The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth
Background The present in vitro study aimed to evaluate the fatigue behavior of teeth filled with a calcium silicate-based sealer (Bio-C Sealer, BC) or an epoxy resin-based sealer (AH Plus, AH), in bulk or associated with gutta-percha as main core material. Methods Seventy-two sound human maxillary anterior teeth were initially selected. Sixty of them, were randomly chosen, and had their root canals prepared using nickel-titanium reciprocating instruments, being again randomly assigned to five experimental groups (n = 12): C+ (control + prepared but not filled); BC-B (BC in bulk); BC-GP (BC+ gutta-percha); AP-B (AH in bulk); AP-GP (AH+ gutta-percha). An additional negative control group (C−) was considered (n = 12), consisting only on sound teeth, without preparation and filling. The specimens were submitted to a survival analysis after the cyclic fatigue test. Results Sound teeth (C−) presented the best fatigue performance (P < 0.05), being similar only to the AP-GP group (P > 0.05). Despite that, all experimental groups showed similar fatigue behavior (P > 0.05) to C+ (BC-B = BC-GP = AP-B = AP-GP = C+). Based on that, it can be seen that the use of gutta-percha, as a main core material, associated with the AH Plus sealer, reestablished the mechanical fatigue performance of endodontically treated teeth comparable to sound teeth, still consisting on the most promising approach to rehabilitate such scenario. Teeth filled in bulk, had discreetly higher risk of premature failures and inferior fatigue performance.
Lena et al. (2024) The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth. PeerJ 12:e18221 https://doi.org/10.7717/peerj.18221
Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L.
Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (i.e., hydro-priming, halopriming by KNO3, and acid priming with HCl) in four ancient and neglected cultivars of Capsicum annuum L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO3 6% for 96 h > KNO3 4% for 48 h > hydropriming for 24 h. In particular, KNO3 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes.
Granata et al. (2024) Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L.. PeerJ 12:e18293 https://doi.org/10.7717/peerj.18293
Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus
Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family’s evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family.
Wang et al. (2024) Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus. PeerJ 12:e18322 https://doi.org/10.7717/peerj.18322
Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia
Background The interplay between chronic kidney disease (CKD) and thyroid dysfunction is becoming more evident in the biomedical community. However, the intricacies of their relationship warrant deeper investigation to understand the clinical implications fully. Objective This study aims to systematically evaluate the correlation between thyroid hormone levels, including thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4), and markers of renal disease severity. These markers include serum creatinine, urea, and parathyroid hormone (PTH) levels in individuals diagnosed with CK). Methods We conducted a cross-sectional observational study involving a cohort of 86 participants with CKD recruited from the renal clinic at King Fahad Hospital in Tabuk. Biochemical parameters, encompassing plasma electrolytes and thyroid hormone concentrations, were quantitatively assessed. These measurements were performed with the aid of a Roche Cobas E411 analyzer. The Pearson correlation coefficient was employed to delineate the strength and direction of the associations between the thyroid function markers and renal disease indicators. Results The statistical analysis highlighted a generally weak correlation between the concentrations of thyroid hormones and the indicators of renal disease severity, with Pearson correlation coefficients between −0.319 and 0.815. Critically, no significant correlation was found between creatinine and thyroid hormones (TSH, T3, T4), nor was any substantial correlation between urea and thyroid hormones. Conversely, a robust positive correlation was noted between the levels of parathyroid hormone and serum creatinine (r = 0.718, p < 0.001). Conclusion The data suggests that thyroid hormone levels have a minimal correlation with the severity of renal disease markers. In contrast, the pronounced correlation between PTH and creatinine underscores the importance of considering PTH as a significant factor in managing and therapeutic intervention of CKD complications. These initial findings catalyze further research to thoroughly investigate the pathophysiological relationships and potential therapeutic targets concerning thyroid dysfunction in patients with renal impairment.
Awwaadh et al. (2024) Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia. PeerJ 12:e18338 https://doi.org/10.7717/peerj.18338
COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression
Background Colorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression. Methods Using the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. The candidate biomarkers were also examined for constructing a prognostic model based on survival analysis. Results Among the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN3, GABRD, and LPAR1, was sufficient to optimize a RandomForest model that achieved > 98% balanced accuracy (and performant recall) of cancer vs. normal on external validation. Design of an optimal multivariate model based on survival analysis yielded a prognostic panel of three stage-IV salient genes, namely HOTAIR, GABRD, and DKK1. Based on the above sparse signatures, we have developed COADREADx, a web-server for potentially assisting colorectal cancer screening and patient risk stratification. COADREADx provides uncertainty measures for its predictions and needs clinical validation. It has been deployed for experimental non-commercial use at: https://apalanialab.shinyapps.io/coadreadx/.
Palaniappan et al. (2024) COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression. PeerJ 12:e18347 https://doi.org/10.7717/peerj.18347
The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures
Background Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ) but not ${\mathrm{NO}}_{2}^{-}$ NO 2 − to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$ NO 3 − to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Furthermore, ${\mathrm{NO}}_{3}^{-}$ NO 3 − is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Methods Both strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$ NO 3 − , or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − / ${\mathrm{NO}}_{2}^{-}$ NO 2 − transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. Results The transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$ NO 3 − . These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − than those in both strains cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Since NnrS senses NO, these results suggest that strain GP59 reduced ${\mathrm{NO}}_{3}^{-}$ NO 3 − to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to ${\mathrm{NO}}_{3}^{-}$ NO 3 − by flavohemoproteins (NO dioxygenase; Hmp), explaining why ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction is not observed in strain GP59 cultured under oxic conditions. Conclusions Understanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities.
Lestin et al. (2024) The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures. PeerJ 12:e18361 https://doi.org/10.7717/peerj.18361
Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis
Objective This study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis. Methods Single-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment. Results Two subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration. Conclusion The study revealed the heterogeneity of TECs in HCC and their potential roles in tumor progression, offering new perspectives and potential therapeutic targets for HCC molecular mechanisms. The findings emphasize the importance of further exploring TECs heterogeneity for understanding HCC pathogenesis and developing personalized treatment strategies.
Sun et al. (2024) Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis. PeerJ 12:e18362 https://doi.org/10.7717/peerj.18362
Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index
Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000–2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran’s Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000–2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000–2020 period, with a relatively stable overