a comprehensive analysis of the cGAS-STING pathway, including its biological composition, activation mechanisms, and physiological functions, as well as its dual roles in LC and the current and emerging LC treatment strategies that target the pathway. By addressing these aspects, we intend to highlight the potential of the cGAS-STING pathway as a novel immunotherapeutic target, while also considering the challenges and future directions for its clinical application.
Wei et al. (2024) Multifaceted roles of cGAS-STING pathway in the lung cancer: from mechanisms to translation. PeerJ 12:e18559 https://doi.org/10.7717/peerj.18559
Serum neuron-specific enolase (NSE) is associated with the overall survival of colorectal cancer: a retrospective study
Background Serum neuron-specific enolase (NSE) had been associated with survival of several cancers. However, its prognostic significance for colorectal cancer (CRC) has not been effectively discussed. We aimed to investigate the relationship between baseline serum NSE and the overall survival (OS) of colorectal adenocarcinoma (CRAD) patients. Methods A retrospective study had been conducted by including 564 histopathology confirmed CRAD patients between January 2013 and December 2018 from Yunnan Provincial Cancer hospital, China. Cox proportional hazards model was used to estimate the crude and adjusted associations between serum NSE measured at diagnosis and the OS of the patients. Restricted cubic spline (RCS) was further applied to delineate dose-response trend of the NSE-OS association. Results After controlling for possible confounding factors, baseline serum NSE was significantly associated with OS in CRAD: when dichotomizing by the median, patients with higher baseline serum NSE (NSE >= 12.93 ng/mL) were observed a worse prognosis (hazard ratio, HR: 1.82, 95% CI [1.30–2.55], p < 0.01). Stratified analysis by tumor stage revealed a stronger NSE-OS association in advanced CRAD patients. RCS disclosed a prominent dose-response relationship in NSE-OS association for all CRAD patients: along with the increase of baseline serum NSE, the adjusted HR of CRAD patients increased gradually. This dose-response trend is also evident in advanced stage CRAD patients, but not in early stage CRAD patients. Conclusions Serum NSE measured at diagnosis might be a useful prognostic indicator for CRAD, especially for advanced stage patients.
Peng et al. (2024) Serum neuron-specific enolase (NSE) is associated with the overall survival of colorectal cancer: a retrospective study. PeerJ 12:e18617 https://doi.org/10.7717/peerj.18617
Estimation and prediction of water conservation in the upper reaches of the Hanjiang River Basin based on InVEST-PLUS model
With the gradual prominence of global water shortage and other problems, evaluating and predicting the impact of land use change on regional water conservation function is of great reference significance for carrying out national spatial planning and environmental protection, and realizing land intelligent management. We first analyzed 8,416 remote sensing images in the upper reaches of the Hanjiang River Basin (URHRB) by GEE platform and obtained the land use and land cover (LULC) results of fours periods. Through our field investigation, the accuracy of remote sensing image interpretation is obviously higher than that of other comprehensive LULC classification results. Then, through the coupling of InVEST-PLUS model, not only the results of URHRB water conservation from 1990 to 2020 were calculated and the accuracy was assessed, but also the LULC results and water conservation of URHRB under different development scenarios in 2030 were predicted. The results showed as follows: From 1990 to 2020, the forest area of URHRB increased by 7152.23 km2, while the area of cropland, shrub and grassland decreased by 3220.35 km2, 1414.72 km2 and 3385.39 km2, respectively. The InVEST model reliably quantifies the water yield and water conservation of URHRB. In the past 30 years, the total amount of water-saving in China has shown a trend of increasing first and then decreasing. From the perspective of vegetation types, URHRB forest land is the main body of water conservation, with an average annual water conservation depth of 653.87 mm and an average annual water conservation of 472.10×108 m3. Under the ecological protection scenario of the URHRB in 2030, the maximum water conservation in the basin is 574.92×108 m3, but compared with the water conservation in 2010, there is still a gap of 116.28×108 m3. Therefore, through the visualization analysis of the LULC changes of URHRB and water conservation function, it is found that the land and resources department should pay attention to the LULC changes of water sources and adjust the territorial spatial planning in time to cope with the huge water conservation gap in the future.
Niu et al. (2024) Estimation and prediction of water conservation in the upper reaches of the Hanjiang River Basin based on InVEST-PLUS model. PeerJ 12:e18441 https://doi.org/10.7717/peerj.18441
Development and validation of a simple clinical nomogram for predicting infectious diseases in pediatric kidney transplantation recipients: a retrospective study
To construct and verify an easy-to-use nomogram for predicting the risk of infectious diseases in pediatric kidney transplant recipients. Clinical data of hospitalized pediatric kidney transplant recipients were retrospectively analyzed. Meaningful variables identified from the multivariate stepwise logistic regression analysis were used to construct the nomogram. Internal validation was performed using Bootstrap resampling 1,000 times. The nomogram was evaluated using calibration, decision and receiver operating characteristic (ROC) curves. A total of 297 pediatric kidney transplant recipients were included (164 infected, 133 non-infected). Multivariate stepwise regression analysis identified white blood cell count (WBC), lymphocyte to monocyte ratio (MLR), platelet to neutrophil ratio (PNR), red cell distribution width-standard deviation (RDW-SD), and albumin (ALB) as significant predictors of postoperative infection. The nomogram, based on the five indicators, showed strong discrimination ability (AUC = 0.756; 95% CI [0.702–0.811]), with a sensitivity of 88.0% and a specificity of 54.3%. The calibration curve and decision curve further demonstrated good consistency and clinical practicality between the predicted and actual values. WBC, MLR, PNR, RDW-SD, and ALB are effective indicators for predicting postoperative infection in pediatric kidney transplant recipients. The nomogram constructed from these indicators can effectively predict and evaluate the early risk of infection in these patients.
Li et al. (2024) Development and validation of a simple clinical nomogram for predicting infectious diseases in pediatric kidney transplantation recipients: a retrospective study. PeerJ 12:e18454 https://doi.org/10.7717/peerj.18454
The diagnostic utility of glycosaminoglycans (GAGs) in the early detection of cancer: a systematic review
Background Glycosaminoglycans (GAGs) are a family of polysaccharides found abundantly in the extracellular matrix (ECM) of tissues. Research has indicated that the dysregulation of ECM, including changes and disruptions in GAGs, contributes to various cancer hallmarks such as metabolic reprogramming, persistent growth signals, immunosuppression, angiogenesis, tumor invasion, and metastasis. Objective This systematic review aims to evaluate the diagnostic accuracy of GAGs, including heparan sulfate (HS), chondroitin sulfate (CS), and hyaluronic acid (HA), in early detection of cancer. Method Four databases (PubMed, Scopus, EBSCO, and Ovid) were searched for studies in English within the last 15 years, involving at least 50 human participants. Using a two-stage process: identification and screening, 11 articles were selected and critically appraised using Critical Appraisal Skills Programme (CASP) checklists and Newcastle-Ottawa Scale (NOS) appropriate for each study design. Result Eleven studies met the inclusion criteria, encompassing various cancers like renal cell carcinoma (RCC), upper GI cancer (UGI), ovarian cancer, prostate cancer, breast cancer, lung cancer, colorectal cancer and oral cancer. Methodological quality was assessed using two established tools, with no studies exhibiting a high risk of bias. Heparan sulfate levels showed diagnostic potential in renal cancer with a maximum accuracy of 98.9%, achieving 94.7% specificity and 100% sensitivity. Chondroitin sulfate disaccharides emerged as a promising diagnostic marker in ovarian cancer and showed potential as diagnostic markers in renal cancer. However, there were no statistically significant differences in urinary chondroitin sulfate levels between patients and controls in prostate cancer. In breast cancer, hyaluronic acid showed moderate accuracy (AUC = 0.792) in distinguishing metastatic from non-metastatic disease, and a composite score incorporating multiple markers, including HA, showed even higher accuracy (AUC = 0.901) in detecting metastatic breast cancer. HA demonstrated moderate diagnostic accuracy for UGI cancers. Serum HA levels were significantly elevated in patients with oral cancer and pleural malignant mesothelioma and associated with tumor progression in patients with lung cancer. Elevated low molecular weight form of hyaluronan (~6 k Da HA) levels were found in colorectal cancer tissues. Conclusion GAGs hold potential as early cancer detection biomarkers. Further validation with larger, diverse populations is needed to validate their diagnostic accuracy and clinical utility.
Douglah et al. (2024) The diagnostic utility of glycosaminoglycans (GAGs) in the early detection of cancer: a systematic review. PeerJ 12:e18486 https://doi.org/10.7717/peerj.18486
Single-cell data revealed the function of natural killer cells and macrophage cells in chemotherapy tolerance in acute myeloid leukemia
Background Acute myeloid leukemia (AML) is highly prevalent and heterogeneous among adult acute leukemias. Current chemotherapeutic approaches for AML often face the challenge of drug resistance, and AML immune cells play an important role in the regulation of AML drug resistance. Thus, it is of key significance to explore the regulatory mechanisms of immune cells in AML to alleviate chemotherapy resistance in AML. Methods Based on AML single-cell transcriptomic data, this study revealed the differences in the expression of immune cell subpopulations and marker genes in AML patients in the complete remission group (CR) compared to AML patients in the non-complete remission group (non-CR) after chemotherapy. Functional enrichment by clusterprofiler revealed the regulatory functions of differentially expressed genes (DEGs) in AML. AUCell enrichment scores were used to assess the immunoregulatory functions of immune cells. Pseudotime analysis was used to construct immune cell differentiation trajectories. CellChat was used for cellular communication analysis to elucidate the interactions between immune cells. Survival analysis with the R package “survival” revealed the role of immune cell marker genes on AML prognosis. Finally, the wound healing and trans-well assay were performed. Results Single-cell clustering analysis revealed that NK/T cells and macrophage cells subpopulations were significantly higher in non-CR AML patients than in CR AML. AUCell enrichment analysis revealed that FCAR+ and FCGR3A+ macrophages were significantly more active in the non-CR group and correlated with processes regulating cellular energy metabolism and immune cell activity. Differentially expressed NK cell marker genes between CR and non-CR groups mainly included HBA1, S100A8, and S100A9, which were associated with cancer drug resistance regulation, these marker genes of (FCAR, FCGR3A, PREX1, S100A8 and S100A9) were upregulated in human chronic myeloid leukemia cells (HAP1) and silencing of S100A8 affected migration and invasion of HAP1 cells. In particular, the differentiation pathways of macrophages and NK cells in non-CR differed from those of patients in the CR group. Cellular communication analyses showed that ligand-receptor pairs between NK cells and macrophage cells mainly included HLA-E-KLRK1, HLA-E-KLRC1, HLA-E-CD94:NKG2A, CLEC2B-KLRB1. In addition, LGALS9-CD45, CCL3L1- CCR1, CCL3-CCR1 between these two immune cells mainly regulate secreted signaling to mediate AML progression. Marker genes in NK/T cells and macrophage cells were significantly associated with AML prognosis. Conclusion This study reveals the potential role of NK cells and macrophages in AML chemoresistance through the analysis of single-cell RNA sequencing data. This provides new ideas and insights into the key mechanisms of immune cells in AML treatment.
Gao et al. (2024) Single-cell data revealed the function of natural killer cells and macrophage cells in chemotherapy tolerance in acute myeloid leukemia. PeerJ 12:e18521 https://doi.org/10.7717/peerj.18521
The ecological niche characteristics and interspecific associations of plant species in the alpine meadow of the Tibetan Plateau affected plant species diversity under nitrogen addition
Background Plant species diversity is of great significance to maintain the structure and function of the grassland ecosystem. Analyzing community niche and interspecific associations is crucial for understanding changes in plant species diversity. However, there are few studies on the response of plant species diversity, species niche characteristics, and interspecific relationships to nitrogen addition in alpine meadows on the Qinghai-Tibet Plateau. Methods This study investigates the effects of different levels of nitrogen addition (0, 15, 30, 45, and 60 g N m−2) on plant species diversity, functional group importance values, niche width, niche overlap, and interspecific associations in an alpine meadow. Results 1) Compared with the control (CK), the Shannon-Weiner index and species richness index significantly increased by 11.36% and 30.77%, respectively, with nitrogen addition at 30 g N m−2, while both indices significantly decreased by 14.48% and 23.08%, respectively, at 60 g N m−2. As nitrogen addition increased, the importance value of grasses showed an upward trend, whereas the importance value of sedges showed a decline. 2) The niche width of Poa pratensis L., Elymus nutans Griseb., and Stipa purpurea Griseb. are increased with higher nitrogen addition. As nitrogen addition increases, the niche overlap values also show a rising trend. At 60 g N m−2, the overall community association in the alpine meadow exhibited a significant negative correlation. These findings suggest that grasses exhibit strong ecological adaptability under high nitrogen addition and gain a competitive advantage in spatial competition, increasing their niche width. Moreover, as nitrogen levels increase, the importance values of grasses rise significantly, and their ecological characteristics become more similar, resulting in reduced niche overlap among plant species. Furthermore, high nitrogen addition intensifies interspecific competition between grasses, sedges, and forbs, disrupting the original balance and reducing species diversity. These insights provide a valuable understanding of changes in species diversity and competitive dynamics in alpine meadow plant communities under high nitrogen addition.
Xiang et al. (2024) The ecological niche characteristics and interspecific associations of plant species in the alpine meadow of the Tibetan Plateau affected plant species diversity under nitrogen addition. PeerJ 12:e18526 https://doi.org/10.7717/peerj.18526
Abnormal hypothalamic functional connectivity and serum arousal-promoting neurotransmitters in insomnia disorder patients: a pilot study
Objective The present study aimed to investigate the functional connectivity (FC) of the anterior and posterior hypothalamus with the whole brain in insomnia disorder (ID) patients. Additionally, we explored the relationship between FC values and serum levels of arousal-promoting neurotransmitters (orexin-A and histamine) in ID patients. Methods This study enrolled 30 ID patients and 30 age- and gender-matched healthy controls. Resting-state functional magnetic resonance imaging (RS-fMRI) was employed to assess the FC of the anterior and posterior hypothalamus with the whole brain. Serum concentrations of orexin-A and histamine were measured using enzyme-linked immunosorbent assay (ELISA). Moreover, Spearman correlation analysis was conducted to investigate the relationship between FC values and serum levels of arousal-promoting neurotransmitters in ID patients. Results Our findings showed decreased FC between the posterior hypothalamus and several brain regions including the bilateral orbital superior frontal gyrus, the bilateral angular gyrus, the right anterior cingulate cortex, the left precuneus, and the right medial superior frontal gyrus in ID patients. Additionally, decreased FC was observed between the anterior hypothalamus and the right anterior cingulate cortex among ID patients. Compared to the healthy controls, ID patients showed significantly elevated serum concentrations of orexin-A and histamine. Furthermore, we identified a positive correlation between the FC of the right medial superior frontal gyrus with posterior hypothalamus and histamine levels in ID patients. Conclusion ID patients exhibited aberrant FC in brain regions related to sleep-wake regulation, particularly involving the default mode network and anterior cingulate cortex, which may correlate with the peripheral levels of histamine. These findings contribute to our understanding of the potential neuroimaging and neurohumoral mechanism underlying ID patients.
Lin et al. (2024) Abnormal hypothalamic functional connectivity and serum arousal-promoting neurotransmitters in insomnia disorder patients: a pilot study. PeerJ 12:e18540 https://doi.org/10.7717/peerj.18540
Health-related quality of life and its associated factors among Chinese seasonal retired migrants in Hainan
Background Seasonal retired migrants are mainly retired or semiretired people who migrate to warmer areas during the winter and then return to their original homes in the following year. Despite its increasing popularity, the evidence concerning the health status of Chinese seasonal retired migrants is controversial. Although some studies have shown that seasonal retired migrants have better health status, other studies note that migrants are driven involuntarily by health concerns and that their mental health suffers during migration. The objective of this study was to provide quantified evidence on the health-related quality of life (HRQoL) of seasonal retired migrants in China and to identify potential factors associated with HRQoL. Methods This was a community-based cross-sectional study of seasonal retired migrants who lived in Wuzhishan, Hainan during the winter. The Chinese version of the EuroQol 5-Dimension 5-Level (EQ-5D-5L) was used to assess participants’ HRQoL. Data on demographic and behavioral characteristics, body mass index, and the presence of chronic diseases were collected using a self-administered survey. Logistic regressions were used to explore the factors associated with responses in each dimension of the EQ-5D-5L descriptive system, and a multiple linear regression model was used to explore the factors associated with EuroQol visual analogue scale (EQ-VAS) scores. Results A total of 992 participants (female: 56.5%) were enrolled in the current study, with a mean age of 67.87 ± 6.98 years. Most participants reported problems in the pain/discomfort dimension (16.7%), followed by the anxiety/depression dimension (8.3%). Few participants reported problems in the first three dimensions of the EQ-5D-5L: mobility (5.4%), usual activities (2.0%), and self-care (1.2%). The median EQ-VAS score was 84 (interquartile range: 80–89). The regression results indicated that poor sleep quality, the presence of chronic diseases, and low-level physical activity were important factors that were negatively associated with multiple dimensions of the EQ-5D-5L. In addition, the EQ-VAS score was negatively associated with age, the presence of chronic diseases, poor sleep quality, and low-level physical activity. Conclusion This study revealed that Chinese seasonal retired migrants have high HRQoL. In addition, this study revealed that sleep quality and physical activity are correlated with multiple dimensions of the EQ-5D-5L descriptive system and EQ-VAS. Therefore, lifestyle interventions related to sleep quality and physical activity are essential for improving HRQoL among Chinese seasonal retired migrants.
Chen et al. (2024) Health-related quality of life and its associated factors among Chinese seasonal retired migrants in Hainan. PeerJ 12:e18574 https://doi.org/10.7717/peerj.18574
Correlation between pre-operative VE-cadherin and DLL4 and the maturation after primary arteriovenous fistula in uremic patients
Aims Uremic patients require dialysis to replace the declined kidney function, and arteriovenous fistula (AVF) is a commonly used dialysis access route. Our study aimed to explore vascular endothelial cells cadherin (VE-cadherin) and Delta-like ligand 4 (DLL4) expression in uremic patients undergoing primary AVF surgery and their correlation with AVF maturation. Methods We conducted a prospective study that included n = 55 voluntary uremic patients receiving their initial AVF procedure for renal replacement therapy, subjects were divided into a mature group and a failure group based on whether the AVF matured within 3 months post-operatively. We analyzed the association of VE-cadherin and DLL4 with AVF maturation by examining their expression levels in serum and the endothelium of cephalic veins. Results Pre-operative serum VE-cadherin, in the mature group measured 125.07 (106.77–167.65) ng/L, and DLL4 was 92.78 (83.83–106.72) pg/mL, while the failure group had VE-cadherin at 95.40 (79.03–107.16) ng/L (P = 0.001), and DLL4 at 60.42 (43.98–80.15) pg/mL with a statistical significant; (P = 0.002), binary logistic regression analysis indicated a significant association between cephalic vein diameter, VE-cadherin, DLL4 levels, and AVF immaturity (P = 0.024, P = 0.014 respectively). Immunohistochemical staining showed slightly higher VE-cadherin levels in the mature group than in the failure group (P = 0.366). DLL4 was primarily located in the cell membrane and cytoplasm, concentrated in the inner membrane, with significantly higher levels in the mature group compared to the failure group (P = 0.027). Conclusion The failure group exhibited lower levels of VE-cadherin and DLL4 in serum and vascular tissue, these results suggest that VE-cadherin and DLL4 might play pivotal regulatory roles in the onset and the progression of fistula immaturity, potentially serving as promising targets for future interventions.
Yin et al. (2024) Correlation between pre-operative VE-cadherin and DLL4 and the maturation after primary arteriovenous fistula in uremic patients. PeerJ 12:e18356 https://doi.org/10.7717/peerj.18356
The role of andrographolide as a potential anticancer agent against gastric cancer cell lines: a systematic review
Objective To critically analyse literature on the anticancer properties of andrographolide in in vitro studies on gastric cancer cells. Method This study systematically reviewed articles from 2013 to 2024 across five prominent databases; PubMed, Google Scholar, Web of Science, Scopus, and Science Direct, EMBASE, Cochrane library and DOAJ. The study eligibility criteria include original studies assessing using gastric cancer cell lines and articles utilizing extracted andrographolide from Andrographis paniculata or standard andrographolide source treatment. The following exclusion criteria were articles written in a different language, review articles, book chapters, conference articles, scientific reports. Duplicated articles were removed using Mendeley software. Result Out of 93 articles, six were relevant, primarily focusing on in vitro analyses with gastric adenocarcinoma cell lines. Conclusion These studies indicate that andrographolide can hinder the cell cycle, suppress cell proliferation, alleviate oxidative stress, and induce apoptosis by prompting gastric cancer cells to undergo self-destruction, which is a crucial mechanism for controlling and eliminating cancerous growths.
Anis Amiera et al. (2024) The role of andrographolide as a potential anticancer agent against gastric cancer cell lines: a systematic review. PeerJ 12:e18513 https://doi.org/10.7717/peerj.18513
Klastomycter conodentatus, gen et sp. nov., a small early Permian parareptile with conical teeth from Richards Spur, Oklahoma
A small, pristinely preserved specimen recently collected from the Dolese Brothers limestone quarry near Richards Spur, Oklahoma provides evidence for the presence of a new early Permian parareptile at this locality. The specimen includes an articulated, nearly complete skull roof, and with the right premaxilla, right quadratojugal, most of the right palate, as well as the right epipterygoid and the sphenethmoid preserved inside. Although similar in many respects to the other contemporary parareptiles Acleistorhinus, Delorhynchus and Colobomycter, it can be distinguished from other acleistorhinids by the presence of a number of autapomorphies related to its dentition. Phylogenetic analysis places it closer to Delorhynchus and Colobomycter within Acleistorhinidae than to Acleistorhinus pteroticus. Unique aspects of the present specimen include the pronounced anterior extension of the lacrimal bone, largely homodont dentition composed of simple conical crowns with slight recurvature in the premaxillary and anterior maxillary teeth, and simple conical crowns in posterior maxillary dentition. The discovery of this new parareptile along with the surprisingly large number of acleistorhinids at Richards Spur highlights the importance of the unique fissure and vertical cave system at this site. No other early Permian site has provided such a wide diversity of parareptilian taxa, part of a complex community of terrestrial vertebrates. The present specimen highlights the fine niche partitioning that appears to have been present among reptiles of this region.
Reisz et al. (2024) Klastomycter conodentatus, gen et sp. nov., a small early Permian parareptile with conical teeth from Richards Spur, Oklahoma. PeerJ 12:e18393 https://doi.org/10.7717/peerj.18393
The use of four-pillar regimen for heart failure management: results from the Jordanian Heart Failure Registry (JoHFR)
Background Heart failure (HF) is a complex cardiovascular disease. Effective management typically involves four main medications: angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, beta-blockers, angiotensin receptor-neprilysin inhibitors, and mineralocorticoid receptor antagonists, along with sodium-glucose co-transporter-2 inhibitors (SGLT2i). The primary objective of this article is to assess and identify the utilization of four-pillar regimen for HF managment and explore the characteristics of the patients being on the four-pillar regimen in Jordan. Methods Data from the Jordanian HF registry (JoHFR) was analyzed, encompassing records of HF patients treated in various cardiology centers from 2021 to 2023. Results The medical records of 2,151 patients with HF who were admitted to cardiology centers throughout Jordan were collected. Males comprised 58.0% of the included patients. Moreover, 71.0% of patients had chronic HF, whereas the rest, 29.0%, had acute HF. Of these, only 0.6% received the complete four-pillar treatment of HF. Beta-blockers were the most frequently used medication, prescribed to 74% of patients, while SGLT2i were the least common, used by only 9%. Notably, patients with type 2 diabetes were more likely to be on the four-pillar regimen (P-value = 0.016). Additionally, patients with a glomerular filtration rate (GFR) below 60 were more likely to be treated using the four-pillar (P-values = 0.044). The analysis revealed no significant difference in mortality rates between the two groups (P-value = 0.475). Conclusion Our study demonstrated an overall low utilization of the four-pillar regimen for HF treatment in Jordan with several patients’ characteristics associated with it. This highlight the need for enhanced collaborative effort and governmental initiatives to address the challenges of the low utilization of these medications.
Izraiq et al. (2024) The use of four-pillar regimen for heart failure management: results from the Jordanian Heart Failure Registry (JoHFR). PeerJ 12:e18464 https://doi.org/10.7717/peerj.18464
Common neural mechanisms supporting time judgements in humans and monkeys
There has been an increasing interest in identifying the biological underpinnings of human time perception, for which purpose research in non-human primates (NHP) is common. Although previous work, based on behaviour, suggests that similar mechanisms support time perception across species, the neural correlates of time estimation in humans and NHP have not been directly compared. In this study, we assess whether brain evoked responses during a time categorization task are similar across species. Specifically, we assess putative differences in post-interval evoked potentials as a function of perceived duration in human EEG (N = 24) and local field potential (LFP) and spike recordings in pre-supplementary motor area (pre-SMA) of one monkey. Event-related potentials (ERPs) differed significantly after the presentation of the temporal interval between “short” and “long” perceived durations in both species, even when the objective duration of the stimuli was the same. Interestingly, the polarity of the reported ERPs was reversed for incorrect trials (i.e., the ERP of a “long” stimulus looked like the ERP of a “short” stimulus when a time categorization error was made). Hence, our results show that post-interval potentials reflect the perceived (rather than the objective) duration of the presented time interval in both NHP and humans. In addition, firing rates in monkey’s pre-SMA also differed significantly between short and long perceived durations and were reversed in incorrect trials. Together, our results show that common neural mechanisms support time categorization in NHP and humans, thereby suggesting that NHP are a good model for investigating human time perception.
Rodriguez-Larios et al. (2024) Common neural mechanisms supporting time judgements in humans and monkeys. PeerJ 12:e18477 https://doi.org/10.7717/peerj.18477
NU7441, a selective inhibitor of DNA-PKcs, alleviates intracerebral hemorrhage injury with suppression of ferroptosis in brain
Neuronal apoptosis, oxidative stress, and ferroptosis play a crucial role in the progression of secondary brain injury following intracerebral hemorrhage (ICH). Although studies have highlighted the important functions of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) in various experimental models, its precise role and mechanism in ICH remain unclear. In this study, we investigated the effects of DNA-PKcs on N2A cells under a hemin-induced hemorrhagic state in vitro and a rat model of collagenase-induced ICH in vivo. The results revealed a notable increase in DNA-PKcs levels during the acute phase of ICH. As anticipated, DNA-PKcs and γ-H2AX had consistent upregulations after ICH. Administration of NU7441, a selective inhibitor of DNA-PKcs, alleviated neurological impairment, histological damage, and ipsilateral brain edema in vivo. Mechanistically, NU7441 attenuated neuronal apoptosis both in vivo and in vitro, alleviated oxidative stress by decreasing ROS levels, and suppressed ferroptosis by enhancing GPX4 activity. These results suggest that inhibition of DNA-PKcs is a promising therapeutic target for ICH.
Gong et al. (2024) NU7441, a selective inhibitor of DNA-PKcs, alleviates intracerebral hemorrhage injury with suppression of ferroptosis in brain. PeerJ 12:e18489 https://doi.org/10.7717/peerj.18489
Metabolomic analysis of rice cultivars from diverse production areas
Rice grown in Yunnan Province is known for its excellent taste and consumer preference. However, the metabolite composition of this unique rice remains unclear. In this study, the metabolic profile of different rice planted in various producing regions was evaluated. A total of 1,005 metabolites were identified, including nucleotides and their derivatives, amino acids and their derivatives, alkaloids, organic acids, phenolic acids, lignans and coumarins, lipids, terpenoids, quinones, flavones, tannins, and others. Procucing region and varieties can be clearly distinguished on the PCA diagram. Differential metabolites accumulated in the MSD502 vs. MSR88 (138)/LHHG (234)/LHR88 (188) comparison groups. The results in this study provide scientific information for the origin tracing and variety differentiation of raw rice materials.
Nie et al. (2024) Metabolomic analysis of rice cultivars from diverse production areas. PeerJ 12:e18496 https://doi.org/10.7717/peerj.18496
Serum metabolite profiles of thyroid autoimmunity patients in early pregnancy
Background Research on serum metabolite profiles in thyroid autoimmunity (TAI) patients during early pregnancy is currently limited. Aim & Methods The current study aimed to identify differential serum metabolites and assess the relationship between pregnancy outcomes and metabolic abnormalities in individuals with TAI. This research included 26 pregnant women with TAI and 30 healthy controls (HC). We employed a liquid chromatograph mass spectrometer (LC-MS) to analyze changes between the two groups. Results Newborns in the TAI patients had lower birth weights than those in the control group (P = 0.007). We identified 92 differential metabolites (including 50 upregulated and 42 downregulated) belonging to amino acids, fatty acyls, glycerophosphocholines, steroid and other categories and four significantly enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including taurine and hypotaurine metabolism, citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism and 2-oxocarboxylic acid metabolism. We further identified 15 characteristic metabolites (6-Methylquinoline, D-erythrose 4-phosphate, 4-Hydroxyisoleucine, phosphatidylcholine (PC)(16:2e/16:0), N3,N4-Dimethyl-L-arginine, N-desmethyltramadol, 3-Methoxybenzaldehyde, sphingomyelin (SM)(d14:3/28:2), gamma-Glutamylleucine, NSI-189, 3-(1-cyano-1,2-dihydroisoquinolin-2-yl)-3-oxopropyl propionate, lysophosphatidylinositol (LPI) 16:0, cis-Aconitic acid, polyamide (PA)(18:1/18:2) and fatty acyl esters of hydroxy fatty acid (FAHFA)(17:0/18:0)) using least absolute shrinkage and selection operator (LASSO) regression. Correlation analyses revealed that 6-Methylquinoline, D-erythrose 4-phosphate, gamma-Glutamylleucine, and LPI 16:0 exhibited a positive correlation with anemia before delivery, while 3-(1-cyano-1,2-dihydroisoquinolin-2-yl)-3-oxopropyl propionate had a negative correlation. LPI 16:0 displayed a positive correlation with uric acid (UA) during both middle and late pregnancy, whereas 3-Methoxybenzaldehyde exhibited a negative correlation with UA in late pregnancy. Cis-Aconitic acid showed a positive correlation with fasting blood glucose (FBG) in middle pregnancy. Conversely, 6-Methylquinoline and 4-Hydroxyisoleucine had a negative correlation with birth weight. Thyroid autoantibodies were found to be associated with 14 metabolites identified using LASSO, with the exception of PA (18:1/18:2). Conclusions Our findings provide new evidence supporting the early screening of serum metabolites and their potential for predicting adverse pregnancy outcomes in women with TAI.
Chen et al. (2024) Serum metabolite profiles of thyroid autoimmunity patients in early pregnancy. PeerJ 12:e18534 https://doi.org/10.7717/peerj.18534
Examining the practical importance of nonstationary cardio-respiratory coupling detection in breathing training: a methodological appraisal
This study investigates changes in cardiorespiratory coupling during clinic breathing training and its impact on autonomic nervous functioning compared with heart rate variability (HRV). A total of 39 subjects undergoing dynamic electrocardiogram-recorded breathing training were analyzed. Subjects were divided into early- and late-training periods, and further categorized based on changes in HRV indexes. Subtypes were identified using time-frequency cardiorespiratory coupling diagrams. Significant differences were observed in the high-frequency (HF) index between training stages in the subgroup with increasing HF-HRV (p = 0.0335). Both unimodal and bimodal subtypes showed significant high-frequency coupling (HFC) in the mid-training period compared with early and late stages (both p < 0.0001), suggesting improved parasympathetic cardiac regulation or reduced sympathetic control. This study highlights the potential of nonstationary cardiorespiratory coupling analysis alongside traditional HRV in evaluating the therapeutic effect of breathing training on autonomic nervous function. Cardiorespiratory coupling analysis could provide valuable adjunctive information to HRV measures for assessing the impact of breathing training.
Li et al. (2024) Examining the practical importance of nonstationary cardio-respiratory coupling detection in breathing training: a methodological appraisal. PeerJ 12:e18551 https://doi.org/10.7717/peerj.18551
Oral health manifestations and the perceived quality of life among Saudi children: a cross-sectional study
Background This cross-sectional study addresses scarcity of evidence on oral health issues among Saudi children and their impact on quality of life (OHRQL). We aimed to investigate parental reports of oral health problems in children and their effect on their OHQRL. Methods Parents of children aged 2–11-years from Five-Saudi regions participated from February 2021 to July 2021 by completing an electronic, self-administered questionnaire structured according to World Health Organization-Oral Health Questionnaire for children. It comprises questions on children experiencing oral pain/discomfort, oral lesions/manifestations and reduction in their OHRQL. Results Among 1,516 responders, 1,107 (73.0%) reported that their children experienced toothache/discomfort. The possibility of parents reporting toothache/discomfort or oral manifestations decreased with younger children. For children aged 2–5 years, the odds ratio (AOR) was 0.18 (95% CI [0.13–0.24], P < 0.001) for toothache and 0.58 (95% CI [0.45–0.74], P < 0.001) for oral manifestations. For children aged 6–8 years, the AOR was 0.57 (95% CI [0.4–0.81], P = 0.002) for toothache. Additionally, parents of younger children less frequently reported reduced OHRQL with AORs of 0.58 (95% CI [0.45–0.73], P < 0.001) for children aged 2–5 years and 0.64 (95% CI [0.49–0.83], P < 0.001) for those aged 6–8 years. Lower parental education increased AORs, with values of 1.575 (95% CI [1.196–2.074], P = 0.001) and 1.505 (95% CI [1.208–1.876], P < 0.001) for younger and 6–8-year-old children, respectively. Conclusion Results revealed notable prevalence of toothache/discomfort and oral manifestations in children reported by parents, which was related to age and parental education; ultimately leading to reduction in their OHRQL.
Sabbagh et al. (2024) Oral health manifestations and the perceived quality of life among Saudi children: a cross-sectional study. PeerJ 12:e18556 https://doi.org/10.7717/peerj.18556
The DUF348 domains of resuscitation promoting factor 2 play important roles in the enzymatic and biological activities in Rhodococcus erythropolis KB1
Rhodococcus erythropolis KB1 is a member of the Actinomycetota and a petroleum-degrading bacterium, isolated from soil contaminated with petroleum products. The resuscitation-promoting factors (Rpf) widely exist among Actinomycetota, which revive the viable but nonculturable (VBNC) state cells and facilitate growth of normal cells. The Rpf2 of the R. erythropolis KB1 is the most complex Rpf protein, which consists of the conserved Rpf domain, one G5 domain and three DUF348 domains. The protein demonstrates muralytic activity and growth-promoting and resuscitation effect, but the exact roles of these DUF348 domains in the enzymic and biological activities remain unclear. In this paper, the recombinant plasmids containing rpf2 genes with different DUF348 domain deletion were constructed and expressed in Escherichia coli. The enzymatic and biological activities of the mutated Rpf2 proteins were examined. The results showed that the enzymatic activities of the mutated Rpf2 proteins with 1, 2, and 3 DUF348 deletion decreased by 26.27%, 38.17%, and 42.56% respectively when compared with that of the wild-type Rpf2. A negative correlation between the number of DUF348 deletions and the growth-promoting and resuscitation effect on R. erythropolis KB1 cells were also observed. The muralytic activities of the mutated Rpf2 proteins showed stability at the temperature range of 20 °C to 40 °C, but showed sharp declines at 50 °C, with the activity dropping by 50.07% to 90.06%, and complete loss at 70 °C and 80 °C, underscoring importance of the DUF348 in thermal stability of the Rpf2. Zn2 + and Mn2 + slightly enhanced the muralytic activity, while Mg2 +, Ca2 + and Co2 + had negligible effects. These findings offered significant insights into mechanism of the Rpf action, emphasizing the critical role of the DUF348 domain.
Fu et al. (2024) The DUF348 domains of resuscitation promoting factor 2 play important roles in the enzymatic and biological activities in Rhodococcus erythropolis KB1. PeerJ 12:e18561 https://doi.org/10.7717/peerj.18561
School well-being in primary school children with chronic illness. A prospective cohort study
Background Children with chronic illness perform poorer at school, and school well-being (SWB) may mediate this association. We investigated the association between chronic illness and three domains of SWB in children in first grade. Methods Data from a German population-based prospective cohort study were used. Children with chronic illness were identified via their preschool health examination and follow-up parent surveys during first grade. Children were grouped as either (i) having current special health care needs (SHCN), (ii) having at least one physician diagnosis of a chronic illness but no current SHCN, or (iii) being healthy. SWB was assessed at the end of first grade and measured by the Questionnaire for the Assessment of Emotional and Social School Experiences of First and Second Grade Primary School Children. Based on SWB theory and previous frameworks, the following subscales were used: School-Related Self-Concept, Social Integration, and Joy of Learning. The sum score for each subscale was converted into area-transformed T-values (mean 50 and standard deviation 10). Associations between chronic illness groups and SWB subscales were investigated by multivariable linear regression models. Effect estimates were adjusted for potential confounding variables and standardized mean differences (SMD) were calculated. Results Of the 1,490 children included, 15% had current SHCN and 37% had a physician diagnosis of a chronic illness but no current SHCN. Compared to healthy children, children with SHCN had lower scores for the School-Related Self-Concept and the Joy of Learning subscale (SMD −0.18 for both) but not for the Social Integration subscale. In contrast, children with a chronic condition but no SHCN had lower scores only for the Social Integration subscale (SMD −0.12). Conclusions Primary school students with a chronic illness with or without SHCN have lower SWB in some domains compared to their healthy peers. SWB may be a mediator in the association between chronic illness and poor school performance.
Schnick-Vollmer et al. (2024) School well-being in primary school children with chronic illness. A prospective cohort study. PeerJ 12:e18280 https://doi.org/10.7717/peerj.18280
Factors associated with work engagement of nurses in the radiology department, Japan: a cross-sectional study
Background Radiology departments present unique challenges compared to other departments due to exposure to radiation and the specialized nature of the work. Nurses must not only manage typical nursing duties but also adhere to strict safety protocols to minimize radiation exposure. These additional responsibilities can significantly impact their work engagement and overall job satisfaction. Objective This study aimed to identify the factors associated with work engagement among nurses working at prefectural designated cancer care hospitals in Japan. Identifying these factors may lead to improvements in future work environments and educational systems. Methods This was a cross-sectional study using an internet-based survey. A questionnaire using the Utrecht Work Engagement Scale (UWES) was conducted among 317 nurses; 140 responded (response rate: 44.2%). Results Significant associations were found between work engagement and several factors. The mean UWES score was 54.3 (Standard deviation (SD): 18.4). Work engagement was positively associated with age (B = 0.179, p = 0.03), being male (B = 0.19, p = 0.015), higher position (B = 0.199, p = 0.012), desire for radiology assignments (B = 0.223, p = 0.003), and presence of a radiation exposure consultation system (B = 0.214, p = 0.034). Conclusions This study identified several factors associated with work engagement among radiology nurses, highlighting the importance of specialized support systems to address radiation-related concerns. These findings can inform interventions to enhance work engagement and well-being in this field.
Tsuchihashi et al. (2024) Factors associated with work engagement of nurses in the radiology department, Japan: a cross-sectional study. PeerJ 12:e18426 https://doi.org/10.7717/peerj.18426
MALAT1 promotes colonic epithelial cell apoptosis and pyroptosis by sponging miR-22-3p to enhance NLRP3 expression
Background Colonic epithelial cell apoptosis and pyroptosis had a close relationship with the pathological progression of ulcerative colitis (UC). LncRNA play a crucial role in the progression of UC. However, the role of the lncRNA MALAT1 in colonic epithelial cell apoptosis and pyroptosis remains unclear. Methods UC colitis cell model was established through lipopolysaccharide (LPS) treatment. MiR-22-3p and MALAT1 expression in fetal human colon (FHC) cells were analyzed by qRT-PCR. Proliferation and apoptosis of FHCs were measured using CCK-8 assay and flow cytometry, respectively. Pyroptosis indicators including interleukin (IL)-1β, IL-18, tumor necrosis factor-α (TNF-α), NLR family pyrin domain containing 3 (NLRP3), caspase-1, and N-gasdermin D (N-GSDMD) in FHCs were detected using ELISA, qRT-PCR, western blotting, and immunofluorescence. Results In this study, apoptosis was facilitated, IL-1β, IL-18, and TNF-α levels were enhanced, NLRP3, caspase-1, N-GSDMD protein were increased, and MALAT1 expression was markedly increased in LPS-treated FHCs (LTFs). MALAT1 knockdown remarkably facilitated proliferation and suppressed apoptosis, reduced IL-1β, IL-18, and TNF-α levels, and decreased the protein of NLRP3, caspase-1, N-GSDMD. Furthermore, NLRP3 overexpression remarkably reversed the effect of MALAT1-downexpression in LTFs. In addition, miR-22-3p could bind with MALAT1 and NLRP3 3′ UTR. Furthermore, miR-22-3p inhibition remarkably reversed the effect of MALAT1 overexpression in LTFs. Conclusions These findings suggest that MALAT1 represents a promising therapeutic target for the treatment of UC by modulating the miR-22-3p/NLRP3 pathway, potentially leading to novel strategies for reducing inflammation and cell death in the colon.
Yan et al. (2024) MALAT1 promotes colonic epithelial cell apoptosis and pyroptosis by sponging miR-22-3p to enhance NLRP3 expression. PeerJ 12:e18449 https://doi.org/10.7717/peerj.18449
Several methods for assessing research waste in reviews with a systematic search: a scoping review
Background Research waste is present in all study designs and can have significant consequences for science, including reducing the reliability of research findings and contributing to the inefficient use of resources. Estimates suggest that as much as 85% of all biomedical research is wasted. However, it is uncertain how avoidable research waste is assessed in specific types of study designs and what methods could be used to examine different aspects of research waste. We aimed to investigate which methods, systematic reviews, scoping reviews, and overviews of reviews discussing research waste, have used to assess avoidable research waste. Materials and Methods We published a protocol in the Open Science Framework prospectively (https://osf.io/2fbp4). We searched PubMed and Embase with a 30-year limit (January 1993–August 2023). The concept examined was how research waste and related synonyms (e.g., unnecessary, redundant, duplicate, etc.) were assessed in reviews with a systematic search: systematic, scoping, or overviews of reviews. We extracted data on the method used in the review to examine for research waste and for which study design this method was applied. Results The search identified 4,285 records of which 93 reviews with systematic searches were included. The reviews examined a median of 90 (range 10–6,781) studies, where the study designs most commonly included were randomized controlled trials (48%) and systematic reviews (33%). In the last ten years, the number of reports assessing research waste has increased. More than 50% of examined reviews reported evaluating methodological research waste among included studies, typically using tools such as one of Cochrane Risk of Bias tools (n = 8) for randomized controlled trials or AMSTAR 1 or 2 (n = 12) for systematic reviews. One fourth of reviews assessed reporting guideline adherence to e.g., CONSORT (n = 4) for randomized controlled trials or PRISMA (n = 6) for systematic reviews. Conclusion Reviews with systematic searches focus on methodological quality and reporting guideline adherence when examining research waste. However, this scoping review revealed that a wide range of tools are used, which may pose difficulties in comparing examinations and performing meta-research. This review aids researchers in selecting methodologies and contributes to the ongoing discourse on optimizing research efficiency.
Rosengaard et al. (2024) Several methods for assessing research waste in reviews with a systematic search: a scoping review. PeerJ 12:e18466 https://doi.org/10.7717/peerj.18466
Comparative transcriptome profiling suggests the role of phytohormones in leaf stalk-stem angle in melon (Cucumis melo L.)
Leaf stalk-stem angle is an important agronomic trait influencing melon architecture, photosynthetic efficiency, and crop yield. However, the mechanisms governing leaf stalk-stem angle, particularly in melon, are not well understood. In this study, we explored the comparative transcriptome in the expanded architecture line Y164 and the compact plant architecture line Z151 at 30 days after pollination. Phytohormones were measured at the leaf stalk-angle site at the same time in these two lines using liquid chromatography (LC) tandem mass spectrometry (MS) (LC-MS/MS). The phytohormones and transcriptomes were jointly analyzed. Differential hormone profiling revealed that the levels of 1-aminocyclopropane-1-carboxylate (ACC) and 12-oxophytodienoic acid (OPDA) in the large-angled line Y164 were significantly higher than those in the small-angled line Z151. These differences were quantified as 2.1- and 2.8-fold increases, respectively. Conversely, the content of isopentenyl adenosine (IPA) was significantly elevated in Z151, with a 3.8-fold higher concentration relative to Y164. Transcriptome analysis identified a total of 1709 differently expressed genes (DEGs), with a predominant enrichment in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to photosynthesis and plant hormone signal transduction. Similarly, photosynthesis and the hormone metabolic process were predominantly enriched in the biological process of Gene Ontology (GO) terms. Further integration of transcriptome and hormone analyses substantiated the close relationship between melon leaf stalk-stem angle and phytohormones, especially ACC, OPDA and IPA. Selected DEGs from phytohormone signal transduction were validated. Detailed analysis of DEGs highlighted the potential role of genes such as GH3s (LOC103490488, LOC103490483), SUARs (LOC107991561, LOC103497281 and LOC103489067), ARFs (LOC103503893, LOC103493078) and five genes in abscisic acid pathway. In summary, our findings strongly suggest a direct correlation between phytohormones and the leaf stalk-stem angles in melon.
Mao et al. (2024) Comparative transcriptome profiling suggests the role of phytohormones in leaf stalk-stem angle in melon (Cucumis melo L.). PeerJ 12:e18467 https://doi.org/10.7717/peerj.18467
Systemic acquired resistance inducing chemicals mitigate black scurf disease in potato by activating defense-related enzymes
The potato, being an underground vegetable crop, faces consistent threats from soil- and tuber-borne fungal and bacterial pathogens. Black scurf and stem canker disease caused by the fungal pathogen Rhizoctonia solani Kuhn is a critical global concern in the potato cultivation system. In this study, we evaluated the disease mitigation potential of five systemic acquired resistance-inducing chemicals viz., salicylic acid, jasmonic acid, β-aminobutyric acid, γ-aminobutyric acid and hydrogen peroxide (H2O2). Two common methods, tuber dipping and foliar spray, were utilized in this experiment to evaluate pathogen inhibition on inoculated tubers. The results revealed that all the systemic acquired resistance inducing chemicals were effective in disease suppression in a concentration-dependent manner compared to an inoculated control. Significant differences (P < 0.005) were evident among the various treatment combinations, with salicylic acid being the most effective in alleviating black scurf disease. Maximum reduction in disease incidence compared to the control was observed with salicylic acid (57.89% and 73.68%), followed by jasmonic acid (52.63% and 65.78%) and H2O2 (49.99% and 60.52%) under the tuber dipping treatment combinations. Whereas, in the foliar application, the maximum reduction in disease incidence compared to the control was observed with salicylic acid (44.73 and 63.15%), followed by jasmonic acid (42.10 and 60.52%) and H2O2 (39.46 and 52.63%). The tuber dipping treatments were significantly more efficacious (P < 0.005) compared to foliar spray for all treatment combinations. The biochemical analysis of defense-related enzymes and metabolites demonstrated the induced resistance activation under these treatments. The activity of peroxidase, polyphenol oxidase, and phenyl ammonia-lyase was significantly higher in treated tubers as compared to inoculated and uninoculated control. The total phenol content was also elevated in treated tubers as compared to the respective control. Altogether, these resistance-inducing chemicals can be successfully included in integrated disease management programs.
Buswal et al. (2024) Systemic acquired resistance inducing chemicals mitigate black scurf disease in potato by activating defense-related enzymes. PeerJ 12:e18470 https://doi.org/10.7717/peerj.18470
Association between circulating CTRP9 levels and coronary artery disease: a systematic review and meta-analysis
Background C1q tumor necrosis factor (TNF) related proteins 9 (CTRP9) is a novel adipocytokine that has been shown to have a cardioprotective effect in coronary artery disease (CAD). However, there are conflicting results on circulating levels of CTRP9 in patients with and without CAD. This meta-analysis was conducted to investigate the association between circulating CTRP9 levels and CAD. Objective The aim of this meta-analysis was to re-examine the relationship between circulating CTRP9 levels and CAD. Methods We searched PubMed, Web of Science, Embase, Cochrane Library, CNKI, VIP, Wanfang Data, and CBM for relevant studies up to October 2023, and 193 articles were identified. After reading the title, abstract and full text, a total of 25 articles were included in this meta-analysis. A prespecified protocol registered at INPLASY was followed (INPLASY202450066). Due to the high heterogeneity, we performed subgroup analyses and meta-regression based on patient characteristics, complications, clinical biochemical indicators, coronary artery lesion, and CAD classification. Publication bias was assessed using Egger’s linear regression tests, Begg’s rank correlation tests, and funnel plots. Results The results showed that the patient with CAD had significantly lower circulating CTRP9 levels than the control group (Z = 3.26, P = 0.001). Subgroup analysis and meta-regression findings demonstrated that observed heterogeneity could be attributed to population distribution. Patient characteristics (year of publication, patients’ age, and BMI), complications (diabetes and type 2 diabetes mellitus (T2DM)), clinical biochemical indicators, coronary artery lesion (stability of coronary atherosclerotic plaque, and the number of diseased coronary vessels), and classification of CAD were not identified as source of heterogeneity. Conclusions The meta-analysis confirmed that circulating CTRP9 levels in CAD patients are significantly lower than those in patients without CAD. The association may be modified by the population distribution.
Zhu et al. (2024) Association between circulating CTRP9 levels and coronary artery disease: a systematic review and meta-analysis. PeerJ 12:e18488 https://doi.org/10.7717/peerj.18488
Systemic immune-inflammation index as an independent risk factor for diabetic nephropathy: a retrospective, single-center study
Purpose Systemic immune-inflammation index (SII) was an indicator which could reflect immune response and systemic inflammation. We aim to explore the relationship between SII and diabetic nephropathy (DN). Methods SII was calculated as neutrophil count × platelet count/lymphocyte count. The receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnosis power of SII. Univariate and multivariate logistic analysis were conducted to assess SII as the risk factor for DN. A restricted cubic spline model was carried out to show the nonlinear association between SII and DN. Results Two hundred participants were enrolled, with an average age of 56.6 ± 13.4 years; 54% participants were categorized as DN. Spearman association analysis showed SII was positive associated with increased urinary albumin to creatinine ratio and serum creatinine, while negative associated with eGFR and serum albumin. The ROC curve revealed that the maximum area under the curve (AUC) was 0.761 (95% CI, 0.694-0.828, P < 0.001). After univariate and multivariate logistic analysis, SII (OR=1.004, P = 0.002) and serum creatinine (OR=1.146, P < 0.001) were risk factors for the occurrence of DN, while age (OR=0.920, P = 0.011) and serum albumin (OR=0.708, P < 0.001) were protective factors for the occurrence of DN. The restricted cubic spline model showed that there was a significant nonlinear association between DN incidence and continuous SII value when it exceeded 624*10 $\hat {}$ ˆ 9/L. Conclusion SII is a novel diagnostic biomarker which is independently associated with DN. Further large-scale prospective studies are needed to validate our findings before SII can be considered a reliable diagnostic or prognostic tool for DN.
Zhang et al. (2024) Systemic immune-inflammation index as an independent risk factor for diabetic nephropathy: a retrospective, single-center study. PeerJ 12:e18493 https://doi.org/10.7717/peerj.18493
Intra-rater and inter-rater reliability of a handheld myotonometer measuring myofascial stiffness of lower lumbar myofascial tissue in healthy adults
Background Biomechanical muscle properties, such as stiffness, can be valuable indicators of tissue health and show promise as a diagnostic and treatment measure for chronic low back pain (CLBP). The development of accessible assessment technologies, such as the MyotonPRO portable device, allows for the convenient quantification of muscle tone and stiffness changes. The aim of this study is to assess the reliability of lumbar erector spinae muscle stiffness with the MyotonPRO in healthy adults and to compare stiffness changes between prone and sitting position. Methods Thirty asymptomatic participants (N = 15 women and N = 15 men) aged between 18 and 65 years were recruited to participate in this study. Two examiners tested muscle stiffness at the palpable muscle belly, one finger away from the spinous process at the level of the L4 vertebra, first from the left and then from the right side, both in prone position and after in sitting position. For inter-rater reliability, all participants were tested by two examiners on the same day, and intra-rater reliability was calculated using the same examiner’s assessment results with an exact 24-h interval. Intraclass correlation coefficients (ICC), standard error measures (SEM) and minimum detectable change (MDC) with a 95% confidence interval were calculated to assess intra-rater and inter-rater reliability. Results Statistical analysis revealed good intra-rater reliability with an ICC of 0.88 (95% CI [0.76–0.94]) for the stiffness of the left erector spinae and excellent intra-rater reliability with an ICC of 0.91 (95% CI [0.82–0.95]) for the right erector spinae, both in the prone position. Intra-rater reliability in the sitting position was excellent to very good with an ICC of 0.91 (95% CI [0.82–0.96]) for the left side and an ICC of 0.89 (95% CI [0.78–0.95]) for the right side. The results for the left-sided prone position showed good inter-rater reliability with an ICC of 0.87 (95% CI [0.73–0.94]). The prone position on the right side also showed good inter-rater reliability with an ICC of 0.84 (95% CI [0.68–0.92]). The inter-rater reliability for the left and right side in the sitting position was excellent with an ICC of 0.96 (95% CI [0.92–0.98]) for the left side and an ICC of 0.95 (95% CI [0.90–0.97]) for the right side. Conclusion This study demonstrated high reliability in measuring lumbar erector spinae muscle stiffness with the MyotonPRO in healthy adults and the ability of the device to detect even small changes in erector spinae muscle stiffness, testing both the right and left sides and measuring in both prone and sitting positions. The use of the sitting position to assess lumbar tissue tension in individuals may serve as a valuable substitute for the prone position, particularly for patients who experience discomfort in the prone position, and could have additional practical significance in clinical settings.
Valenti et al. (2024) Intra-rater and inter-rater reliability of a handheld myotonometer measuring myofascial stiffness of lower lumbar myofascial tissue in healthy adults. PeerJ 12:e18524 https://doi.org/10.7717/peerj.18524
Chemical constituents and biological activities of endophytic fungi from Fagopyrum dibotrys
Background Fagopyrum dibotrys is an important wild food and feed germplasm resource. It has high nutritional and medicinal value and is rich in natural products, including flavonoids, phenolic acids, coumarins, and alkaloids. Endophytic fungi in F. dibotrys have emerged as valuable sources of natural products. However, studies on the biological activity and chemical composition of these endophytic fungi remain limited. Methods In this paper, a new method to obtain natural active ingredients by fermentation of endophytic fungi from medicinal plants was proposed. Then the antioxidant and pathogenic activities of the endophytic fungi extracts were determined in vitro. In addition, secondary metabolites produced by endophytic fungi with medicinal activity were analyzed by high performance liquid chromatography-tandem mass spectrometry (LC-MS). Results Among the 95 endophytic fungal strains in F. dibotrys, four strains with high phenol yields were selected by reaction: Alternaria alstroemeriae (J2), Fusarium oxysporum (J15), Colletotrichum karsti (J74), and Colletotrichum boninense (J61). Compared with those of various extracts, the ethyl acetate fractions of A. alstroemeriae (J2), F. oxysporum (J15), and C. boninense (J61) exhibited superior antioxidant and antibacterial properties. The results indicated that the fungal extract was an excellent natural antioxidant and might be a potential antibacterial agent. The DPPH free radical clearance of A. alstroemeriae was 94.96 ± 0.004%. These findings indicated that A. alstroemeriae had strong antioxidant activity. In addition, the extract of A. alstroemeriae had good antibacterial activity against Escherichia coli and Staphylococcus aureus, with MICs of 0.5 and 0.05 mg/mL, respectively. The chemical constituents of the ethyl acetate extract from A. alstroemeriae were further analyzed by liquid chromatography–mass spectrometry (LC–MS). We noted that A. alstroemeriae can create a variety of medicinal substances that have high value in medicine, such as caffeic acid (884.75 ng/mL), 3-phenyllactic acid (240.72 ng/mL) and norlichexanthone (74.36 ng/mL). Discussion In summary, many valuable active substances and medicinal substances can be obtained through the study of endophytic fungi of F. dibotrys.
Xie et al. (2024) Chemical constituents and biological activities of endophytic fungi from Fagopyrum dibotrys. PeerJ 12:e18529 https://doi.org/10.7717/peerj.18529
Risk factors for postoperative hypokalemia in patients undergoing endoscopic pituitary adenoma resection: a retrospective cohort study
Background Currently, endoscopic transsphenoidal surgery is the primary approach for treating pituitary tumors. While endoscopic surgery offers numerous advantages, it also comes with a series of potential surgical complications. Postoperative hypokalemia is a common complication, with mild cases presenting with atypical symptoms such as dizziness, headache, fatigue, and constipation, while severe cases can lead to arrhythmias, rhabdomyolysis, and even death. Therefore, early identification of risk factors for postoperative hypokalemia is crucial. This study aims to analyze the risk factors for hypokalemia after endoscopic pituitary tumor resection. Methods and Materials This study included 168 patients who underwent endoscopic resection of pituitary tumors between 2019 and 2023. Patients were divided into hypokalemia group and non-hypokalemia group based on whether their postoperative serum potassium concentration was less than 3.0 mEq/L. Identifying independent risk factors through binary logistic regression analysis. Results Among the 168 patients, 18 (10.7%) cases experienced postoperative hypokalemia, with the majority occurring on the fourth day after surgery. The majority of patients did not exhibit clinical symptoms related to hypokalemia. The binary logistic regression analysis revealed that age (OR 1.09; 95% CI [1.03–1.15]; P = 0.001) and postoperative hypoalbuminemia on the first day (OR, 4.35; 95% CI [1.38–13.75]; P = 0.012) were associated with postoperative hypokalemia. Conclusions Patients aged ≥50 years and those presenting with hypoalbuminemia on the first postoperative day were more likely to develop postoperative hypokalemia. Therefore, electrolyte monitoring should be enhanced in such patients postoperatively, especially to actively prevent hypokalemia on the 4th–5th postoperative day.
Li et al. (2024) Risk factors for postoperative hypokalemia in patients undergoing endoscopic pituitary adenoma resection: a retrospective cohort study. PeerJ 12:e18536 https://doi.org/10.7717/peerj.18536
β-Defensin versus conventional markers of inflammation in periprosthetic joint infection: a retrospective study
Background Diagnosing periprosthetic joint infection (PJI) remains a significant challenge for healthcare professionals. Commonly utilized inflammatory markers include erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and white blood cells (WBC). Human β-defensin 1 (β-defensin) is an antimicrobial peptide elevated in infection, yet its diagnostic value for PJI has not been explored. The purpose of this study was to evaluate the efficacy of synovial β-defensin as a diagnostic marker for PJI and to compare its performance with ESR, serum CRP, and WBC. Methods We conducted a single-center retrospective study from October 2022 to June 2023. A total of 105 joint fluid samples from revision patients at the Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra were collected intraoperatively (71 hips, 34 knees) and frozen. According to MSIS criteria, 64 patients were defined as positive for PJI and the remaining 41 were negative. Synovial β-defensin levels were quantified using ELISA, serum CRP levels by immunoturbidimetry, and blood ESR and WBC were analyzed. Sensitivity and specificity were determined using ROC curves, and diagnostic performance was compared using the area under the curve (AUC). Cut-off values for diagnosing PJI were established. Results Levels of synovial β-defensin, ESR, serum CRP, and WBC were significantly higher in the PJI group compared to the non-PJI (P < 0.0001). The AUCs were 0.948 for β-defensin, 0.884 for ESR, 0.902 for CRP, and 0.767 for WBC, with a combined AUC of 0.994. Sensitivity/specificity for β-defensin, ESR, CRP, and WBC were 0.966/0.830, 0.887/0.791, 0.930/0.771, and 0.820/0.682, respectively. Optimal predictive cut-off values were 1105.8 pg/mL for β-defensin, 11.5 mm/h for ESR, 5.55 mg/L for CRP, and 7.3 × 103/mm3 for WBC. Conclusion The synovial β-defensin assay demonstrated greater sensitivity and specificity for the diagnosis of PJI compared to ESR, serum CRP and WBC. Therefore, β-defensin shows promise as a diagnostic marker for PJI. Simultaneous determination of all markers may increase diagnostic confidence.
Fernández-Torres et al. (2024) β-Defensin versus conventional markers of inflammation in periprosthetic joint infection: a retrospective study. PeerJ 12:e18560 https://doi.org/10.7717/peerj.18560
The complete mitochondrial DNA of the carnivorous sponge Lycopodina hypogea is putatively complemented by microDNAs
Carnivorous sponges (Porifera, Demospongiae, Cladorhizidae), contrary to the usual filter-feeding mechanism of sponges, are specialized in catching larger prey through adhesive surfaces or hook-like spicules. The mitochondrial DNA of sponges overall present several divergences from other metazoans, and while presenting unique features among major transitions, such as in calcarean and glass sponges, poriferan mitogenomes are relatively stable within their groups. Here, we report and discuss the mitogenome of Lycopodina hypogea (Vacelet & Boury-Esnault, 1996), which greatly vary from its subordinal counterparts in both structure and gene order. This mitogenome is seemingly multipartite into three chromosomes, two of them as microDNAs. The main chromosome, chrM1, is unusually large, 31,099 bp in length, has a unique gene order within Poecilosclerida, and presents two rRNA, 13 protein and 19 tRNA coding genes. Intergenic regions comprise approximately 40% of chrM1, bearing several terminal direct and inverted repeats (TDRr and TIRs) but holding no vestiges of former mitochondrial sequences, pseudogenes, or transposable elements. The nd4l and trnI(gau) genes are likely located in microDNAs thus comprising putative mitochondrial chromosomes chrM2, 291 bp, and chrM3, 140 bp, respectively. It is unclear which processes are responsible for the remarkable features of the of L. hypogea mitogenome, including a generalized gene rearrangement, long IGRs, and putative extrachromosomal genes in microDNAs.
de Paula et al. (2024) The complete mitochondrial DNA of the carnivorous sponge Lycopodina hypogea is putatively complemented by microDNAs. PeerJ 12:e18255 https://doi.org/10.7717/peerj.18255
Rapid detection of enterobacteria in wastewater treated by microalgal consortia using loop-mediated isothermal amplification (LAMP)
In the present study, nine Enterobacteriaceae species present in wastewater were isolated and identified, and loop-mediated isothermal amplification (LAMP) was developed for the detection of Enterobacteriaceae by designing primers based on the mcr-1, KPC, OXA-23, and VIM genes, which are recognized markers of antimicrobial resistance (AMR) transmission during microalgal bioremediation treatment. The developed assays successfully detected four strains positive for mcr-1 gene-asociated resistance (Acinetobacter baylyi, Klebsiella pneumoniae, Morganella morganii, and Serratia liquefaciens), three strains for KPC gene-associated resistance (Acinetobacter sp., Escherichia coli 15499, and Morganella morganii), seven strains for OXA-23 gene-associated resistance (Acinetobacter baylyi, Enterobacter hormaechi, Enterobacter cloacae, Escherichia coli 15922, Escherichia coli 51446, Morganella morganii, and Serratia liquefaciens), and three strains for resistance to the VIM gene-associated resistance (Acinetobacter baylyi, Acinetobacter sp., and Enterobacter hormaechi) from a single colony. A reduction in microbiological load of 93.6% was achieved at 15 colony-forming units (CFU) mL−1, utilizing EMB agar and LAMP values of 0.142 ± 0.011 for the mcr-1 gene, 0.212 ± 0.02 for the KPC gene, 0.233 ± 0.006 for the OXA-23 gene, and 0.219 ± 0.035 for the VIM gene. Furthermore, bioremediation efficiency values of 71.6% and 75% for total nitrogen and phosphorus, respectively, were observed at 72 h of treatment in open pond microalgal remediation systems (MRS). This study demonstrated that the LAMP technique is faster and more sensitive than traditional detection methods, such as CFU, for Enterobacteriaceae. Consequently, this method may be considered for the detection of microbiological quality indicators within the water treatment industry.
Cameron et al. (2024) Rapid detection of enterobacteria in wastewater treated by microalgal consortia using loop-mediated isothermal amplification (LAMP). PeerJ 12:e18305 https://doi.org/10.7717/peerj.18305
Population size and structure of Grant’s gazelle and lesser kudu in Geralle National Park, Southeastern Ethiopia
Background Grant’s gazelle and lesser kudu remain widespread within and outside protected areas. Current pressures on their populations, human encroachment and disturbance associated habitat modifications, and excessive grazing pose further threats to the species. The estimation of density and abundance of species has significant value for sustainable wildlife management in Geralle National Park (GNP) and also contributes towards a more accurate global population estimate. Result Using distance sampling methods, the lowest Akaike Information Criterion (AIC) (close to zero) and Chi-square tests (P value > 0.05) showed that the hazard rate key function with an un-equal interval group model was selected for estimation of density and abundance. The density of species was 1.7 ± 0.5, 2.07 ± 0.7, gazelle/km2 and 1.39 ± 0.3, 1.92 ± 0.42, lesser kudu/km2 during the dry and wet seasons, respectively. Population density, abundance, and structure showed habitat and seasonal differences in observation. More individuals of both species were recorded during the wet season as compared to the dry season. Grassland was favored by Grant’s gazelle, while lesser kudu preferred woodlands. Both species exhibited a female-biased sex ratio, indicating potential for future population growth prospects. Conclusion It can be concluded that GNP is home to viable populations of Grant’s gazelle and lesser kudu, and season has influenced population abundance and distribution due to resource availability variations among seasons. The female-biased sex ratio indicates the future population growth prospects for the two species.
Aychew et al. (2024) Population size and structure of Grant’s gazelle and lesser kudu in Geralle National Park, Southeastern Ethiopia. PeerJ 12:e18340 https://doi.org/10.7717/peerj.18340
Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony
There is an ongoing debate about the internal systematics of today’s group of hamsters (Cricetinae), following new insights that are gained based on molecular data. Regarding the closely related fossil cricetids, however, most studies deal with only a limited number of genera and statements about their possible relationships are rare. In this study, 41 fossil species from the Late Miocene to the Pliocene, belonging to seven extinct cricetine genera, Collimys, Rotundomys, Neocricetodon, Pseudocricetus, Cricetulodon, Apocricetus and Hattomys are analysed in a phylogenetic framework using traditional maximum parsimony and Bayesian inference approaches. Following thorough model testing, a relaxed-clock Bayesian inference analysis is performed under tip-dating to estimate divergence times simultaneously. Furthermore, so-called ‘rogue’ taxa are identified and excluded from the final trees to improve the informative value of the shown relationships. Based on these resulting trees, the fit of the topologies to the stratigraphy is assessed and the ancestral states of the characters are reconstructed under a parsimonious approach and stochastic character mapping. The overall topologies resulting from Bayesian and parsimonious approaches are largely congruent to each other and confirm the monophyly of most of the genera. Additionally, synapomorphies can be identified for each of these genera based on the ancestral state reconstructions. Only Cricetulodon turns out to be paraphyletic, while ‘Cricetulodon’ complicidens is a member of Neocricetodon. Lastly, this work makes a contribution to a debate that went on for decades, as the genus Kowalskia can be confirmed as junior synonym of Neocricetodon.
Dirnberger et al. (2024) Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony. PeerJ 12:e18440 https://doi.org/10.7717/peerj.18440
Comparative efficacy of Knema retusa extract delivery via PEG-b-PCL, niosome, and their combination against Acanthamoeba triangularis genotype T4: characterization, inhibition, anti-adhesion, and cytotoxic activity
Background Acanthamoeba spp. is a waterborne, opportunistic protozoan that can cause amebic keratitis and granulomatous amebic encephalitis. Knema retusa is a native tree in Malaysia, and its extracts possess a broad range of biological activities. Niosomes are non-ionic surfactant-based vesicle formations and suggest a future targeted drug delivery system. Copolymer micelle (poly(ethylene glycol)-block-poly(ɛ-caprolactone); PEG-b-PCL) is also a key constituent of niosome and supports high stability and drug efficacy. To establish Knema retusa extract (KRe) loading in diverse nanocarriers via niosome, PEG-b-PCL micelle, and their combination and to study the effect of all types of nanoparticles (NPs) on Acanthamoeba viability, adherent ability, elimination of adherence, and cytotoxicity. Methods In this study, we characterized niosomes, PEG-b-PCL, and their combination loaded with KRe and tested the effect of these NPs on Acanthamoeba triangularis stages. KRe-loaded PEG-b-PCL, KRe-loaded niosome, and KRe-loaded PEG-b-PCL plus niosome were synthesized and characterized regarding particle size and charge, yield, encapsulation efficiency (EE), and drug loading content (DLC). The effect of these KRe-loaded NPs on trophozoite and cystic forms of A. triangularis was assessed through assays of minimal inhibitory concentration (MIC), using trypan blue exclusion to determine the viability. The effect of KRe-loaded NPs was also determined on A. triangularis trophozoite for 24–72 h. Additionally, the anti-adhesion activity of the KRe-loaded niosome on trophozoites was also performed on a 96-well plate. Cytotoxicity activity of KRe-loaded NPs was assessed on VERO and HaCaT cells using MTT assay. Results KRe-loaded niosome demonstrated a higher yielded (87.93 ± 6.03%) at 286 nm UV-Vis detection and exhibited a larger size (199.3 ± 29.98 nm) and DLC (19.63 ± 1.84%) compared to KRe-loaded PEG-b-PCL (45.2 ± 10.07 nm and 2.15 ± 0.25%). The EE (%) of KRe-loaded niosome was 63.67 ± 4.04, which was significantly lower than that of the combination of PEG-b-PCL and niosome (79.67 ± 2.08). However, the particle charge of these NPs was similar (−28.2 ± 3.68 mV and −28.5 ± 4.88, respectively). Additionally, KRe-loaded niosome and KRe-loaded PEG-b-PCL plus niosome exhibited a lower MIC at 24 h (0.25 mg/mL), inhibiting 90–100% of Acanthamoeba trophozoites which lasted 72 h. KRe-loaded niosome affected adherence by around 40–60% at 0.125–0.25 mg/mL and removed Acanthamoeba adhesion on the surface by about 90% at 0.5 mg/mL. Cell viability of VERO and HaCaT cells treated with 0.125 mg/mL of KRe-loaded niosome and KRe-loaded PEG-b-PCL plus niosome exceeded 80%. Conclusion Indeed, niosome and niosome plus PEG-b-PCL were suitable nanocarrier-loaded KRe, and they had a greater nanoparticle property to test with high activities against A. triangularis on the reduction of adherence ability and demonstration of its low toxicity to VERO and HaCaT cells.
Chimplee et al. (2024) Comparative efficacy of Knema retusa extract delivery via PEG-b-PCL, niosome, and their combination against Acanthamoeba triangularis genotype T4: characterization, inhibition, anti-adhesion, and cytotoxic activity. PeerJ 12:e18452 https://doi.org/10.7717/peerj.18452
Treatment of the terrible triad of the elbow by olecranon osteotomy: a retrospective cohort study
Background This study aims to evaluate the surgical techniques and outcomes of treating elbow dislocations with coronoid and radial head fractures, commonly referred to as the terrible triad of the elbow (TTE), through a single olecranon osteotomy. Methods A retrospective analysis was performed on 73 patients diagnosed with TTE between January 2015 and April 2022. The cohort included 44 men and 29 women, with an average age of 40.0 ± 15.1 years (range, 18–68 years). Among these patients, Mason Type I, II, and III fractures were identified in 11, 42, and 20 cases, respectively, while Morrey Type I, II, and III fractures were observed in 45, 23, and five cases, respectively. All patients underwent treatment via a single olecranon osteotomy. The average interval between injury and surgery was 5.6 ± 1.6 days (range, 3–8 days). Elbow function was assessed using the Mayo Elbow Performance Score (MEPS), pain was measured via the Visual Analogue Scale (VAS), and quality of life was evaluated using the SF-36 questionnaire. Results Patients were followed for 15 to 60 months (mean, 37.1 ± 13.3 months). All coronoid and radial head fractures achieved complete healing, with an average recovery time of 4.3 ± 1.1 months (range, 3–6 months). By the final follow-up, all patients had regained normal elbow function. The mean elbow flexion was 124.4° ± 9.2°, extension was 9.6° ± 6.5°, and the total range of flexion-extension was 114.8° ± 11.7°. Forearm pronation averaged 77.3° ± 4.8°, supination 79.2° ± 6.5°, and total forearm rotation 156.5° ± 8.4°. The mean MEPS was 89.3 ± 6.4, with 36 patients achieving excellent scores and 37 obtaining good scores. Preoperative VAS scores averaged 8.78 ± 1.11, which significantly dropped to 0.97 ± 0.83 at the final follow-up (p = 0.000). The SF-36 preoperative PCS and MCS scores were 45.77 ± 3.59 and 60.67 ± 3.91, respectively, with postoperative improvements to 93.85 ± 2.65 (p = 0.000) and 95.79 ± 3.11 (p = 0.000). Conclusion This retrospective analysis indicates that a single olecranon osteotomy could be a viable treatment option for TTE. However, additional research involving a control group is essential to substantiate the efficacy of this technique.
Zhou et al. (2024) Treatment of the terrible triad of the elbow by olecranon osteotomy: a retrospective cohort study. PeerJ 12:e18469 https://doi.org/10.7717/peerj.18469
Evaluating the efficacy of curcumin in the management of oral potentially malignant disorders: a systematic review and meta-analysis
Background Oral potentially malignant disorders (OPMDs) not only harbour the risk of malignant transformation but can also affect patients’ quality of life owing to severe symptoms. Therefore, there is an urgent need for therapeutic strategies to improve patients’ quality of life. The objective of this meta-analysis was to comprehensively assess the efficacy of curcumin in the management of OPMDs. Methods PubMed, Embase, the Cochrane Library, and Web of Science were searched for clinical trials evaluating the efficacy of curcumin in the treatment of OPMDs from inception until March 2024. RevMan 5.4 software was used to perform statistical and subgroup analyses. Results Sixteen randomised controlled trials (1,089 patients) were selected. Curcumin exhibited comparable efficacy to conventional controls in alleviating pain (I2 = 98%, P = 0.49) and improving tongue protrusion (I2 = 94%, P = 0.51) in oral submucous fibrosis (OSF). Additionally, topical use of curcumin had an efficacy equivalent to that of conventional therapy in reducing pain (I2 = 83%, P = 0.31) and facilitating clinical remission (I2 = 67%, P = 0.38) of oral lichen planus (OLP). Conclusion The topical use of curcumin may palliate pain and promote clinical healing in OLP patients. Systemic curcumin can ameliorate the degree of pain and tongue protrusion in OSF. Therefore, our study suggests that curcumin could serve as an alternative treatment for managing OPMDs with lower medical toxicity than steroids, especially when steroids are not suitable. Further studies with larger sample sizes and adequate follow-up periods are required to validate our results.
Shi et al. (2024) Evaluating the efficacy of curcumin in the management of oral potentially malignant disorders: a systematic review and meta-analysis. PeerJ 12:e18492 https://doi.org/10.7717/peerj.18492
Cirsilineol improves anesthesia/surgery-induced postoperative cognitive dysfunction through attenuating oxidative stress and modulating microglia M1/M2 polarization
Background Cirsilineol is a trimethoxy and dihydroxy flavonoid isolated from plant species such as Artemisia vestita and has a variety of pharmacological properties. This study analyzed whether cirsilineol could prevent postoperative cognitive dysfunction (POCD). Methods A POCD mouse model induced by anesthesia/surgery induction and a cell model established with hydrogen peroxide (H2O2)-induced microglia BV-2 were employed to explore the efficacy of cirsilineol on POCD. The cognition function of the mice were assessed by carrying out behavioral tests (Morris water maze test and Y-maze test). We assessed the activation and polarization status of microglia using immunofluorescence analysis and detected the expression levels of CD86 and CD206 using the quantitative PCR (qPCR). Subsequently, cell viability was determined by CCK-8 assay and apoptosis was assessed using Calcein-AM/PI staining. Meanwhile, superoxide dismutase (SOD) and malondialdehyde (MDA) levels in plasma and cell culture medium were detected using chemiluminescence. Finally, the phosphorylation levels of JAK/STAT signaling pathway-related proteins were analyzed by Western blot. Results Cirsilineol reduced the escape latency and times of crossing island and increased spontaneous alternation (SA) rate, restoring the cognitive dysfunctions of POCD-modeled mice. Meanwhile, POCD elevated CD86 expression and malondialdehyde content and lowered the level of SOD; however, cirsilineol promoted CD206 expression and generation of SOD and inhibited malondialdehyde production. In H2O2-induced microglia BV-2, cirsilineol treatment increased SOD content and suppressed the generation of reactive oxygen species (ROS) and malondialdehyde, modulating microglia M1/M2 polarization and JAK/STAT pathway. Conclusion Cirsilineol prevented against POCD by attenuating oxidative stress and modulating microglia M1/M2 polarization, providing novel insights for the management of POCD.
Du et al. (2024) Cirsilineol improves anesthesia/surgery-induced postoperative cognitive dysfunction through attenuating oxidative stress and modulating microglia M1/M2 polarization. PeerJ 12:e18507 https://doi.org/10.7717/peerj.18507
Heavy metal concentrations in soil and ecological risk assessment in the vicinity of Tianzhu Industrial Park, Qinghai-Tibet Plateau
Industrial parks in China are centers of intensive chemical manufacturing and other industrial activities, often concentrated in relatively small areas. This concentration increases the risk of soil pollution both within the parks and in surrounding areas. The soils of the Tibetan Plateau, known for their high sensitivity to environmental changes, are particularly vulnerable to human activity. In this study, we examined the concentrations (mg/kg) of 10 metal elements (As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Se, and Zn) in soils at depths of 0–10 cm, 10–20 cm, and 20–30 cm from the surface at three distances (500 m, 1000 m, and 1500 m from the park boundary) on the east, south, west, and north sides of the Tianzhu Industrial Park on the Qinghai-Tibet Plateau. The concentrations of As, Cr, Mn, and Pb were close to the standard reference values for the Qinghai-Tibet Plateau, while Cu, Ni, Se, and Zn levels were found to be 1.6-2.2 times higher than the reference values. Cd and Hg concentrations were particularly concerning, at 8.0 and 6.5 times higher than reference values, respectively. The potential ecological risk indexes indicated persistent risk levels for Cd and Se across various directions and distances. Variations in soil depth and direction were observed for the concentrations of As, Cd, Hg, Pb, Se, and Zn, underscoring the need for regular or long-term monitoring. Cd, in particular, presents a significant hazard due to its high concentration and its propensity for uptake by plants in the study area.
Qi et al. (2024) Heavy metal concentrations in soil and ecological risk assessment in the vicinity of Tianzhu Industrial Park, Qinghai-Tibet Plateau. PeerJ 12:e18510 https://doi.org/10.7717/peerj.18510
Wavelet transform-based mode decomposition for EEG signals under general anesthesia
Background Mode decomposition methods are used to extract the characteristic intrinsic mode function (IMF) from various multidimensional time series signals. We analyzed an electroencephalogram (EEG) dataset for sevoflurane anesthesia using two wavelet transform-based mode decomposition methods, comprising the empirical wavelet transform (EWT) and wavelet mode decomposition (WMD) methods, and compared the results with those from the previously reported variational mode decomposition (VMD) method. Methods To acquire the EEG data, we used the software application EEG Analyzer, which enabled the recording of raw EEG signals via the serial interface of a bispectral index (BIS) monitor. We also created EEG mode decomposition software to perform empirical mode decomposition (EMD), VMD, EWT, and WMD operations. Results When decomposed into six IMFs, the EWT enables narrow band separation of the low-frequency bands IMF-1 to IMF-3, in which all central frequencies are less than 10 Hz. However, in the upper IMF of the high-frequency band, which has a center frequency of ≥ 10 Hz, the dispersion within the frequency band covered was widespread among the individual patients. In WMD, a narrow band of clinical interest is specified using a bandpass filter in a Meyer wavelet filter bank within a specific mode-decomposition discipline. When compared with the VMD and EWT methods, the IMF that was decomposed via WMD was accommodated in a narrow band with only a small variance for each patient. Multiple linear regression analyses demonstrated that the frequency characteristics of the IMFs obtained from WMD best tracked the changes in the BIS upon emergence from general anesthesia. Conclusions The WMD can be used to extract subtle frequency characteristics of EEGs that have been affected by general anesthesia, thus potentially providing better parameters for use in assessing the depth of general anesthesia.
Yamochi et al. (2024) Wavelet transform-based mode decomposition for EEG signals under general anesthesia. PeerJ 12:e18518 https://doi.org/10.7717/peerj.18518
Accuracy of self-reported height, weight, and waist circumference in poor, rural areas of China
Objectives There are differing opinions and findings about the accuracy of self-reported data. This study sought to assess the accuracy of self-reported height, weight, and waist circumference (WC) data among adult residents in poor, rural areas of China. Methods Multi-stage stratified cluster random sampling was used to sample rural adult residents in Jinzhai County. Intraclass correlations (ICCs), Bland-Altman plots with limits of agreements (LOAs), and Cohen’s kappa were used to examine the accuracy of self-reported data. Multiple linear regression was used to explore the effect of demographic and socioeconomic variables. Results Height was over-reported by an average of 0.67 cm, weight and WC were both under-reported, by an average of 0.004 kg and 1.09 cm, respectively. The ICC for height was 0.92, the ICC for weight was 0.93, and the ICC for WC was 0.93. Bland-Altman plots showed no trend in variability with increasing height, weight, and WC, but 95% of the LOAs were wide, especially for WC. The percentage agreement (kappa) for BMI was 82.10% (0.71), and the percentage agreement for WC was 83.56% (0.66). Overall, obesity, overweight, and increased WC were underestimated by 0.56%, 2.64%, and 6.89%, respectively. Assessments of which demographic and socioeconomic factors were associated with statistically significant differences between self-reported and measured data showed that education (junior school vs. primary or below: β = −0.56, 95% CI [−1.01 to −0.11]) and occupation (others vs. professionals: β = 2.16, 95% CI [0.62–3.70]) were associated with differences between measured and self-reported height; occupation (industrial and commercial service vs. professionals: β = 1.57, 95% CI [0.52–2.61]) was associated with differences between measured and self-reported weight; and gender (women vs. men: β = −1.74, 95% CI [−2.51 to −0.97]) and age (60– vs. 18–44: β = −1.62, 95% CI [−2.88 to −0.36]) were associated with differences between measured and self-reported WC. Conclusions Self-reported height and weight were shown to be reliable in poor, rural areas of China, but self-reported WC should be used with caution. To improve the accuracy of self-reported data, certain subgroups should be targeted for educational interventions.
Cao et al. (2024) Accuracy of self-reported height, weight, and waist circumference in poor, rural areas of China. PeerJ 12:e18525 https://doi.org/10.7717/peerj.18525
Clinical outcomes of arthroscopic suture fixation combined with loop plate vs. posterior approach open reduction and cannulated screw fixation for treating tibial avulsion fractures of the posterior cruciate ligament: a retrospective study
Background Comparison of the efficacy of arthroscopic suture fixation combined with loop plate vs. the posterior approach involving open reduction and intramedullary nail fixation in treating posterior cruciate ligament tibial avulsion fractures (PCLTAFs). Methods A retrospective analysis was conducted on the clinical data of patients diagnosed with PCLTAF who were admitted to Northern Jiangsu People’s Hospital between June 2019 and March 2022. Based on distinct surgical procedures, the patients were categorized into two groups: arthroscopic group (33 cases), involving a single bone tunnel, high-strength suture, loop plate, and anchor screw fixed under arthroscopy, and open reduction and internal fixation (ORIF) group (13 cases), involving a modified posterior medial approach and fixation using 1–2 cannulated screws. Key parameters, including surgical duration, postoperative fracture alignment, fracture-healing duration, range of motion changes, postoperative Lysholm scores, and VAS scores were documented and compared between the two groups. Results The study cohort comprised 46 patients, with 28 males and 18 females, and the median age was 29 years old (range: 15–69). There were no significant differences in the baseline characteristics, including knee Lysholm scores, between the two groups. The arthroscopic group exhibited significant improvement in all eight Lysholm score indicators (all P < 0.001). The total Lysholm score also exhibited significant improvement before and after surgery in both groups (P < 0.001). Following surgery, the arthroscopic group demonstrated improvements in all indicators, but had a slightly longer operating time compared to the ORIF group. No significant differences were observed in the Lysholm scores for the knee joint between the two patient groups before and after surgery (P > 0.05). Conclusions Arthroscopic suture fixation in conjunction with looped plate binding can significantly improve knee function and clinical effect for patients in the treatment of PCLTAF, promotingearly postoperative functional recovery of patients.
Zhang et al. (2024) Clinical outcomes of arthroscopic suture fixation combined with loop plate vs. posterior approach open reduction and cannulated screw fixation for treating tibial avulsion fractures of the posterior cruciate ligament: a retrospective study. PeerJ 12:e18532 https://doi.org/10.7717/peerj.18532
miR-101-3p suppresses proliferation of orbital fibroblasts by targeting pentraxin-3 in thyroid eye disease
Background Excessive proliferation of orbital fibroblasts (OFs) is an essential factor in the pathogenesis of thyroid eye disease (TED). While existing evidence indicates that various microRNAs (miRNAs) significantly contribute to TED development, the precise function and targets of miR-101-3p in TED pathogenesis remain unknown. This research aims to elucidate the effects of miR-101-3p on TED-OFs and identify its potential targets. Methods Orbital adipose tissues were harvested from both TED patients and healthy controls to culture their fibroblasts. MiR-101-3p mimic or mimic negative control (mimic NC) was transfected into OFs from TED patients, with untreated OFs serving as an additional blank control group. Cell proliferation was assessed using cell counting kit-8 (CCK-8) assay, Ki-67 immunofluorescence staining, and the EdU assay, while apoptosis was evaluated via flow cytometry. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to measure the expression levels of miR-101-3p and pentraxin-3 (PTX3), and PTX3 protein levels were quantified using western blot. A dual-luciferase assay was conducted to ascertain how miR-101-3p and PTX3 interacted. Results The results demonstrated a significant downregulation of miR-101-3p in fibroblasts and TED orbital adipose tissues. Transfection with the miR-101-3p mimic upregulated miR-101-3p levels, significantly reducing OFs proliferation without affecting apoptosis. Overexpression of miR-101-3p led to the downregulation of PTX3 in OFs. The dual-luciferase assay validated miR-101-3p binding to PTX3’s 3’UTR, thereby repressing its expression. Moreover, overexpression of PTX3 partially rescued the miR-101-3p mimic’s inhibitory effect on TED-OFs proliferation. Conclusion Our findings illustrate miR-101-3p’s role in targeting PTX3 to regulate TED-OFs proliferation, providing novel insights into the pathological mechanisms underlying TED development.
Zhu et al. (2024) miR-101-3p suppresses proliferation of orbital fibroblasts by targeting pentraxin-3 in thyroid eye disease. PeerJ 12:e18535 https://doi.org/10.7717/peerj.18535
Microglial depletion rescues spatial memory impairment caused by LPS administration in adult mice
Recent studies have highlighted the importance of microglia, the resident macrophages in the brain, in regulating cognitive functions such as learning and memory in both healthy and diseased states. However, there are conflicting results and the underlying mechanisms are not fully understood. In this study, we examined the effect of depleting adult microglia on spatial learning and memory under both physiological conditions and lipopolysaccharide (LPS)-induced neuroinflammation. Our results revealed that microglial depletion by PLX5622 caused mild spatial memory impairment in mice under physiological conditions; however, it prevented memory deficits induced by systemic LPS insult. Inactivating microglia through minocycline administration replicated the protective effect of microglial depletion on LPS-induced memory impairment. Furthermore, our study showed that PLX5622 treatment suppressed LPS-induced neuroinflammation, microglial activation, and synaptic dysfunction. These results strengthen the evidence for the involvement of microglial immunoactivation in LPS-induced synaptic and cognitive malfunctions. They also suggest that targeting microglia may be a potential approach to treating neuroinflammation-associated cognitive dysfunction seen in neurodegenerative diseases.
Zong et al. (2024) Microglial depletion rescues spatial memory impairment caused by LPS administration in adult mice. PeerJ 12:e18552 https://doi.org/10.7717/peerj.18552
Biopsy-based normalizations of gill monogenean-infected European catfish (Silurus glanis L., 1758) stocks for laboratory-based experiments
Ectoparasites cause serious problems during the aquaculture production of food fishes. In this study, we set out to develop and test protocols for maintenance and sampling European catfish (Silurus glanis L., 1758) stocks infected with a gill monogenean, Thaparocleidus vistulensis (Siwak 1932) Lim 1996. When we compared the feasibility of two cohabitation-based parasite culture systems (i.e., static vs. flow-through), we found that the life cycle of T. vistulensis was completed in both habitats. In our experience, static tank systems with regular water exchange allowed better daily quality control of the parasite culture than continuous flow-through systems. We investigated the microhabitat preference of T. vistulensis on the gills of infected European catfish. A balanced distribution on the two lateral gill sets and a decreasing trend in parasite numbers from anterior gill holobranches towards the posterior ones was observed. Using these results, we developed a minimally invasive sampling protocol to estimate the parasite load of individuals. The biopsy aimed at four sectors (#6, #7, #10, and #11) situated within the distal and middle zones of the first holobranch on the left side, encompassing both rows of filaments. Biopsy-based estimates of parasite loads were validated by comparing them to full parasite counts of the same individuals and showed statistically significant correlations. Our biopsy-based method is designed to identify experimental animals with similar parasite loads and create groups of hosts with comparable burdens. This setup is expected to generate reduced between-group differences for expensive experiments (e.g., high throughput transcriptomic or epigenetic studies). We propose that the biopsy-based pre-sorting procedure should be considered in similar experiments with other cultured fish species and their gill monogeneans following a thorough fine-tuning of the experimental conditions.
Bognár et al. (2024) Biopsy-based normalizations of gill monogenean-infected European catfish (Silurus glanis L., 1758) stocks for laboratory-based experiments. PeerJ 12:e18288 https://doi.org/10.7717/peerj.18288
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma
Background Lung adenocarcinoma (LUAD) is a widely occurring cancer with a high death rate. Radiomics, as a high-throughput method, has a wide range of applications in different aspects of the management of multiple cancers. However, the molecular mechanism of LUAD by combining transcriptomics and radiomics in order to probe LUAD remains unclear. Methods The transcriptome data and radiomics features of LUAD were extracted from the public database. Subsequently, we used weighted gene co-expression network analysis (WGCNA) and a series of machine learning algorithms including Random Forest (RF), Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression, and Support Vector Machines Recursive Feature Elimination (SVM-RFE) to proceed with the screening of diagnostic genes for LUAD. In addition, the CIBERSORT and ESTIMATE algorithms were utilized to assess the association of these genes with immune profiles. The LASSO algorithm further identified the features most relevant to the expression levels of LUAD diagnostic genes and validated the model based on receiver operating characteristic (ROC), precision-recall (PR), calibration curves and decision curve analysis (DCA) curves. Finally, RT-qPCR, transwell and cell counting kit-8 (CCK8) based assays were performed to assess the expression levels and potential functions of the screened genes in LUAD cell lines. Results We screened a total of 214 modular genes with the highest correlation with LUAD samples based on WGCNA, of which 192 genes were shown to be highly expressed in LUAD patients. Subsequently, three machine learning algorithms identified a total of four genes, including UBE2T, TEDC2, RCC1, and FAM136A, as diagnostic molecules for LUAD, and the ROC curves showed that these diagnostic molecules had good diagnostic performance (AUC values of 0.989, 0.989, 989, and 0.987, respectively). The expression of these diagnostic molecules was significantly higher in tumor samples than in normal para-cancerous tissue samples and also correlated significantly and negatively with stromal and immune scores. Specifically, we also constructed a model based on TEDC2 expression consisting of seven radiomic features. Among them, the ROC and PR curves showed that the model had an AUC value of up to 0.96, respectively. Knockdown of TEDC2 slowed down the proliferation, migration and invasion efficiency of LUAD cell lines. Conclusion In this study, we screened for diagnostic markers of LUAD and developed a non-invasive radiomics model by innovatively combining transcriptomics and radiomics data. These findings contribute to our understanding of LUAD biology and offer potential avenues for further exploration in clinical practice.
Huang et al. (2024) Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma. PeerJ 12:e18310 https://doi.org/10.7717/peerj.18310
A new moradisaurine captorhinid reptile (Amniota: Eureptilia) from the upper Permian of India
Upper Permian rocks of the former supercontinent Gondwana record climax late Paleozoic terrestrial vertebrate faunas that were dominated numerically and ecologically by therapsid synapsids. Older faunal elements of earlier Paleozoic faunas, such as captorhinid reptiles, are rare and scattered components of the first amniote faunas to inhabit high-latitude regions. Here we describe a new genus and species of moradisaurine captorhinid that represents an archaic faunal element of the high-fibre herbivore fauna of the late Permian of what is now peninsular India. The presence of a relatively broad parietal and three rows of conical teeth on the maxilla and the dentary distinguishes Indosauriscus kuttyi gen. et sp. nov. from other moradisaurines. The hypodigm of I. kuttyi comprises skulls that range in length from 39 mm to 54 mm, and high ossification of the braincase elements and well developed skull-roof sutures, indicate that I. kuttyi adults were smaller than those of most moradisaurines. Results of our phylogenetic analyses suggest that moradisaurines, despite appearing first in the paleotropics, dispersed into temperate, high-latitude regions of Pangea early in their evolutionary history. Moradisaurines in dicynodont-dominated faunas, viz. Indosauriscus kuttyi and Gansurhinus naobaogouensis, were the smallest high-fibre herbivores in their respective faunas. This suggests that small body size may have evolved in these moradisaurines as they co-evolved with the more numerous and diverse dicynodont therapsids.
Reisz et al. (2024) A new moradisaurine captorhinid reptile (Amniota: Eureptilia) from the upper Permian of India. PeerJ 12:e18394 https://doi.org/10.7717/peerj.18394
Evaluation of traditional and bootstrapped methods for assessing data-poor fisheries: a case study on tropical seabob shrimp (Xiphopenaeus kroyeri) with an improved length-based mortality estimation method
Background Unrealistic model assumptions or improper quantitative methods reduce the reliability of data-limited fisheries assessments. Here, we evaluate how traditional length-based methods perform in estimating growth and mortality parameters in comparison with unconstrained bootstrapped methods, based on a virtual population and a case study of seabob shrimp (Xiphopenaeus kroyeri, Heller, 1862). Methods Size data were obtained for 5,725 seabob shrimp caught in four distinct fishing grounds in the Southwestern Atlantic. Also, a synthetic population with known parameter values was simulated. These datasets were analyzed using different length-based methods: the traditional Powell-Wetheral plot method and novel bootstrapped methods. Results Analysis with bootstrapped ELEFAN (fishboot package) resulted in considerably lower estimates for asymptotic size (L∞), instantaneous growth rate (K), total mortalities (Z) and Z/K values compared to traditional methods. These parameters were highly influenced by L∞ estimates, which exhibited median values far below maximum lengths for all samples. Contrastingly, traditional methods (PW method and Lmax approach) resulted in much larger L∞ estimates, with average bias >70%. This caused multiplicative errors when estimating both Z and Z/K, with an astonishing average bias of roughly 200%, with deleterious consequences for stock assessment and management. We also present an improved version of the length-converted catch-curve method (the iLCCC) that allows for populations with L∞ > Lmax and propagates the uncertainty in growth parameters into mortality estimates. Our results highlight the importance of unbiased growth estimates to robustly evaluate mortality rates, with significant implications for length-based assessments of data-poor stocks. Thus, we underscore the call for standardized, unconstrained use of fishboot routines.
de Barros et al. (2024) Evaluation of traditional and bootstrapped methods for assessing data-poor fisheries: a case study on tropical seabob shrimp (Xiphopenaeus kroyeri) with an improved length-based mortality estimation method. PeerJ 12:e18397 https://doi.org/10.7717/peerj.18397
The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents
Tuberculosis (TB) caused by Mycobacterium tuberculosis has been a threat to human health for thousands of years and still leads to millions of deaths each year. TB is a disease that is refractory to treatment, partially due to its capacity for in-host persistence. The cell wall of mycobacteria, rich in mycolic acid, is broadly associated with bacterial persistence together with antimicrobial and immunological resistance. Enzymes for the biosynthesis of bacterial peptidoglycan, an essential component of the cell wall, have been addressed and considered as appealing drug targets in pathogens. Significant effort has been dedicated to finding inhibitors that hinder peptidoglycan biosynthesis, many with demonstrated enzymatic inhibition in vitro being published. One family of critical biosynthetic enzymes are the Mur enzymes, with many enzyme specific inhibitors having been reported. However, a lesser developed strategy which may have positive clinical implications is to take advantage of the common structural and catalytic characteristics among Mur enzymes and to allow simultaneous, multiple Mur inhibition, and avert the development of drug resistance. M. tuberculosis relies on these essential Mur enzymes, with the best-known subset being Mur ligases, but also utilizes unique functions of atypical transpeptidases resulting in peptidoglycan peptide cross-linking beneficial to the bacteria’s capacity for chronic persistence in humans. A systematic review is now needed, with an emphasis on M. tuberculosis. The urgent development of novel anti-TB agents to counter rapidly developing drug resistance requires a revisit of the literature, past successes and failures, in an attempt to reveal liabilities in critical cellular functions and drive innovation.
Chiang et al. (2024) The fall of the mycobacterial cell wall: interrogating peptidoglycan synthesis for novel anti-TB agents. PeerJ 12:e18404 https://doi.org/10.7717/peerj.18404
Digital eye strain syndrome among higher education health sciences students in Saudi Arabia: severity and preventive ergonomic practices
Background The increased utilization of digital screens is an unavoidable consequence of the technology era. Digital eye strain (DES) is a prevalent health problem among higher education students in Saudi Arabia, especially health sciences students due to the frequent use of digital sources and virtual classes. Thus, this study aimed to assess the severity of digital eye strain syndrome (DESS) symptoms and preventive ergonomic practices among higher education health science students in Saudi Arabia. Methods A cross-sectional study using multistage cluster sampling in three cities (Dammam, Riyadh, Jeddah) in Saudi Arabia. A convenient sample of 328 health science students was selected using an equal allocation technique. The researchers designed and used an online survey of three sections: personal and digital device use-related data, the DESS questionnaire, and the self-reported preventive ergonomic practices scale. Results DESS is a widespread problem among 72.0% of health science students, and 58.2% had unsatisfactory ergonomics. The frequently reported symptoms were blurred vision (32.9%) and increased sensitivity to light (33.5%). The severe eye-related symptoms were headache (45.85%), foreign body inside the eye (43.71%), eye burning (40.19%), and dryness (39.76%). Logistic regression analysis revealed that the female sex, years of screen utilization and the number of hours per day, screen use without rest, and frequency of virtual classes per week, eye disease, digital screen utilization for studying, nonuse of protective eye measures, and using numerous digital devices were significant predictors of DESS risk (P < 0.05). Conclusions DESS is a common problem among many health science students, with headaches and foreign body sensations in the eye being the most frequent symptoms. Screen utilization time and eye disease are significant predictors of DESS, while most items’ application of ergonomic practices was low. Educational programs are needed to increase student’s awareness of ergonomic practices.
Gushgari et al. (2024) Digital eye strain syndrome among higher education health sciences students in Saudi Arabia: severity and preventive ergonomic practices. PeerJ 12:e18423 https://doi.org/10.7717/peerj.18423
A review of advancements in the theory and characterization of soil macropore structure
Soil has an intricate pore structure, with the macropore structure serving as a pivotal component of gas exchange, liquid flow, and solute transport within the soil matrix. Scientifically understanding the macropore structure is important for the exploration of soil ecological functions. Drawing upon research literature from diverse nations, this study presents a comprehensive summary of past research findings, thoroughly examining the definition and taxonomy of soil macropores. Additionally, we delve into the factors that affect macropore structure, the effects of macropores on soil ecological functions, and the indicators that describe the nature of macropores. Furthermore, the principles, suitability conditions, benefits, and limitations of the widely utilized techniques for characterizing soil macropore structure were outlined, including staining observation, soil water retention curve, mercury intrusion porosimetry, gas adsorption, nuclear magnetic resonance, scanning electron microscopy, and computed tomography (CT). A comparative analysis was conducted to assist scholars in comprehending the theory of soil macropores, facilitating the selection of suitable macropore structure characterization techniques, and enabling the development of collaborative application modes among these techniques. Using the Web of Science core collection database, bibliometric software such as VOSviewer and CiteSpace were employed to explore the research hotspots and trends in CT, which is currently the most popular technique for characterizing soil macropore structure. This analysis offers insights into the future prospects of CT in the field of soil macropore structure characterization techniques. This article is of particular interest to readers engaged in the characterization of soil macropores.
Cao et al. (2024) A review of advancements in the theory and characterization of soil macropore structure. PeerJ 12:e18442 https://doi.org/10.7717/peerj.18442
Comparative electromyography analysis of subphase gait disorder in chronic stroke survivors
Abnormal lower limb muscle activity is the most common cause of the alterative pattern of gait in stroke survivors, resulting from spastic and paralytic muscles around the hip, knee, and ankle joints. However, the activity of the major lower limb muscles that control the legs to facilitate walking in stroke patients have not been clearly understood in each subphase of the gait. This study differentiated the characteristics of surface electromyography (sEMG) signals of lower limb muscles during four subphases of gait cycle between stroke patients and healthy subjects. Sixteen chronic stroke patients and sixteen healthy subjects were recruited. All participants completed three walking trials with a self-selected walking speed. The sEMG signals were recorded on the gluteus medius, rectus femoris, long head of biceps femoris, medial gastrocnemius, tibialis anterior, and peroneus longus muscles. The characteristics of sEMG signals were processed and analyzed in the time and frequency features, considering the first double support, single support, second double support, and swing phases of the gait cycle.The stroke patients had altered sEMG characteristics on both paretic and non-paretic sides compared to healthy subjects across the sub-phases of gait cycle for all six muscles. All time domain features of sEMG signal showed that the medial gastrocnemius muscle has the most significant impaired activity (p < 0.05) and affected gait disturbance during all four subphases of the gait cycle. The findings demonstrated that the medial gastrocnemius muscle had impaired activity and was most affected during all four sub-phases of the gait cycle. This indicates that sEMG of medial gastrocnemius muscle can be used to measure the improvement of gait rehabilitation.
Hohsoh et al. (2024) Comparative electromyography analysis of subphase gait disorder in chronic stroke survivors. PeerJ 12:e18473 https://doi.org/10.7717/peerj.18473
New insights into the impact of wood vinegar on the growth and rhizosphere microorganisms of cherry radish (Raphanus sativus L.)
Understanding the impact of wood vinegar on the growth of cherry radish is indispensable for use in crop production and environmental safety. Our study explored the regulation of rhizosphere microbial abundance and activity by wood vinegar, as well as the relationship between microbial community and growth factors in-depth and systematically. Bacterial communities at the phylum and genus levels were significantly changed after wood vinegar treatment. Application of 200-fold diluted wood vinegar significantly boosted Actinobacteriota and Firmicutes abundances by 40.88% and 126.67%, respectively, while Proteobacteria was promoted in carbon-rich soil. Fungi positively responded to cherry radish root traits and were correlated with aboveground biomass and fruit production. The fungi that correlated with photosynthesis included Albifimbria, Allomyces, Calcarisporiella, Clonostachys, Fusarium, Fusicolla, Knufia, Nigrospora, Paraconiothyrium, Preussia, Talaromyces, and Mortierellomycota. Wood vinegar treatment significantly affected the composition and abundance of soil bacterial and fungal communities in cherry radish rhizosphere, while simultaneously enhancing photosynthetic efficiency (e.g., Pn: 80.45% and Tr: 56.75%) and resulting in a 44.91% increase in crop yield. The promotion of cherry radish growth by wood vinegar may be attributed to the stimulation of soil microorganisms that degraded aromatic compounds and drove nitrogen cycling. This study provided novel insights into the significant promotion of cherry radish growth using wood vinegar diluted 200 times and identified potential microbial targets for agricultural applications.
Gu et al. (2024) New insights into the impact of wood vinegar on the growth and rhizosphere microorganisms of cherry radish (Raphanus sativus L.). PeerJ 12:e18505 https://doi.org/10.7717/peerj.18505
An experimental analysis of graph representation learning for Gene Ontology based protein function prediction
Understanding protein function is crucial for deciphering biological systems and facilitating various biomedical applications. Computational methods for predicting Gene Ontology functions of proteins emerged in the 2000s to bridge the gap between the number of annotated proteins and the rapidly growing number of newly discovered amino acid sequences. Recently, there has been a surge in studies applying graph representation learning techniques to biological networks to enhance protein function prediction tools. In this review, we provide fundamental concepts in graph embedding algorithms. This study described graph representation learning methods for protein function prediction based on four principal data categories, namely PPI network, protein structure, Gene Ontology graph, and integrated graph. The commonly used approaches for each category were summarized and diagrammed, with the specific results of each method explained in detail. Finally, existing limitations and potential solutions were discussed, and directions for future research within the protein research community were suggested.
Vu et al. (2024) An experimental analysis of graph representation learning for Gene Ontology based protein function prediction. PeerJ 12:e18509 https://doi.org/10.7717/peerj.18509
Intra-rater and inter-rater reliability of the fixed plumb line for postural and scoliosis assessment in the sagittal plane: a pilot study
Background The plumb line (PL) is a common tool for assessing the sagittal curvatures of the spine, but its accuracy depends on the ability of the physician to use it correctly. This study aimed to present a fixed plumb line (FPL) no longer held by a physician but fixed to a support, evaluating the reliability in posture assessment, comparing it with PL in both adolescent with and without scoliosis. Methods The study evaluated the sagittal distances of the spine using a PL and a FPL in 80 young adults aged between 28.7 ± 7.2 and 55 adolescents aged between 12.4 ± 2.3, with and without scoliosis. Two expert and two novice clinicians tested the patients to evaluate the intra-rater and inter-rater reliability of FPL. Each clinician assessed participants twice on the same day, with a predetermined time interval (>1 h) to reduce recall bias. Multi-factor multivariate analysis of variance and two-way analysis of variance assessed the statistical significance, while intraclass correlation coefficient (ICC), standard error of measurement (SEM) and minimum detectable change (MDC) validated FPL consistency. Results FPL provided an ICC coefficient >0.90 for all the measures, while PL an average of 0.70. On AIS patients, PL and FPL showed a significant difference for C7 p < 0.001 and T12 p < 0.001. The measured parameters were sensitive to gender and age for the FPL, furthermore, the C7 and L3 measurements were statistically different between PL and FPL (p < 0.001). Intra-rater reliability results for FPL ranged from 0.94 to 0.98 across various parameters, while the SEM and MDC values underscore the valuable precision of the FPL with changes exceeding 1 cm being meaningful. These findings suggest that FPL could be a reliable and accurate tool for measuring sagittal distances of the spine in both scoliotic and non-scoliotic patients.
Roggio et al. (2024) Intra-rater and inter-rater reliability of the fixed plumb line for postural and scoliosis assessment in the sagittal plane: a pilot study. PeerJ 12:e18121 https://doi.org/10.7717/peerj.18121
Intention to use short messaging services for promoting drug adherence among individuals with diabetes in Addis Ababa, Ethiopia
Background Suboptimal medication adherence among individuals with diabetes presents a significant challenge in low-income nations. Growing evidence demonstrates the effectiveness of text messaging interventions to enhance medication adherence. This study assesses the intention to use Short Messaging Service (SMS) based reminder services in promoting drug adherence among diabetic patients and associated factors in Addis Ababa, Ethiopia. Methods An institution-based cross-sectional study was conducted from February 06, 2023, to March 27, 2023, in Addis Ababa, Ethiopia. A sample of 351 patients was selected using systematic random sampling. Structured questionnaires were used for data collection. Binary and multivariable logistic regression models were used to analyze the association between intention to use SMS reminders to promote drug adherence among individuals with diabetes and related factors. Results A total of 333 respondents, with a 94.87% response rate, were interviewed for this study. The majority of respondents, 66.4 % (95% CI [61.9–71.2]), expressed an intention to use SMS-based reminder services to promote their drug adherence. Age < 45 years (AOR = 5.73, 95% CI [2.07–15.73]), higher educational level (AOR = 3.03, 95% CI [1.16–7.90]), type of diabetes (AOR = 3.71, 95% CI [1.16–7.90]), oral medication users (AOR = 2.99, 95% CI [1.42–6.32]), SMS as a preferred medium for communication (AOR = 2.86, 95% CI [1.17–7.00]) were deemed to be important variables linked to intention to use SMS reminders to promote drug adherence among individuals with diabetes. Conclusion The findings suggest the majority of individuals with diabetes have intention to use SMS reminders to enhance adherence. This result indicates the potential for utilization of SMS reminders to enhance adherence to diabetic medications. Furthermore, the findings highlight the importance of tailored interventions that take into account patient characteristics and preferences as factors that influence intention when designing such an intervention.
Alem et al. (2024) Intention to use short messaging services for promoting drug adherence among individuals with diabetes in Addis Ababa, Ethiopia. PeerJ 12:e18297 https://doi.org/10.7717/peerj.18297
Effect of vitamin C injections on exercise muscular performance and biochemical parameters in Trichinella spiralis-infected mice
Background Trichinella spiralis is a worldwide intestinal nematode that can parasitize the striated muscles of its hosts at the larval stage. This study aims to evaluate potential of vitamin C for treating trichinellosis-related pathological problems in the infected muscles of mice. Materials and Methods Thirty CD1 male Albino mice were divided into three groups (10 mice per group). Negative and positive control groups (0.9% NaCl) and the infected vitamin C group (10 mg/kg body weight). Two weeks post-infection, each group was intraperitoneally injected daily for two weeks with Vitamin C or saline. The performance of the muscles was assessed both before and after the treatment. After dissection, constant parts of striated muscles were removed for further assays. The scoring of the histological changes of infected muscles was carried out. In addition to muscle malondialdehyde levels, superoxide dismutase and catalase activities were measured for the oxidative and antioxidant states. Creatine kinase and aspartate aminotransferase were also measured in tissues to reflect the degree of muscular damage. Results Vitamin C enhances the weakness of the muscular performance resulting from the infection. Vitamin C was able to repair some of the histological lesions that resulted from the infection. Trichinellosis caused severe changes in the biochemical markers in positive control animals. Muscle damage biomarkers and, besides, oxidative and antioxidant conditions were greatly ameliorated in infected vitamin C animals. Summing up, vitamin C can be used as a complementary drug due to its efficiency in improving pathogenesis following a trichinellosis infection. The supplement also must be tested in the intestinal stage of infection after showing promising results in the muscular stage.
Rashed et al. (2024) Effect of vitamin C injections on exercise muscular performance and biochemical parameters in Trichinella spiralis-infected mice. PeerJ 12:e18381 https://doi.org/10.7717/peerj.18381
Characteristics and development of steepland gullies in the dry valleys of Southwest China
In semi-arid and arid areas, gully erosion is one of the most destructive forms of erosion and causes serious land degradation and resource destruction. Steepland gullies are widely distributed in the dry valleys of southwest China, and their formation is one of the main causes of soil erosion and the destruction of sloping farmland in the region. Previous research on the development of steepland gullies is limited, and further study is needed. In this study, 11 steepland gullies at various stages of development located in Guobu Village, Xide County, Liangshan, Sichuan Province, were selected for investigation using a digital elevation model (DEM) derived from unmanned aerial vehicle data as the primary data source. These data had a spatial resolution of 0.1 m. Fundamental parameters such as the gully length, width, depth, area, and volume were extracted from the remote sensing data. Other characteristic parameters, including the coefficient of main and tributary gullies, vertical gradient, gully elongation, and gully openness, were also investigated. The results indicate a significant linear positive correlation between the gully’s degree of openness and elongation as the gully’s length, width, and depth increase. Furthermore, the vertical gradient and coefficient of main and tributary gullies exhibit power-law relationships with these gully dimensions. The development of steepland gullies was divided into infancy, youth, maturity, and old age based on the use of the gully length as an ergodic indicator in space-for-time substitution. The morphological characteristics of these different stages were quantitatively analyzed, and a proposed mechanism for how the evolution of the gullies proceeds was developed. An empirical model of volume–length erosion was established to investigate the development process of steepland gullies in the dry valleys. It has been observed that the development law of steepland gullies is essentially consistent with the very active stage of typical gully formation, suggesting that steepland gully may represent the initial stage of gully development. The results show that these steepland gullies have their origin in high-intensity rainfall events that are accompanied by the formation of steps and drop water. The effects of gravity erosion and hydraulic erosion then cause the gullies to expand rapidly, forming gullies with a large head and a small tail before they gradually stabilize. The results of this study will help with the understanding of the formation and evolution of steepland gullies and will be of practical significance for the prevention of gully erosion and the protection of sloping farmland in the dry valley region of southwest China.
Cui et al. (2024) Characteristics and development of steepland gullies in the dry valleys of Southwest China. PeerJ 12:e18411 https://doi.org/10.7717/peerj.18411
Exploring the interplay between body mass index and passive muscle properties in relation to grip strength and jump performance in female university students
Background Women typically have a higher body fat content than men. Fat accumulation is associated with muscle weakness and alterations in mechanical properties. This study aims to determine the relationship between BMI and weight status with the mechanical properties of muscle and tendon. It was hypothesized that the stiffness and tone of the forearm muscle and Achilles tendon would be correlated with weight status and BMI. Methods A cross-sectional study was conducted with 136 female university students. Grip strength was assessed using a dynamometer, body composition was analyzed through bioimpedance, and countermovement jump performance was evaluated with a force platform. Stiffness and tone were measured using the MyotonPro device. ANOVA was used to compare grip strength and countermovement jump performance according to body composition. The Pearson correlation coefficient was used to examine bivariate associations. Results Relative grip strength decreased with an increase in fat content, while forearm muscle stiffness and tone decreased with rising weight status and BMI. Stiffness of the Achilles tendon increased with an increase in fat content and showed a significant positive correlation with BMI. Multiple regression analysis revealed a weak correlation between BMI, body composition, and stiffness of the forearm muscles. Conclusion The results of this study support the notion that the stiffness of the forearm muscles and Achilles tendon is correlated with BMI in young adult women. Furthermore, an increase in body fat percentage is linked to a decrease in mechanical properties and poorer muscle function.
Pérez et al. (2024) Exploring the interplay between body mass index and passive muscle properties in relation to grip strength and jump performance in female university students. PeerJ 12:e18430 https://doi.org/10.7717/peerj.18430
Anti-inflammatory role of low-intensity pulsed ultrasound in inhibiting lipopolysaccharide-induced M1 polarization of RAW264.7 cells via Wnt2b/AXIN/β-catenin
Background Low-intensity pulsed ultrasound (LIPUS) is a special type of low-intensity ultrasound. In periodontal disease, LIPUS is applied as an adjuvant and non-invasive treatment. It has been reported that LIPUS significantly shifts the macrophage phenotype from M1 to M2, but the specific mechanism behind this shift is still unknown. Methods RAW264.7 cells were induced to M1/M2 polarization with lipopolysaccharide (LPS)/interleukin-4 (IL4). LIPUS was performed for 25 min two times, 24 h apart, at an intensity of 45 mW/cm2 to stimulate RAW264.7 cells. PolyA mRNA sequencing was conducted of both the LPS-induced RAW264.7 cells and the LPS-induced RAW264.7 cells with LIPUS treatment. The expression of Wnt2b in RAW264.7 cells was downregulated by siRNA. The macrophage surface markers and downstream inflammatory cytokines were detected using flow cytometry. The relative expression of proteins in the Wnt2b/AXIN/β-catenin pathway was assessed using reverse transcription real-time polymerase chain reaction (RT-qPCR) and Western blot. Results LIPUS reversed the M1 polarization of RAW264.7 cells, with decreased expression of CD80 and CD86. In addition, LIPUS enhanced the M2 polarization of RAW264.7 cells, with upregulated expression of CD163 and CD206. The polyA mRNA sequencing results indicated that the Wnt signaling pathway participated in the M1 polarization of LIPUS-treated RAW264.7. The results of the RT-qPCR showed a higher expression of Wnt2b in LIPUS-treated and M1- or M2-polarized RAW264.7 cells. Knocking down Wnt2b was shown to reverse the inhibitory effect of LIPUS on M1 polarization and increase the expression of CD80 and CD86. Wnt2b knockdown also regulated downstream AXIN, β-catenin, and inflammatory factors such as tumor necrosis factor alpha (TNFα) and interleukin-6 (IL6). Conclusions LIPUS plays an anti-inflammatory role by inhibiting LPS-induced M1 polarization of RAW264.7 cells in a Wnt2b/AXIN/β-catenin-dependent way. LIPUS may play a therapeutic role in periodontal diseases by inhibiting inflammation through the regulation of macrophage differentiation.
Yin et al. (2024) Anti-inflammatory role of low-intensity pulsed ultrasound in inhibiting lipopolysaccharide-induced M1 polarization of RAW264.7 cells via Wnt2b/AXIN/β-catenin. PeerJ 12:e18448 https://doi.org/10.7717/peerj.18448
The CLEC3B inhibits cellular proliferation and metastasis of cholangiocarcinoma through Wnt/β-catenin pathway
Purpose Cholangiocarcinoma (CCA) is a cancer of the biliary system, including intrahepatic and extrahepatic cholangiocarcinoma, and is highly aggressive. C-type lectins family member 3b (CLEC3B) is a Ca2+ binding transmembrane protein with different biological functions in a variety of cancers. The objective of this study was to explore the biological function of CLEC3B in CCA. Methods The CLEC3B gene was identified using the TCGA database and survival analysis of the cholangiocarcinoma clinical cohort. The expression CLEC3B cholangiocarcinoma and correlation with prognosis was investigated in our patient cohort. The effects of CLEC3B on proliferation, apoptosis, migration and invasion were verified in QBC939 and HUCCT1 cells. The effect of CLEC3B on the tumor formation was proved by xenograft tumor model in nude mice. The signaling pathway of CLEC3B in regulating CCA progression was further analyzed RNA sequencing and western blot. Results CLEC3B was decreased in the cholangiocarcinoma in the database. The mRNA and protein expression level of CLEC3B were significantly lower and correlated with poor overall survival in cholangiocarcinoma of our patient cohort. In vitro experiments proved that overexpression of CLEC3B can inhibit proliferation, migration and invasion in bile duct cancer cells. The CLEC3B was correlated with epithelial–mesenchymal transition and apoptosis. The calcium could promote the biological function of CLEC3B. The vivo study indicated that CLEC3B inhibited tumor formation. RNA sequencing indicating CLEC3B may transduce signal through e Wnt/β-catenin signaling pathway. Conclusions The CLEC3B inhibits cellular proliferation and migration of cholangiocarcinoma through the Wnt/β-catenin pathway.
Wu et al. (2024) The CLEC3B inhibits cellular proliferation and metastasis of cholangiocarcinoma through Wnt/β-catenin pathway. PeerJ 12:e18497 https://doi.org/10.7717/peerj.18497
Myoferlin alleviates pressure overload-induced cardiac hypertrophy and dysfunction by inhibiting NLRP3-mediated pyroptosis
Myoferlin (MYOF) is a muscle-derived secretory protein. Recent studies have found that MYOF protects against cell damage. However, the role of MYOF in cardiac hypertrophy remains unclear. Increasing evidence suggests that NLRP3 (NOD-like receptor protein 3) and the pyroptosis cascade play critical roles in the development of cardiac hypertrophy and inflammation. To investigate the role of MYOF in cardiac hypertrophy, we conducted a transverse aortic constriction (TAC) experiment in a mouse model. We found that MYOF can improve cardiac hypertrophy and cardiac function. Furthermore, our study confirmed a connection between cardiac hypertrophy and myocardial pyroptosis. Cardiac hypertrophy significantly increased the proportion of apoptotic cells and upregulated apoptosis-associated speck-like protein containing a CARD (ASC), caspase-1, and gasdermin D (GSDMD). This suggests that pharmacological or genetic inhibition of NLRP3 can effectively reduce cardiac hypertrophy. An abnormal increase in NLRP3 can reverse the cardioprotective effects of MYOF. Our findings indicate that MYOF is a potential therapeutic agent for cardiac hypertrophy.
Zhou et al. (2024) Myoferlin alleviates pressure overload-induced cardiac hypertrophy and dysfunction by inhibiting NLRP3-mediated pyroptosis. PeerJ 12:e18499 https://doi.org/10.7717/peerj.18499
Comparing the effectiveness of five traditional Chinese exercises in improving balance function in older adults: a systematic review and Bayesian network meta-analysis
Background Despite numerous studies affirming the potential of traditional Chinese exercises (TCEs) in enhancing balance in older adults, systematic integration is lacking. This study evaluated the effectiveness of five TCEs—Baduanjin, Liuzijue, Tai Chi, Wuqinxi, and Yijinjing—in improving balance among older adults using network meta-analysis. Methods This meta-analysis was registered in PROSPERO with the registration number CRD42023481450. Related articles indexed by Web of Science, Cochrane, PubMed, Embase, China National Knowledge Infrastructure (CNKI), Wanfang, and VIP databases before October 2023 were searched. Randomized controlled trials (RCTs) involving TCEs interventions to improve balance function conducted in older adults who aged ≥60 years were included. Two researchers used Review Manager to assess the quality of the studies, and analyzed the data using Stata and R. Results In total, 46 RCTs and 3,333 older adults were included. The aforementioned TCEs had positive effects on improving balance in older adults. Tai Chi revealed significant intervention effects in performing the Single-Leg Stand with eyes Closed (SLSC), 6-Min Walk Test (6MWT), and Short Form 36-Item Physical Component Summary (SF-36PCS). Liuzijue significantly improved performance in the Timed Up and Go Test (TUGT), 6MWT, SF-36PCS, and Berg Balance Scale (BBS). Baduanjin, Wuqinxi, and Yijinjing showed noteworthy intervention effects on the BBS. Tai Chi ranked highest in the SLSC, 6MWT, and SF-36PCS in the surface under the cumulative ranking, while Liuzijue and Yijinjing ranked highest in the TUGT and BBS, respectively. Conclusion Tai Chi, Liuzijue, and Yijinjing improved the static, dynamic, and overall balance outcomes, respectively. Older adults can make a reasonable choice among these TCEs based on their needs.
Xie et al. (2024) Comparing the effectiveness of five traditional Chinese exercises in improving balance function in older adults: a systematic review and Bayesian network meta-analysis. PeerJ 12:e18512 https://doi.org/10.7717/peerj.18512
Assessment of patient knowledge and perceptions towards orthodontic treatment in the Aljouf Region, Saudi Arabia: a cross-sectional study
Background In orthodontic treatment, it is most important to assess the patient’s perspective of malocclusion because these perceptions are fundamental to determining the patient’s demands and level of treatment satisfaction. This study was done to assess the knowledge and perception of residents of the Aljouf Region of Saudi Arabia seeking orthodontic treatment. Furthermore, we determined the factors associated with the patients’ knowledge and perception of orthodontic treatment. Methods This cross-sectional study was conducted using a pre-tested and validated questionnaire among patients seeking orthodontic treatment who were registered at King Abdulaziz Hospital, Sakaka, and primary health centers. We identified the associated factors using binomial logistic regression analysis. Finally, we applied Spearman’s correlation test to identify the correlation between knowledge and perception. Results A total of 282 individuals participated in the current study, of which 53.3% were female and 46.1% were male. About one-third (36.9%) of patients had a low level of knowledge, 35.5% had a medium level of knowledge, and 27.7% had a high level of knowledge regarding orthodontic treatment. A total of 20.6% had low perceptions, 42.9% had medium perceptions, and 36.5% had high perceptions of orthodontic care. A significant correlation was found between age and gender, knowledge (p = 0.001), and perception (p = 0.040). Moreover, we observed a positive correlation between knowledge and perception (Spearman’s rho = 0.297, p = 0.001). Conclusion People in Aljouf have poor knowledge and medium perception regarding orthodontic treatment. We recommend that the concerned authorities make a health educational plan for the patients seeking orthodontic treatment.
Alqahtani et al. (2024) Assessment of patient knowledge and perceptions towards orthodontic treatment in the Aljouf Region, Saudi Arabia: a cross-sectional study. PeerJ 12:e18516 https://doi.org/10.7717/peerj.18516
Calibrations without raw data—A response to “Seasonal calibration of the end-cretaceous Chicxulub impact event”
A recent article by DePalma et al. reported that the season of the End-Cretaceous mass extinction was confined to spring/summer on the basis of stable isotope analyses and supplementary observations. An independent study that was concurrently under review reached a similar conclusion using osteohistology and stable isotope analyses. We identified anomalies surrounding the stable isotope analyses reported by DePalma et al. Primary data are not provided, the laboratory where the analyses were performed is not identified, and the methods are insufficiently specified to enable accurate replication. Furthermore, isotopic graphs for carbon and oxygen contain irregularities such as missing data points, duplicate data points, and identical-length error bars for both elements despite different scales, that appear inconsistent with laboratory instrument outputs. A close examination of such methodological omissions and data irregularities can help to raise the standards for future studies of seasonality and prevent inaccurate claims or confirmation bias.
During et al. (2024) Calibrations without raw data—A response to “Seasonal calibration of the end-cretaceous Chicxulub impact event”. PeerJ 12:e18519 https://doi.org/10.7717/peerj.18519
Investigation of the efficacy of siRNA-mediated KRAS gene silencing in pancreatic cancer therapy
Aim Pancreatic carcinoma is an aggressive cancer that progresses without many symptoms. The difficulty of early diagnosis and an inadequate response to traditional treatments also cause the survival rate of pancreatic cancer to be low. Current research is focusing on methods of diagnosis and treatment, such as gene therapy, to increase survival rates. Small interfering ribonucleic acid (siRNA) has emerged as a promising advanced therapeutic strategy for cancer treatment. This study sought to silence the KRAS gene in the human pancreatic carcinoma cell line using a complex of small interfering ribonucleic acid (siRNA) and gold nanoparticles (AuNP). Methods In this study, 25 nM siRNA and gold nanoparticles at 0.5 mg/ml, 0.25 mg/ml, and 0.125 mg/ml concentrations were used to silence the KRAS gene in the CAPAN-1 cell line. Real-time PCR analysis, agarose gel electrophoresis, and double staining were carried out, and xCelligence real-time cell analysis (RTCA) was used to measure proliferation. Results The PCR analysis revealed crossing point (CP) values of actin beta (ACTB) ranging from 33.04 to 35.98, which was in the expected range for all samples. The interaction between the gold nanoparticle/siRNA complex in the double staining analysis revealed that the most effective concentration of gold nanoparticle was 0.125 mg/ml. The WST-1 technique showed that siRNA/AuPEI cells in application groups had a viability rate of over 90%, indicating no toxicity or side effects. The xCELLigence RTCA® showed that at hour 72, there was a significant difference in proliferation in the 0.5 mg/mL PEI/AuNP-siRNA, 0.25 mg/mL PEI/AuNP-siRNA, and 0.125 mg/mL PEI/AuNP-siRNA application groups compared to the control and siRNA groups (p < 0.05). By hour 96, all three groups were statistically different from the control and siRNA groups in terms of proliferation (p < 0.05). Conclusions The results of this analysis suggest that the AuPEI/siRNA complex can be effectively used to silence the target gene, but more studies are needed to verify these results.
Küçükekmekci et al. (2024) Investigation of the efficacy of siRNA-mediated KRAS gene silencing in pancreatic cancer therapy. PeerJ 12:e18214 https://doi.org/10.7717/peerj.18214
Coral recruits demonstrate thermal resilience
Marine heatwaves are becoming more frequent during summer and pose a significant threat to coral reef ecosystems. Restoration efforts have the potential to support native coral populations and guard them against some degree of environmental change, while global action against climate change takes place. Interspecific hybridization is one approach through which resilient coral stock could be generated for restoration. Here we compared the performance of Acropora kenti and A. loripes hybrid and purebred coral recruits under a simulated thermal stress event. A. kenti eggs were successfully fertilized by A. loripes sperm to produce ‘KL’ hybrids, but no ‘LK’ hybrids could be produced from A. loripes eggs and A. kenti sperm. Despite corals in the elevated treatment accruing thermal stress (>12 degree heating weeks over 2 months) known to result in mass bleaching, both purebred and hybrid recruits showed no signs of stress under the simulated temperature regime, based on the performance indicators survivorship, size, color (a proxy of bleaching), and photochemical efficiency of photosystem II. Comparisons between the hybrids and purebreds studied here must be interpreted with caution because hybrid sample sizes were small. The hybrids did not outperform both of their purebred counterparts for any metrics studied here, demonstrating that there are limitations to the extent to which interspecific hybridization may boost the performance of coral stock. In general, the purebred A. loripes recruits performed best under both ambient and elevated conditions. The performance of the KL hybrid corals was similar to the maternal parental species, A. kenti, or not significantly different to either parental purebred species. The Symbiodiniaceae communities of the KL hybrids were characteristic of their maternal counterparts and may have underpinned the performance differences between the A. kenti/KL hybrid and A. loripes recruits.
Lamb et al. (2024) Coral recruits demonstrate thermal resilience. PeerJ 12:e18273 https://doi.org/10.7717/peerj.18273
Developing a quality indicator system for evaluating internet plus home care nursing services based on the SERVQUAL model: a Delphi-analytic hierarchy process study
Background In the context of global population aging and the rapid development of information technology, the demand for Internet Plus Home Care Nursing (Internet+ HCN) services have been on the rise, especially in China. Internet+ HCN services have the potential to maximize existing human resources to counter the shortage of medical healthcare services. However, at present, Internet+ HCN services are difficult to scale due to the lack of standardized service quality governance. Quality indicators for service evaluation of Internet+ HCN services are under-defined. Objective To develop a quality indicator system for evaluating Internet+ HCN services, and to shed theoretical light on assessing mHealth service quality from a user experience perspective. Methods An initial quality indicator system was established based on scenarios related to Internet+ HCN services. The Delphi Method was applied to modify the indicators according to experts’ opinions, and the analytic hierarchy process (AHP) was applied to calculate the indicator weight. Finally, a quality indicator system for evaluating Internet+ HCN services was developed based on the SERVQUAL model. Results Altogether, 17 experts from relevant fields such as nursing education, clinical nursing, health management, and health informatics were consulted through email surveys. The response rates in both rounds of Delphi and the AHP were 100%. The average expert authority coefficients were 0.912 and 0.925 respectively in the two rounds of Delphi. Kendall’s W, indicating variation coefficients, ranged from 0.262 to 0.265. Finally, a quality indicator system for evaluating Internet+ HCN services, comprising five primary indicators and 15 secondary indicators, was developed. Primary indicators and their AHP generated the following weights: assurance (0.245), reliability (0.240), tangibles (0.192), responsiveness (0.190), and empathy (0.132). Conclusions By measuring the services quality gap between user expectations and perceptions, the proposed SERVQUAL model-based quality indicator system shows potential in improving the quality of Internet+ HCN services through the perspective of user experiences.
Ye et al. (2024) Developing a quality indicator system for evaluating internet plus home care nursing services based on the SERVQUAL model: a Delphi-analytic hierarchy process study. PeerJ 12:e18281 https://doi.org/10.7717/peerj.18281
Feasibility of continuous physical activity monitoring: first-month recovery markers following joint replacement surgery
Background The role of physical activity (PA) monitoring during the recovery after orthopaedic surgeries is unclear. This study aimed to explore early changes in the pattern and level of PA following orthopedic surgeries. Methods This observational feasibility study included 11 hip replacement patients (four females) with a mean age of 66 years and five knee replacement patients (four females) with a mean age of 65 years. A PA tracker was used to collect the patients’ daily PA data, including duration of various activity categories, steps taken, and activity intensity count. The PA tracker recorded data from two weeks prior to surgery until four weeks after the surgery. Ratios of PA parameters for each of the first four weeks following surgery were calculated in relation to preoperative measurements. Results Compared to preoperative measurements, during the first four weeks after the surgery, the time spent in a recumbent position decreased from 112% to 106%, while continuous walking time and activity intensity count increased from 27% to 77% and from 35% to 73%, respectively. Step counts increased from 18% to 67%, and sit-to-stands rose from 65% to 93%. No significant changes were found in sitting, standing, sporadic walk time, and sporadic steps. Conclusion Continuously measuring PA using wearable sensors was feasible in orthopedic patients during the perioperative period. Continuous step count, walking time, activity intensity count showed noticeable changes and stable patterns demonstrating their potential for remote monitoring of patients during the early postoperative period.
Ghaffari et al. (2024) Feasibility of continuous physical activity monitoring: first-month recovery markers following joint replacement surgery. PeerJ 12:e18285 https://doi.org/10.7717/peerj.18285
The influence of parenting styles and coping strategies on anxiety symptoms in adolescents: a comparative study of groups with and without non-suicidal self-injury behavior
Background During the COVID-19 pandemic, the global incidence of non-suicidal self-injury (NSSI) has been increasing year by year, especially among adolescents, and it is highly correlated with the level of anxiety among teenagers, particularly within Chinese cultural contexts where parenting styles significantly influence adolescent behavior. Objective This study examines the role of culturally-influenced parenting styles and adolescent coping strategies in relation to anxiety and NSSI behavior, aiming to clarify these multivariate interactions for better understanding and intervention. Methods A cross-sectional survey was conducted with NSSI-diagnosed adolescents from Affiliated Kangning Hospital, Ningbo, China, and healthy adolescents from urban schools. Data on background, parenting styles, coping strategies, and anxiety levels were analyzed using chi-square tests, independent sample t-tests, MANOVA, and regression analysis. Results Adolescents with NSSI reported higher anxiety levels, more punishment and interference, and less emotional warmth from their fathers compared to the non-NSSI group (p < 0.001). The NSSI group also relied more on emotion-oriented coping strategies, while the non-NSSI group favored problem-oriented approaches (p < 0.001). Multivariate analyses confirmed significant effects of NSSI behavior, parenting styles, and coping strategies on anxiety levels. Conclusion This study found that the anxiety levels of NSSI adolescents were significantly higher than those of non-NSSI adolescents in China, which was closely related to less emotional warmth from parents, more punishment and interference, and emotion-focused coping strategies. The results demonstrate that family environment and coping strategies play a critical role in NSSI behavior and anxiety levels, highlighting the importance of emphasizing emotional support and positive coping strategies in the prevention and intervention of NSSI behavior.
Liu et al. (2024) The influence of parenting styles and coping strategies on anxiety symptoms in adolescents: a comparative study of groups with and without non-suicidal self-injury behavior. PeerJ 12:e18378 https://doi.org/10.7717/peerj.18378
The associations between well-being and Cloninger’s personality dimensions in a Korean community sample
Background Well-being is a multidimensional construct comprising affective and non-affective components. Previous research has consistently linked personality traits to well-being, yet cultural variations in this association remain underexplored, particularly in collectivistic cultures such as Korea. Therefore, this study aims to identify universal and culture-specific characteristics of personality in relation to well-being. Methods A sample of 527 Korean university students participated, providing data through the Korean version of the Temperament and Character Inventory-RS (TCI-RS), self-rated health (SRH), social support (SS), Satisfaction With Life Scale (SWLS), and positive and negative affect schedule (PANAS). Pearson correlation analysis and ANCOVA, with sex and age as covariates, were employed to examine linear associations. Multidimensional personality profiles were utilized to investigate non-linear associations among character dimensions on different aspects of well-being. All analysis was performed using jamovi 2.3.12. Results Self-directedness and cooperativeness exhibited positive linear associations with both affective (positive and negative affect) and non-affective (SRH, SS, SWLS) components of well-being. Self-directedness emerged as a key predictor across various well-being aspects. Cooperativeness was strongly associated with perception of social support. Self-transcendence showed positive associations with both positive and negative affect, considering interactions with other character dimensions. Discussion While self-directedness played a pivotal role universally, the impact of cooperativeness and self-transcendence appeared to be influenced by cultural factors, enhancing perception of social support and affecting both positive and negative affect in a collectivistic culture. This study illustrates the importance of considering cultural nuances in the relationship between personality and well-being. Future research should delve deeper into cultural differences, emphasizing the need for subtle interpretations of specific personality traits within diverse cultural contexts.
Lee et al. (2024) The associations between well-being and Cloninger’s personality dimensions in a Korean community sample. PeerJ 12:e18379 https://doi.org/10.7717/peerj.18379
Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data
Classifiers trained on high-dimensional data, such as genetic datasets, often encounter situations where the number of features exceeds the number of objects. In these cases, classifiers typically rely on a small subset of features. For a robust algorithm, this subset should remain relatively stable with minor changes in the training data, such as the replacement of a few samples. While the stability of feature selection is a common focus in studies of feature selection algorithms, it is less emphasized in classifier evaluation, where only metrics such as accuracy are commonly used. We investigate the importance of feature selection stability through an empirical study of four classifiers (logistic regression, support vector machine, convex and piecewise Linear, and Random Forest) on seven high dimensional, publicly available, gene datasets. We measure the stability of feature selection using Lustgarten, Nogueira and Jaccard Index measures. We employed our own cross-validation procedure that guarantees a difference of exactly p objects between any two training sets which allows us to control the level of disturbance in the data. Our results show the existence of a drop in feature selection stability when we increase disturbance in the data in all 28 experiment configurations (seven datasets and four classifiers). The relationship is not linear, but resembles more of a hyperbolic pattern. In the evaluation of the tested classifiers, logistic regression demonstrated the highest stability. It was followed in order by support vector machine, convex and piecewise linear, with Random Forest exhibiting the lowest stability among them. This work provides evidence that all tested classifiers are very sensitive to even small changes in learning data in terms of features used by the model, while showing almost no sensitivity in terms of accuracy. The data and codes to reproduce the results in the article are available publicly on GitHub: https://github.com/tlukaszuk/feature-selection-stability-in-classifier-evaluation.
Łukaszuk et al. (2024) Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data. PeerJ 12:e18405 https://doi.org/10.7717/peerj.18405
Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study
Background Pulpotomy is a widely recommended treatment for deep caries and reversible pulpitis in primary teeth. However, there is a significant lack of large-scale clinical studies evaluating the long-term efficacy of pulpotomy in primary molars, especially in studies with follow-up periods extending beyond a two years. Aim This study aimed to evaluate the long-term efficacy of mineral trioxide aggregate (MTA) and iRoot BP Plus for pulpotomy in primary molars performed under general anesthesia and to investigate factors influencing the success rate. Methods In this retrospective study, a total of 942 primary molars from 422 children who met the inclusion criteria underwent pulpotomy. Propensity score matching method (PSM) was used to match the MTA and iRoot BP Plus groups in a 1:1 ratio based on covariates. Efficacy was assessed using the Zurn & Seale criteria. Kaplan-Meier survival analysis and Cox proportional hazards model were performed to analyze the outcomes. Results PSM resulted in 266 pairs of matched teeth from 532 teeth of 291 children (mean age: 4.64 ± 1.07 years, ranging from 2 to 8 years). Long-term clinical and radiographic evaluations revealed higher success rates for iRoot BP Plus (24-month: 99.54%/97.25%; 36-month: 97.22%/95.83%) compared to MTA (24-month: 94.76%/95.29%; 36-month: 92.50%/91.25%). Survival analysis indicated a statistically significant difference between two groups (P = 0.0042). Age, gender, tooth position, and decayed tooth surface showed no significant impact on pulpotomy success, whereas the choice of pulp capping materials significantly influenced the outcome (HR [95% CI]=0.3745[0.1857-0.7552], P = 0.006). Conclusion Clinical and radiographic evaluations support the use of iRoot BP Plus for pulpotomy in primary molars.
Zhao et al. (2024) Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study. PeerJ 12:e18453 https://doi.org/10.7717/peerj.18453
Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age
Background SARS-CoV-2 infection during pregnancy and pandemic circumstances could negatively impact infant development. This study aimed to investigate the physical development, common pediatric illness incidence, and healthcare utilization over the first 2 years of life of infants born to COVID+ and COVID- patients. Comparisons were also made with infants born pre-pandemic. Methods This is a retrospective observational study at a major academic health system in New York City. Participants include all infants born to birthing persons with SARS-CoV-2 infection during pregnancy (N = 758) and without (N = 9,345) from 03/01/2020 to 08/17/2022, infants born pre-pandemic (N = 3,221) from 03/01/2017 to 08/17/2019, and birthing persons of all infants. Results There were no differences in weight, length, or head circumference curves between pandemic infants born to COVID+ and COVID- patients over the first 2 years of life (p > 0.05, repeated ANOVA). Annualized incidence of illness occurrence and healthcare utilization were similar between groups. Compared to pre-pandemic infants, the length of pandemic (COVID-) infants was lower from birth to 9 months (p < 0.0001). Pandemic infants additionally had more adverse perinatal outcomes including increased stillbirth (0.75% vs. 0.12%, p = 0.0001) and decreased gestational age (38.41 ± 2.71 vs. 38.68 ± 2.55 weeks, Cohen’s d = −0.10, p < 0.0001), birthweight (2,597 ± 335 vs. 3,142 ± 643 g, Cohen’s d = −1.06, p < 0.0001), and birth length (48.08 ± 4.61 vs. 49.09 ± 3.93 cm, Cohen’s d = −0.24, p < 0.0001). Conclusions Birthing persons’ SARS-CoV-2 infection status, birthing persons’ profiles, and pandemic circumstances negatively affected perinatal outcomes, newborn physical development, and healthcare utilization. These findings draw clinical attention to the need to follow infants closely and implement enrichment to ensure optimal developmental outcomes.
Eligulashvili et al. (2024) Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age. PeerJ 12:e18481 https://doi.org/10.7717/peerj.18481
Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.)
Aging induces many deteriorative changes to seeds during storage like protein degradation, enzyme inactivation and loss of membrane integrity. In this study, we investigate the impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of maize. Three genotypes African Tall, MAH 14-5 and a local landrace were selected and artificially aged for 96 and 120 h. The aging process led to a decrease in germination, vigour, and total dehydrogenase in seeds, while the electrical conductivity of seed leachates increased, indicating a decline in seed quality. Additionally, there was a variation in the microsculpture pattern of seed coats between genotypes. There was an accumulation of damage on the seed coat surface as the seeds aged and higher damage occurred in African Tall followed by MAH 14-5 and local landrace. Higher catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity were reported in the seed coat of Local landrace and MAH 14-5 that resisted aging and deterioration while, lower catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity was reported in African Tall seed coat that deteriorated during aging. Decrease antioxidant activity in aged seeds might be a possible cause of seed deterioration due to the accumulation of free radicals. Thus, these results clearly show the influence of seed coat structure and antioxidant activity on seed quality during aging.
Satya Srii et al. (2024) Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.). PeerJ 12:e17988 https://doi.org/10.7717/peerj.17988
Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study
Introduction This research explores the intricate relationships between mental health indicators (depression, stress, and anxiety) and various dimensions of quality of life among first-year law students. The study aims to understand how affective valence, mood states, physical activity, body image perception, and social relations influence mental health outcomes. Methods Data were collected from 75 first-year law students (46 females, 29 males), a group predominantly composed of young adults with limited financial means, living in various housing situations, primarily within urban environments, and generally reporting low levels of physical activity. Standardized questionnaires were used to assess mental health and quality of life, including the Depression, Anxiety, and Stress Scale-21 Items (DASS-21), Feeling Scale (FS), Exercise-Induced Feeling Inventory (EIFI), Modified Baecke Physical Activity Questionnaire (MBPAQ), World Health Organization Quality of Life-BREF (WHOQOL-BREF), and Contour Drawing Rating Scale (CDRS). Descriptive statistics, Pearson correlation, and regression analysis were employed to analyze the data. Results The analysis revealed significant correlations between depression (mean = 5.97, SD = 4.21), stress (mean = 7.81, SD = 4.80), and anxiety (mean = 6.17, SD = 4.58) with affective valence (p < 0.05), mood states (p < 0.05), physical activity (p < 0.05), body image perception (p < 0.05), and social relations quality (p < 0.05). Additionally, mood states (mean = 20.73, SD = 10.60), physical activity (mean = 8.43, SD = 1.35), body image perception (mean = 4.21, SD = 1.91), and social relations quality (mean = 12.46, SD = 2.33) were identified as significant predictors of mental health outcomes (p < 0.05). Conclusions These findings underscore the complex interplay between mental health indicators and various dimensions of quality of life, emphasizing the necessity for a comprehensive approach to mental health care. By identifying these predictors, we have gained a clearer understanding of the factors that impact mental health in this specific population. The insights gained highlight the value of interventions aimed at improving mood, increasing physical activity, enhancing body image, and strengthening social connections. These targeted strategies could effectively address mental health issues and promote well-being among law students. Future research should further investigate these relationships and develop tailored interventions to better support students’ mental health. This study contributes to understanding the complex interplay between mental health and quality of life, offering a foundation for both practical interventions and future research.
Muntean et al. (2024) Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study. PeerJ 12:e18245 https://doi.org/10.7717/peerj.18245
Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation
Plant somatic embryogenesis encompasses somatic cells switch into embryogenic cells that can later produce somatic embryos with the ability to produce plantlets. Previously, we defined in vitro culture settings for the somatic embryogenesis process of Coffea canephora that comprise adequate plantlets with auxin plus cytokinin followed by cut-leaf explant cultivation with cytokinin, producing embryos with the ability to regenerate plantlets. Here, we confirmed that cultivating cut-leaf explants with cytokinin is sufficient to promote somatic embryos proliferation and the high yield of somatic embryos in the protocol requires adequate plantlets with auxin plus cytokinin. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels reveal auxin-plus cytokinin-dependent regulated proteins in plantlets with up and down abundance. Chitinase A class III, proteins involved in the metabolism and folding of proteins, photosynthesis, antioxidant activity, and chromatin organization were identified. The RPN12 protein, which is a subunit of the proteasome 26S, has an abundance that is not associated with transcript changes, suggesting post-translational regulation.
Carrillo-Bermejo et al. (2024) Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation. PeerJ 12:e18372 https://doi.org/10.7717/peerj.18372
Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis
Background Oxidative stress caused by exposure to ultraviolet (UV) light on the skin can damage deoxyribonucleic acid (DNA) and cause keratinocytes to undergo apoptosis. Endogenous antioxidants which play a role in trapping free radicals are also unable to overcome excess reactive oxygen species (ROS) in the body due to UV exposure, so exogenous antioxidants are needed. Polyphenolic compounds extracted from natural ingredients such as flavonoids, quercetin, and epicatechin have quite strong antioxidant activity. This is influenced by the chemical structure of these compounds which are rich in hydroxyl groups and aromatic groups. This structure allows the compound to become an electron donor so that it can neutralize free radicals. In vitro research was used to see the potential effectiveness of epicatechin as an antiaging and antioxidant. The study aims to confirm the potential of epicatechin as an antiaging by in vitro assay. Methods The viability test of epicatechin on human skin fibroblast (BJ) cells was carried out using the water-soluble tetrazolium (WST) assay. BJ cells were UV-induced as a cell model of premature aging. Epicatechin 6.25, 12.5, and 25 µg/mL were administered to UV-induced BJ cells. The gene expression of Collagen I Alpha 1 (COL1A1), matrix metalloproteinase-1 (MMP-1), fibroblast growth factor-2 (FGF-2), and glutathione peroxidase-1 (GPX-1) were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Elastin (ELN), hyaluronidase (HAase), cyclooxigenase-2 (COX-2), 8-hydroxydeoxyguanosine (8-OhdG), and melatonin (MT) protein levels were analyzed by enzyme-linked immunosorbent assay (ELISA). The apoptosis of BJ cells was analyzed using flow cytometry. Results Treatment with epicatechin increased relative gene expression including COL1A1 (5.94), FGF-2 (8.34), and GPX-1 (8.09), and also decreased MMP-1 (2.90) relative gene expression compared to the UV-induced BJ cells. Epicatechin also increased levels of ELN (107.7 ng/mg protein) and MT (830 ng/mg protein) levels compared to the UV-induced BJ cells. Epicatechin treatment decreased levels of HAase (505.96 ng/mg protein), COX-2 (33.69 ng/mg protein), and 8-OHdG (97.87 ng/mg protein) compared to the UV-induced BJ cells. Epicatechin also succeeded in maintaining the percentage of live cells and reducing apoptosis, necrotic of UV-induced skin fibroblast cells. Conclusions Epicatechin has the potential to be an antiaging agent by in vitro assay.
Widowati et al. (2024) Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis. PeerJ 12:e18382 https://doi.org/10.7717/peerj.18382
Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study
Background Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022. Methods In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI. Results A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%–6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23–22.9], p < 0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7–29.6], p < 0.001). Conclusions We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.
Vollmer et al. (2024) Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study. PeerJ 12:e18384 https://doi.org/10.7717/peerj.18384
Examination of optical coherence tomography findings in patients with pregabalin use disorder
Background Pregabalin abuse is a rapidly growing health problem worldwide, and little is known about the effects of prolonged high-dose use in patients with pregabalin use disorder. Objective In this study, the effects of pregabalin abuse on retinal layers were investigated in patients with pregabalin use disorder (PGUD). Methods This study included 35 controls and 34 patients with PGUD, according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria. Optic coherence tomography (OCT) measurements including the retinal nerve fiber layer (RNFL), ganglion cell layer-inner plexiform layer (GCL-IPL) and ganglion cell complex (GCC) were performed. RNFL thickness was evaluated in four quadrants (inferior, superior, nasal, temporal). GCL-IPL and GCC thickness were evaluated in six sectors (superior, superonasal, inferonasal, inferior, inferotemporal, superotemporal). Results GCC inferonasal (p = 0.040, r = 0.354), GCC inferior (p = 0.018, r = 0.402) GCL-IPL inferior (p = 0.031, r = 0.370) and GCL-IPL inferotemporal (p = 0.029, r = 0.376) thickness were positively correlated with the duration of pregabalin use. There was no significant sector or quadrant-wise difference between groups (p > 0.05). Conclusion Our findings emphasized the drug’s potential neuroprotective effect. It should be taken into consideration that neurodegenerative changes due to substance use disorder occur with long-term. Longitudinal prospective studies investigating dose-duration relationship are needed.
Kılıç et al. (2024) Examination of optical coherence tomography findings in patients with pregabalin use disorder. PeerJ 12:e18395 https://doi.org/10.7717/peerj.18395
Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study
Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
Xiao et al. (2024) Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study. PeerJ 12:e18424 https://doi.org/10.7717/peerj.18424
CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1
Background Cancer-associated fibroblasts (CAFs) and hepatocellular carcinoma (HCC) cells interact to promote HCC progression, but the underlying mechanisms remain unclear. Serpin family E member 1 (SERPINE1) has conflicting roles in HCC, and microRNAs (miRNAs) are known to regulate tumor progression through intercellular communication. Therefore, we investigated the potential involvement of miRNA/SERPINE1 axis in crosstalk between CAFs and HCC cells. Methods In this study, candidate miRNAs targeting SERPINE1 3′ UTR were predicted using multiple miRNA databases. The miRNAs and SERPINE1 mRNA expression in Huh7 cells was assessed after co-culture with CAFs using RT-qPCR. Huh7 cell proliferation and invasion were detected after SERPINE1 siRNA. The functions of the CAF-derived miR-642a-3p/SERPINE1 axis in HCC cells were examined using CCK-8, wound healing, transwell assays, western blot, and dual-luciferase reporter assays. Moreover, a orthotopic xenograft model was used to investigate the contribution of miR-642a-3p knockdown in HCC. Results SERPINE1 mRNA expression decreased, while miR-642a-3p expression increased in Huh7 cells co-cultured with CAFs. SERPINE1 knockdown enhanced Huh7 cell proliferation and invasion as well as miR-642a-3p expression. miR-642a-3p overexpression promoted migration, invasion, and epithelial-mesenchymal transition (EMT) in Huh7 cells by targeting SERPINE1, while miR-642a-3p knockdown yielded the opposite effect. Rescue experiments confirmed that SERPINE1 knockdown attenuated the inhibitory effects of miR-642a-3p knockdown on migration, invasion, and EMT in Huh7 cells. Importantly, miR-642a-3p knockdown suppressed growth and EMT in orthotopic liver tumors. Conclusion CAF-derived miR-642a-3p/SERPINE1 axis facilitated migration, invasion, and EMT in the HCC cells, suggesting miR-642a-3p/SERPINE1 axis can be a potential therapeutic target for HCC.
Zhang et al. (2024) CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1. PeerJ 12:e18428 https://doi.org/10.7717/peerj.18428
Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores
The mammalian adult dentition is a non-renewable resource. Tooth attrition and disease must be accommodated by individuals using behavioral, physiological, and/or musculoskeletal shifts to minimize impact on masticatory performance. From a biomechanical perspective, the musculoskeletal system becomes less efficient at producing bite force for a given amount of muscle input force over an individual’s life, because tooth-food contact area increases as cusps wear. In this study we ask the question: does mandibular biomechanical performance show evidence of compensation with increasing tooth wear? We use representative taxa of three carnivoran ecomorphologies (meat specialist, scavenger, bone cracker) as a study system to compare morphofunctional data on tooth macrowear, jaw depth, bite mechanical efficiency, and jaw stress during biting. No significant shifts in adult mandibular corpus dimensions occurs in the sampled taxa as canine and carnassial teeth wear. In bone cracking spotted hyenas carnassial biting mechanical efficiency increases significantly with increasing tooth wear, with no significant change in mandibular stress. Analyses of the fossil carnivore Hyaenodon suggests an increase in canine biting efficiency with increased tooth wear, but this may reflect interspecific variation or phylogenetic contingency rather than a life history shift. Overall, these findings indicate that scavenging hyaenids and felid meat specialists do not exhibit morphofunctional compensation for the decreased mechanical capability of worn and dull teeth. Behavioral modifications, rather than musculoskeletal adjustments, may instead play a major role in maintaining food acquisition and processing capabilities for individuals surviving into advanced ontogenetic age and tooth wear. These observations highlight the mammalian masticatory system as having a dynamic performance profile through its useful lifespan, and encourage a more nuanced understanding of past and present carnivore guilds by considering wear-dependent performance changes as a possible source of selection.
Tseng et al. (2024) Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores. PeerJ 12:e18435 https://doi.org/10.7717/peerj.18435
Cryophysiology of coral microfragments: effects of chilling and cryoprotectant toxicity
Coral reefs are being degraded at alarming rates and decisive intervention actions are urgently needed. One such intervention is coral cryopreservation. Although the cryopreservation of coral sperm and larvae has been achieved, preservation of coral fragments including both its tissue and skeleton, has not. The overarching aim of this study was to understand and assess the physiological stressors that might underlie coral fragment cryopreservation, understand the long-term consequences of these exposures to continued growth, and develop a health metrics scale for future research. Therefore, we assessed small fragments (~1 cm2) from the Hawaiian coral, Porites compressa, examining: (1) chill sensitivity; (2) chemical sensitivity to complex cryoprotectants; (3) methods to safely remove algal symbionts of coral for cryopreservation; (4) continued growth over time of coral fragments exposed to chilling and cryoprotectants; and (5) assessment of health and viability of coral fragments post the applied treatments. Corals were able to withstand chilling to 0 °C for 1 min and after 2 weeks were not significantly different from the live controls, whereas, corals exposed to complex cryoprotectants needed 3 weeks of recovery. Most importantly, it appears that once the coral fragments had surpassed this initial recovery, there was no difference in subsequent growth. Technological advances in cryo-technology promise to support successful coral fragment cryopreservation soon, and its success could help secure much of the genetic and biodiversity of reefs in the next decade.
Lager et al. (2024) Cryophysiology of coral microfragments: effects of chilling and cryoprotectant toxicity. PeerJ 12:e18447 https://doi.org/10.7717/peerj.18447
Digital competence of faculty members in health sciences measured via self-reflection: current status and contextual aspects
This descriptive study aims to determine the digital competence level of faculty members who teach in the health sciences, empirically considering possible contextual aspects. Two data collection instruments were used: a self-reflection questionnaire to assess digital competence, and a survey querying demographics and aspects of teaching and learning context. In total, 306 health sciences faculty members from six universities voluntarily participated the study. The results revealed that a majority of the faculty members have intermediate (integrator or expert) level of digital competence, which is described as being aware of the potential use of digital technology in teaching and having a personal repertoire for its use under various circumstances. Age, digital teaching experience, perception of work environment, and previous teaching experience in fully- or partially-online courses were identified as influencing factors for digital competence. Faculty members in health sciences were able to integrate digital technologies in their teaching practices. Health education institutions may facilitate the use of digital technologies in teaching and learning environments. Moreover, institutions or stakeholders should consider that digital competence requires practice and experience in meaningfully-designed digital environments and tools.
Ersoy et al. (2024) Digital competence of faculty members in health sciences measured via self-reflection: current status and contextual aspects. PeerJ 12:e18456 https://doi.org/10.7717/peerj.18456
Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly
Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics–particularly coding gene content and read recruitment profiles–were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses.
Smith et al. (2024) Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly. PeerJ 12:e18132 https://doi.org/10.7717/peerj.18132
Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus
A new species of Helicascus satunensis sp. nov. was collected on mature dead fruits of the Nypa palm in Satun Province, southern Thailand. Its morphological characteristics are similar to those of the genus Helicascus. Recently, a genus Helicascus with three species from marine habitats worldwide was studied. The morphology of this fungus was investigated and combined with multigene sequence analyzes of small subunit (SSU), large subunit (LSU), internal transcribed spacer (ITS) ribosomal DNA, translation elongation factor 1-alpha (TEF-1α) and RNA polymerase II (RPB2) genes. Morphologically, H. satunensis sp. nov. is characterized by semi-immersed, lenticular ascomata, multilocules, a bitunicate ascus and smooth, obovoid, dark brown ascospores that are one-septate and unequally two-celled. In addition, 3D visualization using synchrotron X-ray tomography was performed to investigate the interaction between fruiting body and substrata. Molecular phylogeny with multigene revealed that H. satunensis sp. nov. belongs to the family Morosphaeriaceae, order Pleosporales, class Dothideomycetes. Furthermore, H. satunensis sp. nov. forms a well-supported clade with Helicascus species described from marine habitats. Based on the unique morphological and molecular evidence, we propose this fungus, H. satunensis sp. nov., as a new species for Helicascus.
Preedanon et al. (2024) Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus. PeerJ 12:e18341 https://doi.org/10.7717/peerj.18341
YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines
Background The Internet has transformed global information access, particularly through platforms like YouTube, which launched in 1995 and has since become the second largest search engine worldwide with over two billion monthly users. While YouTube offers extensive educational content, including health topics like cardiopulmonary resuscitation (CPR) and basic life support (BLS), it also poses risks due to potential misinformation. Our study focuses on evaluating the accuracy of CPR and BLS videos on YouTube according to the latest 2020 American Heart Association (AHA) guidelines. This research aims to highlight inconsistencies and provide insights into improving YouTube as a reliable educational resource for both lay rescuers and healthcare professionals. Methods In this cross-sectional observational study, English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were searched using keywords related to CPR and basic life support. Videos were assessed for their source, duration, views, use of human or mannequin models, and mean assessment scores by two emergency medicine physicians. A third physician’s opinion was sought in cases of disagreement. The first assessment evaluated video validity based on specified information criteria, while the second assessed their ability to convey advanced medical information aligned with the 2020 AHA guidelines. Results In this study, 201 English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were evaluated based on search terms related to CPR and BLS, resulting in 95 videos meeting inclusion criteria after excluding 106 due to various reasons. Most included videos were from healthcare professionals (49.5%), followed by anonymous sources (29.5%) and official medical organizations (21.1%). Video durations ranged widely from 43 to 6,019 seconds, with an average of 692 seconds. Videos featuring mannequins predominated (91.6%), followed by those using human subjects (5.3%) or both (3.2%). Healthcare professional and official medical organization videos scoring significantly higher than those of unknown origin (p = 0.001). Video length did not correlate significantly with view counts, although shorter videos under 5 minutes tended to have higher average views. Discussion The results presented in this study demonstrated that English-language videos on YouTube related to BLS and CPR, throughout the study period, did not conform to the 2020 AHA guidelines in terms of providing basic information for lay rescuers. Furthermore, healthcare professionals cannot obtain advanced medical knowledge through these videos. We recommend a professional oversight mechanism in health-related videos that does not tolerate such misinformation.
Yazla et al. (2024) YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines. PeerJ 12:e18344 https://doi.org/10.7717/peerj.18344
Stable dominance of parasitic dinoflagellates in Antarctic sponges
Background Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies. Results The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges. Conclusions The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.
López-Rodríguez et al. (2024) Stable dominance of parasitic dinoflagellates in Antarctic sponges. PeerJ 12:e18365 https://doi.org/10.7717/peerj.18365
Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance
We investigated the convergent validity and intrasession reliability of force, velocity, and power (FVP) variables and the dynamic strength index (DSI) obtained from isometric midthigh pull (IMTP) and squat jump (SJ) testing. Fifteen male combat sports athletes (27 ± 5 years, 77 ± 9 kg, 1.76 ± 0.1 m, 14 ± 6% body fat) participated in a 2-days study. The first day involved testing familiarization, while the second was dedicated to IMTP and SJ testing. Maximal isometric force (Fiso) was obtained from IMTP, while mean force, mean velocity, jump height, and jump impulse (J) were gathered from SJ. To analyze the FVP, we calculated the linear relationship between force and velocity, which allowed us to obtain the slope of the relationship (SFV), the theoretical velocity at zero force (V0), and the theoretical maximal power (Pmax). DSI was obtained as a ratio from SJ peak force and Fiso. The convergent validity was investigated using Spearman’s ρ coefficients to assess the relationships between jump height and J with Fiso, V0, SFV, Pmax, and DSI. The intrasession reliability was assessed using intraclass correlation coefficients (ICC) and coefficient of variations (CV). All variables demonstrated acceptable reliability scores. ICC ranged from moderate to excellent, and the mean CV was <10%. We found a “very large” correlation between jump J and Pmax, while jump height was not correlated with any variable. In conclusion, the IMTP and SJ combination is a practical way to determine FVP producing capacities that can be reliably measured (intrasession). The Pmax, derived from FVP, was correlated with jump performance, which might evidence the convergent validity of the method.
Vieira et al. (2024) Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance. PeerJ 12:e18371 https://doi.org/10.7717/peerj.18371
Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis
Background Phragmites australis is a common foundation species found in inland and brackish estuarine ecosystems. P. australis stands provide a wide range of habitats for wetland organisms and perform essential functions, such as nutrient cycling, pollutant filtration, wave energy reduction, and soil stabilization. However, excessive growth of P. australis can degrade the quality of wetland habitats, thereby reducing the functions of restored wetlands. Methods In this study, we investigated the effectiveness of vegetation management techniques, such as aboveground cutting and temporal inundation with varying depth and periodicity, in controlling the growth performance of P. australis and adjacent vegetation, Bolboschoenus planiculmis. Differences in growth responses to manipulated inundation stress between P. australis and B. planiculmis were measured. Results Inundation stress of 10–50 cm caused significantly greater inhibition of growth performance in B. planiculmis compared to P. australis. The combination of aboveground-cutting and inundation treatments resulted in a significant inhibitory effect on the growth performance and survival rate of P. australis. The growth performance of P. australis, including stem volume and biomass, decreased and its mortality rate increased. Our manipulated experiment suggests a combined treatment approach of moderate inundation, such as 5–10 cm for 20–30 days, and aboveground cutting to manage the overgrowth of P. australis in restored brackish wetlands.
Park et al. (2024) Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis. PeerJ 12:e18402 https://doi.org/10.7717/peerj.18402
Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections
Background Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses. Methods In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology. Results A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively. Conclusion Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection.
Liu et al. (2024) Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections. PeerJ 12:e18471 https://doi.org/10.7717/peerj.18471
The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation
Background Breast cancer (BC) is one of most frequent female malignancies that poses multiple challenges in treatment and prevention. This study aimed to explore the role of miRNAs and their target genes during the BC progression. Methods Based on the BC data (113 normal and 1,118 tumor samples) from the TCGA-BRCA dataset, a single-sample gene set enrichment analysis (ssGSEA) was applied to calculate the cancer migration scores, and weighted gene co-expression network analysis (WGCNA) were performed using the WGCNA R package, with a focus on the set of genes associated with cancer migration. Key modules and hub genes related to cell migration and signaling pathways were identified. Survival analysis of hub genes was conducted using the survminer R package, and prediction of regulatory miRNAs were performed to analyze their impact on BC prognosis. In addition, the BC cell lines MCF-7 and MDA-MB-231 were used to further explore the effect of hsa-miR-1972 mimics on the gene expression and angiogenic factor regulation. Results The study classified important modules (MEblue, MEmagenta, MEpink, and MEfloralwhite) associated with cell migration and identified three hub genes, namely, MRPL20, COL4A1 and VWF. Survival analysis showed that certain hub genes with a low expression were related to a poor prognosis, whereas low-expressed COL4A1 and VWF were related to better survival outcomes. We also found that hsa-miR-1972 mimics significantly downregulated critical genes involved in BC metastasis and angiogenesis and effectively inhibited the proliferation of BC cell lines, showing a strong therapeutic potential. Manipulation of VWF expression in cells overexpressing hsa-miR-1972 had significant effects on the malignant markers and angiogenic factors, suggesting a novel therapeutic direction for BC treatment. Conclusion Our study highlighted the complex interplay of genetic factors in BC progression as well as the therapeutic potential of targeting specific miRNAs and their related hub genes. These findings provided novel insights into the pathogenesis of BC and suggested new direction for the therapeutic development for the cancer.
Yu et al. (2024) The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation. PeerJ 12:e18476 https://doi.org/10.7717/peerj.18476
Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022
Black carbon (BC) is a pollutant produced by the combustion of fossil fuels and biomass fuels, which has a huge impact on regional climate, atmospheric environment, and human health. In this study, based on MERRA-2 reanalysis data and ground-based observation data, the Mann-Kendall (MK) test and random forest (RF) model were used to explore the spatiotemporal variation characteristics of atmospheric BC concentration in Xinjiang, China and its correlation with meteorological and environmental covariates in 2010–2022. The results showed that the use of MERRA-2 reanalysis data to explore the spatiotemporal variation characteristics of BC concentration in Xinjiang had high reliability (relative average deviation (RAD) = 0.65). From 2010 to 2022, the annual average concentration of atmospheric BC in Xinjiang was 195.40 ± 15.55 ng/m3, and the multi-year average change rate was −0.05%. The winter season had the highest atmospheric BC concentration (145.52 ± 39.31 ng/m3), followed by autumn (124.95 ± 28.82 ng/m3), spring (74.05 ± 9.96 ng/m3), and summer (73.41 ± 5.69 ng/m3). The atmospheric BC concentration had a significant spatial variation, showing two high-BC-concentration areas on the northern slope of the Tianshan Mountains (centered on Urumqi-Changji-Shihezi region) and the urban agglomeration around the Tarim Basin (centered on Kashgar). The RF model analysis showed that meteorological factors including snow depth, surface temperature, and humidity as well as environmental factors including NO2, PM10, and SO2 were the main factors affecting the BC concentration. This work is of great significance for clarifying the accumulation and spatial distribution characteristics of atmospheric BC in northwest China and the factors influencing the atmospheric BC concentration, and helps to raise public attention to the increasingly serious climate change and public health problems caused by BC.
Xie et al. (2024) Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022. PeerJ 12:e18187 https://doi.org/10.7717/peerj.18187
High variability in the attractiveness of municipally-planted decorative plants to insects
Insect populations are declining globally. A major driver of this decline is land use change, including urbanisation. However, urban environments can also offer a wide range of floral resources to pollinators, through ornamental plantings, but these can vary widely in their attractiveness to insects. Often, the largest single planter of ornamental plants in an urban area is the municipality. Here we evaluated the decorative plantings carried out by the city municipality of Regensburg, Germany, by systematically surveying insect visitations on different plant types in late summer, when forage is often limited for pollinators. We found a 130-fold difference from the least to the most attractive plants, and high variation in which insect groups were attracted to which plants. While honey bees, which are not a conservation concern, were the most common insect visitors, some decorative plants attracted a very large proportion of wild bees, flies, and wasps. Our results demonstrate that there is great scope for increasing the supply of urban forage to pollinators in general, and specific groups in particular, without requiring new decorative plant types to be sourced or planted. We argue that providing local evidence-based guidance to municipalities offers a quick and potentially cost-neutral method for supporting urban insect populations.
Czaczkes et al. (2024) High variability in the attractiveness of municipally-planted decorative plants to insects. PeerJ 12:e17762 https://doi.org/10.7717/peerj.17762
Reliability and utility of blood glucose levels in the periodontal pockets of patients with type 2 diabetes mellitus: a cross-sectional study
Background Several studies have measured gingival blood glucose (GBG) levels, but few have confirmed systematic bias using Bland–Altman analysis. This study compared the effectiveness of GBG levels with that of fingertip blood glucose (FTBG) levels using Bland–Altman and receiver operating characteristic (ROC) analyses. Methods A total of 15 healthy volunteers and 15 patients with type 2 diabetes were selected according to inclusion and exclusion criteria. Each group comprised eight male and seven female participants. The GBG and FTBG levels were measured using a self-monitoring blood glucose device after periodontal examination. Pearson’s product‒moment correlation and simple linear regression analyses were performed. In addition, Bland‒Altman analysis was also performed to assess the degree of agreement between the two methods. ROC analysis was conducted to determine the sensitivity, specificity, and cutoff values for patients with diabetes. The area under the ROC curve (AUC) was used to identify significant differences. Results The mean GBG and FTBG levels were 120 ± 44.8 mg/dL and 137 ± 45.1, respectively, for the whole sample. The mean GBG and FTBG levels were 145 ± 47.2 mg/dL and 163 ± 49.1, respectively, in the diabetes group. The mean GBG and FTBG levels in the nondiabetes group were 95.3 ± 25.2 and 111 ± 18.8, respectively. Patients with diabetes were more likely to have a probing pocket depth (PPD) of ≥4 mm at the sampled site. Pearson’s product‒moment correlation and simple linear regression analyses revealed a significant correlation between the GBG and FTBG measurements. Bland–Altman analysis revealed that GBG and FTBG measurements differed significantly among all participants; however, no significant differences were observed among the patients with diabetes (mean difference (MD) ± standard deviation (SD) = −18.1 ± 34.2, 95% confidence interval (CI) [−37.0 to 0.88]) or among the participants with a PPD of ≥4 mm (MD ± SD = −15.2 ± 30.4, 95% CI [−30.8 to 0.43]). The sensitivity, specificity, and cutoff values of the GBG measurements for detecting diabetes were 80%, 93%, and 123.5 mg/dL, respectively. The sensitivity, specificity, and cutoff values of the FTBG measurements for detecting diabetes were 73%, 87%, and 134.0 mg/dL, respectively. No significant differences were observed between the AUCs (0.078, 95% CI [−0.006 to 0.161]). Conclusions The GBG measurements aligned with the FTBG measurements in the patients with diabetes and among the participants with a PPD of ≥4 mm. Patients with diabetes were more likely to have a PPD of ≥4 mm at the sampled site, GBG levels can be used to screen for type 2 diabetes in dental clinics.
Terada et al. (2024) Reliability and utility of blood glucose levels in the periodontal pockets of patients with type 2 diabetes mellitus: a cross-sectional study. PeerJ 12:e18239 https://doi.org/10.7717/peerj.18239
Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis
Purpose The aim is to offer a comprehensive overview of oral submucous fibrosis (OSF) prevalence and explore its epidemiological characteristics across various demographic groups and geographical locations, thereby helping the formulation of public health management policies. Methods Studies reporting OSF prevalence were identified from electronic databases including the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OVID, and Web of Science. Pooled prevalence and quality assessment using the New-Ottawa Scale were conducted. Two reviewers screened and selected records, assessed quality, and independently extracted data. This systematic review and meta-analysis followed the PRISMA guidelines and was registered on PROSPERO (CRD42024532975). Results Sixty-three studies, encompassing 11,434 cases in a total population of 769,860, reported OSF prevalence. The majority of studies (forty-one) were from India. The pooled prevalence of OSF across all populations was 3.0% (95% CI [2.8–3.2]%). In non-risk populations, risk populations, and consecutive dental patients, the pooled prevalence stood at 2.4% (95% CI [2.1–2.6]%), 4.5% (95% CI 3.5-5.6%), and 5.6% (95% CI [3.8–7.5]%), respectively. Subgroup analysis by age, sex, and geographical region revealed higher prevalence rates among those aged 50 and above (4.2%, 95% CI [3.0–5.4]%), males (3.3%, 95% CI [2.9–3.7]%), and in India (4.0%, 95% CI [3.7–4.3]%). As the exposure to risk factors exceeded 50% in the surveyed population, the prevalence of OSF notably increased. Most studies met satisfactory quality standards. Conclusions Our research findings reveal a comprehensive prevalence of OSF across all populations at 3.0% (95% CI [2.8–3.2]%). And, existing evidence indicates a relatively low prevalence of OSF associated with tobacco, alcohol, and Areca (betel) nut use. However, further large-scale studies are recommended to validate these findings. Understanding the prevalence and distribution patterns of OSF may assist in healthcare intervention planning and alleviate the oral cancer burden associated with OSF.
Wang et al. (2024) Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis. PeerJ 12:e18385 https://doi.org/10.7717/peerj.18385
Long-term changes in soil biological activity and other properties of raised beds in Longan orchards
Introduction The Longan fruit tree of the Vietnam Mekong Delta is grown in raised beds to improve water drainage during the rainy season and can live as long as 100 years. Objective This research explores the extent to which the soil microorganisms as well as soil physical and chemical properties of these raised beds degrade over a period of 60 years under traditional management practices. Materials and Methods Raised bed topsoil samples at depths of 0–20 cm were obtained from four different Longan orchards raised bed age groups: group 1) 15–25 years (L1–L5); group 2) 26–37 years (L6–L10); group 3) 38–45 years (L11–L15); and group 4) 46–60 years. Soil biological properties were tested for nitrogen-fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria, calcium solubilizing bacteria and silicate solubilizing bacteria, β-glucosidase, urease, phosphomonoesterase, and phytase. Soil samples were also tested for moisture content, soil texture, soil porosity, and bulk density as well as soil chemical properties including pH, electrical conductivity (EC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (NH4+, NO3−), available phosphorus (AP), exchangeable potassium (K+), exchangeable calcium (Ca2 +), available silicate (SiO2), available copper (Cu), zinc (Zn), boron (B) and manganese (Mn). Key findings: The results showed that soil moisture, soil porosity, sand content, SOM, TP, TK, available P, exchangeable Ca2 +, available Si, nitrogen fixing bacteria number, β-glucosidase, urease, phosphomonoesterase, and phytase gradually and significantly decreased in the raised bed soil as the Longan orchard increased in age. Pearson correlation analysis between the ages of Longan orchards and soil properties revealed that raised bed ages were positively correlated with soil bulk density, but negatively correlated with soil moisture content, soil porosity, SOM, TN, β-glucosidase, urease, phosphomonoesterase, and phytase. Principal component analysis (PCA) showed Longan yields had a positive correlation with available NO3− but negative correlation with NFB, exchangeable Ca2 +, pH, and available B. These findings reveal that traditional long-term management of Longan trees in raised beds significantly reduce soil organic matter, moisture content, porosity, and soil fertility with impacts on soil microbial numbers and activity within raised bed soils. Future Directions This suggests that more sustainable management practices, such as mulch and cover crops that decrease soil compaction and increase soil organic matter, improve soil porosity, total N, and feed soil microorganisms that are critical to nutrient cycling are needed to improve raised bed soil quality.
Nguyen et al. (2024) Long-term changes in soil biological activity and other properties of raised beds in Longan orchards. PeerJ 12:e18396 https://doi.org/10.7717/peerj.18396
Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass
Background Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding. Methods Therefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs). Results Initially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data from the F1 population, further verifying the map’s reliability.
Ma et al. (2024) Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass. PeerJ 12:e18409 https://doi.org/10.7717/peerj.18409
Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China
Root-knot nematode disease severely affects the yield and quality of the mandarin variety Citrus reticulata Blanco “Orah” in Guangxi, China. Nevertheless, the pathogen and the effects of this disease on microbial communities remain inadequately understood. This study identified the root-knot nematode Meloidogyne panyuensis in the rhizosphere of infected Orah using morphological and molecular biological methods. Soil chemical properties indicated that organic matter, total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), total potassium (TK), and available potassium (AK) were significantly higher in the rhizosphere soil of M. panyuensis-infected Orah than in that of healthy plants. The relative abundance of the bacteria Bacillus, Sphingomonas, and Burkholderia-Caballeronia-Paraburkholderia, as well as the fungi Lycoperdon, Fusarium, Neocosmospora, Talaromyces, and Tetragoniomyces, was elevated in the rhizosphere soil of M. panyuensis-infected plants. Furthermore, organic matter, TN, available nitrogen (AN), TP, AP, TK, and AK exhibited positive correlationswith these bacteria and fungi in the rhizosphere soil of M. panyuensis-infected Orah. Potential biocontrol strains, such as Burkholderia spp., were identified by comparing the differences in rhizosphere microbial composition between healthy Orah and M. panyuensis-infected Orah. Our findings provide a foundation for the early warning and prevention of root-knot nematode disease in Orah.
Zhang et al. (2024) Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China. PeerJ 12:e18495 https://doi.org/10.7717/peerj.18495
MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2
Background Breast cancer (BC) is a serious health threat to the patients. The present work explored the mechanism of miR-301b-3p and transforming growth factor-beta receptor 2 (TGFBR2 ) in affecting BC progression. Methods The miR-301b-3p-inhibitor and si-TGFBR2 solution were added to the DEME/F12 medium to culture the BC and normal breast epithelial cell lines to prepare negative control, miR-301b-3p-IN and miR-301b-3p-IN+si-TGFBR2 in the two types of cell lines. The relative expression of target genes and the interference effect were analyzed by quantitative real-time PCR (qRT- PCR). Cell viability was detected applying cell counting kit-8 (CCK-8) assay. Transwell and wound healing assay were conducted to evaluate the invasion and migration of BC cells after miR-301b-3p inhibition. Additionally, cell apoptosis and the expression STAT protein were measured by flow cytometry and Western blot, respectively Results The qRT-PCR results showed that miR-301b-3p were high-expressed but the level of TGFBR2 was significantly inhibited in BC cells. The miR-301b-3p-inhibitor significantly downregulated the expression of miR-301b-3p and upregulated that of TGFBR2. Meanwhile, inhibition of miR-301b-3p suppressed the cell viability, invasion, and migration of BC cells, which, however, were restored by the inhibition of TGFBR2. MiR-301b-3p conferred anti-apoptosis ability to BC cells, while TGFBR2 promoted apoptosis of BC cells through producing an antagonistic effect with miR-301b-3p. We found that miR-301b-3p played a crucial role in the phosphorylation of STAT1 and STAT3 to promote BC progression. Conclusion The present findings demonstrated that miR-301b-3p played a crucial role in promoting BC cell growth, invasion and migration and anti-apoptosis, and that targeting TGFBR2 could inhibit the tumor-promoting effect of miR-301b-3p.
Lou et al. (2024) MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2. PeerJ 12:e18324 https://doi.org/10.7717/peerj.18324
Optimizing chlorine dioxide treatment for enhanced post-harvest storage quality of Toona Sinensis
This study investigated the impact of chlorine dioxide (ClO2) treatment on the storage quality of Toona sinensis after harvesting. Toona sinensis samples treated with different concentrations (0.2, 0.4, 0.8, 1.6 mg/L) of chlorine dioxide and stored at (4 ± 1) °C, with sampling test every 2nd day. The changes in sensory, nutritional, and chlorine dioxide residues of T. sinensis were checked regularly. Results revealed that moderate (0.4~0.8 mg/L) chlorine dioxide concentrations maintained sensory quality, inhibited T. sinensis weight loss, slowed flavonoid and vitamin C content depletion, reduced nitrite content, and enhanced superoxide dismutase activity. The chlorine dioxide resides in T. sinensis were below the national standards (<2.0 mg/kg; GB 5009.244-2016). Overall, 0.4~0.8 mg/L chlorine dioxide treatment showed optimal effects on T. sinensis, providing a scientific basis for extended storage and preservation of T. sinensis.
Zeng et al. (2024) Optimizing chlorine dioxide treatment for enhanced post-harvest storage quality of Toona Sinensis. PeerJ 12:e18346 https://doi.org/10.7717/peerj.18346
Long-term alfalfa planting mediates the coupling of soil water and organic carbon storage in a semi-arid area of the Loess Plateau, China
The key to restoring arid and semi-arid ecosystems is maintaining soil water and organic carbon contents. Alfalfa (Medicago sativa L.) is a high-yield perennial forage crop and performs ecological functions as a drought-resistance leguminous herb. It has been widely planted for reconstruction of degraded soils in the Loess Plateau in northwestern China, but long-term planting may affect soil carbon–water coupling and lead to crop yield reduction. To maximize the benefits of reconstructed grassland, this study explored the couplings of soil water, organic carbon, and alfalfa productivity along a reconstruction chronosequence in a semi-arid area of the Loess Plateau. Space-for-time substitution approach was used to select different-aged stands of reconstructed grassland (1, 5, 7, 10, 15, 20, 30 years old). Alfalfa above-ground biomass (AGB), soil water storage (SWS), organic carbon storage (SOCS), and carbon–water coupling coordination degree (D) were measured in the 0–100 cm soil profile. Alfalfa AGB reached a peak in the 7th year, and the degradation began in the 10th year. Both SWS and SOCS varied nonlinearly with stand age. The greatest loss of SWS occurred in the 15th year (80–100 cm depth), whereas the largest increase of SOCS occurred in the 30th year (0–20 cm depth). There was a negative feedback relationship between AGB and SWS over the 30-year study period (Pearson r = −0.835, P = 0.098). AGB and SOCS initially showed a trade-off within the first 10 years (Pearson r = −0.7431, P = 0.2569), in contrast to their positive feedback in the 20–30th years (Pearson r = 0.9978, P = 0.0421). A decoupling between SWS and SOCS (D < 0.6) was observed after 12 years of alfalfa planting. For agricultural production, a greater supply of water and organic fertilizer is required from the 7th year of alfalfa planting, and reseeding may be needed around the 10th year to prolong the life of alfalfa community. Alfalfa should be planted for no more than 12 consecutive years in the study area for ecological protection.
Ma et al. (2024) Long-term alfalfa planting mediates the coupling of soil water and organic carbon storage in a semi-arid area of the Loess Plateau, China. PeerJ 12:e18373 https://doi.org/10.7717/peerj.18373
Citizen science enhances understanding of sea turtle distribution in the Gulf of California
Citizen science is a valuable tool for addressing spatial distribution gaps in endangered species, especially in data-limited regions. Given the logistical and financial challenges of studying migratory species, this cost-effective approach contributes to strategic conservation planning. The Bay of La Paz, located in Baja California Sur, México, is considered an ecologically important region within the larger Gulf of California. Due to its rich biodiversity and abundant natural resources, the region serves as a hub for ecotourism and fishing, affording diverse opportunities for community-based scientific initiatives. This paper examines the value of citizen science contributions from three diverse community groups (i.e., coastal residents, SCUBA divers, and artisanal fishers) to help scientists obtain information on sea turtle distribution in the Bay of La Paz. Our findings represent the first records of loggerhead turtles (Caretta caretta) in the bay based on ten citizen science reports that include live and dead turtles (either observed swimming, as bycatch, or stranded), providing new information on an endangered pelagic species identified in a coastal bay. Although the sample size is small, our diversity of sources and sighting types highlight the value of collaborative citizen science initiatives in complementing traditional research methods.
Rousso et al. (2024) Citizen science enhances understanding of sea turtle distribution in the Gulf of California. PeerJ 12:e18203 https://doi.org/10.7717/peerj.18203
Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning
Background Acute bouts of exercise have been shown to improve motor learning. However, whether these benefits can be observed from habitual physical activity (PA) levels remains unclear and has important implications around PA guidelines to promote motor learning across the lifespan. This study investigated the effect of habitual PA levels on brain activity within the dorsolateral prefrontal cortex (DLPFC) during procedural motor skill acquisition. Methods Twenty-six right-handed healthy young adults had physical activity levels quantified by calculating the metabolic equivalent of task (METs) in minutes per week, derived from the International Physical Activity Questionnaire (IPAQ). Functional near-infrared spectroscopy (fNIRS) over the DLPFC was recorded to measure neural activation during a serial reaction time task (SRTT). Behavioural indicators of procedural motor skill acquisition were quantified as reaction time and accuracy of correct trials during the SRTT. DLPFC activation was characterised as task-related changes in oxyhaemoglobin (∆[HbO2]). Results Findings showed that higher PA levels were associated with improvements in reaction time during procedural motor skill acquisition (p = 0.03). However, no significant effects of PA levels on accuracy or ∆[HbO2] during procedural motor skill acquisition were observed. These findings show that while habitual PA may promote motor performance in young adults, this is not reflected by changes in the DLPFC area of the brain.
Tan et al. (2024) Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning. PeerJ 12:e18217 https://doi.org/10.7717/peerj.18217
Genomic complexity and clinical significance of the RCCX locus
Nearly identical, repetitive elements in the genome contribute to the variability in genetic inheritance patterns, particularly in regions like the RCCX locus, where such repeats can lead to structural variations. In addition, during the formation of gametes as a result of meiosis, variants of loci with repetitive elements that do not code for the required proteins may occur. As a result, an individual with certain genetic rearrangements in this region may have an increased risk of developing a congenital disorder, particularly in cases where the non-functional allele is inherited dominantly. At the same time, there is still no routine or generally recognized diagnostic method to determine the sequence of the repetitive fragments. The functionally important RCCX locus consists of such repetitive fragments. The available knowledge about the genomic variants of the RCCX locus is fragmented, as there is no standardized method to determine its structure. It should be noted that in some structural variants of the RCCX locus, the sequence of protein-coding genes is disrupted, leading to the development of diseases such as congenital adrenal hyperplasia (CAH). Although genetic testing is generally accepted as a gold standard for CAH diagnosis, there are a myriad of strategies on which exact methods to use and in which order. The reason for this inconsistency lies in the complexity of the RCCX locus and the fact that each patient or carrier may have a highly individualized mutation or combination thereof. In this review, we have discussed all known methods that can be used to study the structure of the RCCX locus. As a result, optimal approaches are proposed for the diagnosis of the most common disease caused by lesions in the RCCX–CAH due to CYP21A2 deficiency.
Shiryagin et al. (2024) Genomic complexity and clinical significance of the RCCX locus. PeerJ 12:e18243 https://doi.org/10.7717/peerj.18243
Dietary reference intake for military operations: a scoping review
Background Reports that collect and organize dietary reference intake (DRI) data for military operations in different countries and regions worldwide are limited.This scoping review aimed to collect and organize information on the status of formulating a DRI for military operations in each country. Methodology For the information search, we queried PubMed and Google for literature and reports on the DRI for military operations and summarized the content of the adopted literature and reports. Results The content and rationale for DRI for military operations in Australia, the United Kingdom (UK), the United States of America (USA), and the North Atlantic Treaty Organization (NATO) can be summarized as follows: (1) Energy requirements: Four reports formulated physical activity levels (PALs) and corresponding energy requirements that differed from those for the civilian public. The PAL range for the military was set as high as 1.50–3.20, as opposed to the standard civilian upper PAL set at 1.20–2.20. (2) Protein: Three military reports outside of the UK had different standards than those for the civilian public with an increased intake in accordance with the high PAL while simultaneously preventing excessive intake.In the military, values were formulated 1.2–4.8 times higher than the standards for civilians (45–65 g/day to 55–307 g/day). (3) Macronutrient energy distribution: Four military reports established macronutrient energy distributions that differed from those for the civilian public. The DRI for the Australian and UK militaries was formulated such that as PAL increased, protein decreased, fat decreased or remained unchanged, and carbohydrate increased. (4) Sodium: Considering that military personnel sweat more due to high physical activity and their environment, two Australian and NATO reports were established with sodium levels that were twice as high as that of the civilian public (460–2,300 mg/day to 920–3,200 mg/day). Increasing sodium intake to <4,800 mg/day is recommended for individuals who sweat a lot or are not accustomed to hot environments. Conclusions The DRI in Australia, the UK, USA, and NATO consider the physical activity and operating environment of military personnel, differing from those of the civilian population in terms of (1) energy requirements, (2) protein, (3) macronutrient energy distribution, and (4) sodium.
Mizushima et al. (2024) Dietary reference intake for military operations: a scoping review. PeerJ 12:e18353 https://doi.org/10.7717/peerj.18353
Common laboratory results-based artificial intelligence analysis achieves accurate classification of plasma cell dyscrasias
Background Plasma cell dyscrasias encompass a diverse set of disorders, where early and precise diagnosis is essential for optimizing patient outcomes. Despite advancements, current diagnostic methodologies remain underutilized in applying artificial intelligence (AI) to routine laboratory data. This study seeks to construct an AI-driven model leveraging standard laboratory parameters to enhance diagnostic accuracy and classification efficiency in plasma cell dyscrasias. Methods Data from 1,188 participants (609 with plasma cell dyscrasias and 579 controls) collected between 2018 and 2023 were analyzed. Initial variable selection employed Kruskal-Wallis and Wilcoxon tests, followed by dimensionality reduction and variable prioritization using the Shapley Additive Explanations (SHAP) approach. Nine pivotal variables were identified, including hemoglobin (HGB), serum creatinine, and β2-microglobulin. Utilizing these, four machine learning models (gradient boosting decision tree (GBDT), support vector machine (SVM), deep neural network (DNN), and decision tree (DT) were developed and evaluated, with performance metrics such as accuracy, recall, and area under the curve (AUC) assessed through 5-fold cross-validation. A subtype classification model was also developed, analyzing data from 380 cases to classify disorders such as multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS). Results 1. Variable selection: The SHAP method pinpointed nine critical variables, including hemoglobin (HGB), serum creatinine, erythrocyte sedimentation rate (ESR), and β2-microglobulin. 2. Diagnostic model performance: The GBDT model exhibited superior diagnostic performance for plasma cell dyscrasias, achieving 93.5% accuracy, 98.1% recall, and an AUC of 0.987. External validation reinforced its robustness, with 100% accuracy and an F1 score of 98.5%. 3. Subtype Classification: The DNN model excelled in classifying multiple myeloma, MGUS, and light-chain myeloma, demonstrating sensitivity and specificity above 90% across all subtypes. Conclusions AI models based on routine laboratory results significantly enhance the precision of diagnosing and classifying plasma cell dyscrasias, presenting a promising avenue for early detection and individualized treatment strategies.
Yao et al. (2024) Common laboratory results-based artificial intelligence analysis achieves accurate classification of plasma cell dyscrasias. PeerJ 12:e18391 https://doi.org/10.7717/peerj.18391
Application of composite reference intervals in the diagnosis of subclinical hypothyroidism in the elderly: a retrospective study
Background Thyroid stimulating hormone releasing hormone (TSH) is a key indicator for diagnosing subclinical hypothyroidism (SCH). We evaluated factors affecting TSH levels in elderly SCH, establishing a composite reference interval, and comparing it with traditional one in diagnosis. Methods We collected data on patients aged ≥60 undergoing physical examinations in Chengdu, screening the influencing factors associated with TSH. Then, a two-dimensional composite reference interval was established for TSH and FT4, and the differences between the new and traditional diagnosing methods were compared. Results The incidence of subclinical thyroid dysfunction was about 14%, with SCH accounting for 97%. Regression analysis found that TSH levels increase as FT4 and uric acid levels decrease. Compared with the two-dimensional composite reference interval, the traditional one has a higher incidence rate of SCH. Conclusion Compared with the two-dimensional composite reference interval, the traditional one is more likely to overestimate the incidence rate of SCH, leading to excessive diagnosis and treatment.
Li et al. (2024) Application of composite reference intervals in the diagnosis of subclinical hypothyroidism in the elderly: a retrospective study. PeerJ 12:e18417 https://doi.org/10.7717/peerj.18417
Quality improvement bundles to decrease hypothermia in very low/extremely low birth weight infants at birth: a systematic review and meta-analysis
Background Numerous studies have demonstrated that hypothermia in preterm infants correlates with increased morbidity and mortality, especially among those with very low or extremely low birth weights (VLBW/ELBW). An increasing number of healthcare facilities are implementing quality improvement (QI) bundles to lower the incidence of hypothermia at birth in this vulnerable population. However, the effectiveness and safety of these interventions have yet to be fully assessed. A meta-analysis is necessary to evaluate the efficacy and safety of QI bundles in reducing hypothermia at birth among VLBW/ELBW infants. Methods We searched PubMed, Embase, the Cochrane Library and Web of Science through April 22nd, 2024. Study selection, data extraction, quality evaluation and risk bias assessment were performed independently by two investigators. Meta-analysis was performed using Review Manager 5.4.1. Results A total of 18 studies were included for qualitative analysis and 12 for meta-analysis. For VLBW infants, meta-analysis revealed a reduction in hypothermia and an increase in hyperthermia following the introduction of QI bundles (mild hypothermia, OR 0.22, 95% CI [0.13–0.37]; moderate hypothermia, OR 0.18, 95% CI [0.15–0.22]; hyperthermia, OR 2.79, 95% CI [1.53–5.09]). For ELBW infants, meta-analysis showed a decrease in hypothermia but no increase in hyperthermia after implementing QI bundles (mild hypothermia, OR 0.46, 95% CI [0.26–0.81]; moderate hypothermia, OR 0.21, 95% CI [0.08–0.58]; hyperthermia, OR 1.10, 95% CI [0.22–5.43]). Conclusion QI bundles effectively reduce hypothermia in VLBW/ELBW infants, but they may also increase hyperthermia, especially in VLBW infants.
Zhong et al. (2024) Quality improvement bundles to decrease hypothermia in very low/extremely low birth weight infants at birth: a systematic review and meta-analysis. PeerJ 12:e18425 https://doi.org/10.7717/peerj.18425
Applying stacking ensemble method to predict chronic kidney disease progression in Chinese population based on laboratory information system: a retrospective study
Background and Objective Chronic kidney disease (CKD) is a major public health issue, and accurate prediction of the progression of kidney failure is critical for clinical decision-making and helps improve patient outcomes. As such, we aimed to develop and externally validate a machine-learned model to predict the progression of CKD using common laboratory variables, demographic characteristics, and an electronic health records database. Methods We developed a predictive model using longitudinal clinical data from a single center for Chinese CKD patients. The cohort included 987 patients who were followed up for more than 24 months. Fifty-three laboratory features were considered for inclusion in the model. The primary outcome in our study was an estimated glomerular filtration rate ≤15 mL/min/1.73 m2 or kidney failure. Machine learning algorithms were applied to the modeling dataset (n = 296), and an external dataset (n = 71) was used for model validation. We assessed model discrimination via area under the curve (AUC) values, accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1 score. Results Over a median follow-up period of 3.75 years, 148 patients experienced kidney failure. The optimal model was based on stacking different classifier algorithms with six laboratory features, including 24-h urine protein, potassium, glucose, urea, prealbumin and total protein. The model had considerable predictive power, with AUC values of 0.896 and 0.771 in the validation and external datasets, respectively. This model also accurately predicted the progression of renal function in patients over different follow-up periods after their initial assessment. Conclusions A prediction model that leverages routinely collected laboratory features in the Chinese population can accurately identify patients with CKD at high risk of progressing to kidney failure. An online version of the model can be easily and quickly applied in clinical management and treatment.
Du et al. (2024) Applying stacking ensemble method to predict chronic kidney disease progression in Chinese population based on laboratory information system: a retrospective study. PeerJ 12:e18436 https://doi.org/10.7717/peerj.18436
Potential molecular mechanisms of ETV6-RUNX1-positive B progenitor cell cluster in acute lymphoblastic leukemia revealed by single-cell RNA sequencing
Aim This study was to explore role of immune landscape and the immune cells in acute lymphoblastic leukemia (ALL) progression. Background The most prevalent genetic alteration in childhood ALL is the ETV6-RUNX1 fusion. The increased proliferation of B progenitor cells could expedite the disease’s progression due to irregularities in the cell cycle. Nevertheless, the mechanisms by which particular cell clusters influence the cell cycle and promote the advancement of ALL are still not well understood. Objective This study was to explore role of immune landscape and the immune cells in ALL progression. Methods Single-cell RNA sequencing (scRNA-seq) data of ETV6-RUNX1 and healthy pediatric samples obtained from GSE132509 were clustered and annotated using the Seurat package, and differentially highly expressed genes identified in each cluster were analyzed using DAVID for pathway annotation. Chromosome amplification and deletion were analyzed using the inferCNV package. SCENIC evaluated the regulation of transcription factors and target gene formation in cells. cellphoneDB and CellChat were served to infer ligand-receptor pairs that mediate interactions between subpopulations. The role of the target gene in regulating ALL progression was assessed using RT-qPCR, Transwell and scratch healing assays. Results The bone marrow mononuclear cells (BMMCs) from ETV6-RUNX1 and healthy pediatric samples in GSE132509 were divided into 11 clusters, and B cell cluster 1 was identified as B progenitor cell, which was amplified on chromosome 6p. B progenitor cells were divided into seven clusters. Expression levels of amplified genes in chromosome 6p of B progenitor cell cluster 5 were the highest, and its specific highly expressed genes were annotated to pathways promoting cell cycle progression. Regulons formed in B progenitor cell cluster 5 were all involved in promoting cell cycle progression, so it was regarded as the B progenitor cell cluster that drives cell cycle progression. The key regulator of the B progenitor cell is E2F1, which promotes the migration and invasion ability of the cell line HAP1. The major ligand-receptor pairs that mediate the communication of B progenitor cell cluster 5 with cytotoxic NK/T cells or naive T cells included FAM3C−CLEC2D, CD47−SIRPG, HLAE−KLRC2, and CD47−KLRC2. HLAE−KLRC1 and TGFB1−(TGFBR1+TGFBR2). Conclusion This study outlined the immune cell landscape of ETV6-RUNX1 ALL and identified chromosome 6p amplification in B progenitor cells, described the major B progenitor cell cluster driving cell cycle progression and its potential regulatory mechanisms on NK cells and T cells, providing cellular and molecular insights into ETV6-RUNX1 ALL.
Qu et al. (2024) Potential molecular mechanisms of ETV6-RUNX1-positive B progenitor cell cluster in acute lymphoblastic leukemia revealed by single-cell RNA sequencing. PeerJ 12:e18445 https://doi.org/10.7717/peerj.18445
Prognosis of hepatitis B virus reactivation in newly diagnosed multiple myeloma in modern era therapy: a retrospective study
Studies on the prognosis of hepatitis B virus (HBV) reactivation following modern therapies for newly diagnosed MM (NDMM) are lacking. In this retrospective study, we aimed to assess the incidence, risk factors and prognosis of HBV reactivation in NDMM. A total of 33 of 355 patients with NDMM and HBV reactivation were included in this study. Multivariable analysis showed that hepatitis B surface antigen-positivity, hepatitis B core antibody-positivity, bortezomib-containing regimens, autologous stem cell transplantation, and gain of 1q21 were identified as independent risk factors of HBV reactivation in NDMM patients. The NDMM patients with HBV reactivation had poorer 3-year overall survival (OS) and progression-free survival (PFS) than did those without HBV reactivation, as confirmed by multivariate analysis. In conclusion, HBV reactivation in patients with NDMM constitutes a significant complication, correlating with reduced OS and PFS, and emerges as a potential adverse prognostic factor in the contemporary era of treatment.
Lv et al. (2024) Prognosis of hepatitis B virus reactivation in newly diagnosed multiple myeloma in modern era therapy: a retrospective study. PeerJ 12:e18475 https://doi.org/10.7717/peerj.18475
A novel nomogram to predict the risk of requiring mechanical ventilation in patients with sepsis within 48 hours of admission: a retrospective analysis
Objective To establish a model that can predict the risk of requiring mechanical ventilation within 48 h after admission in patients with sepsis. Methods Data for patients with sepsis admitted to Dongyang People’s Hospital from October 2011 to October 2023 were collected and divided into a modeling group and a validation group. Independent risk factors in the modeling group were analyzed, and a corresponding predictive nomogram was established. The model was evaluated for discriminative power (the area under the curve of the receiver operating characteristic curve, AUC), calibration degree (Hosmer-Lemeshow test), and clinical benefit (decision curve analysis, DCA). Models based on the Sequential Organ Failure Assessment (SOFA) scores, the National Early Warning Score (NEWS) scores and multiple machine learning methods were also established. Results The independent factors related to the risk of requiring mechanical ventilation in patients with sepsis within 48 h included lactic acid, pro-brain natriuretic peptide (PRO-BNP), and albumin levels, as well as prothrombin time, the presence of lung infection, and D-dimer levels. The AUC values of nomogram model in the modeling group and validation group were 0.820 and 0.837, respectively. The nomogram model had a good fit and clinical value. The AUC values of the models constructed using SOFA scores and NEWSs were significantly lower than those of the nomogram (P < 0.01). The AUC value of the integrated machine-learning model for the validation group was 0.849, comparable to that of the nomogram model (P = 0.791). Conclusion The established nomogram could effectively predict the risk of requiring mechanical ventilation within 48 h of admission by patients with sepsis. Thus, the model can be used for the treatment and management of sepsis.
Wang et al. (2024) A novel nomogram to predict the risk of requiring mechanical ventilation in patients with sepsis within 48 hours of admission: a retrospective analysis. PeerJ 12:e18500 https://doi.org/10.7717/peerj.18500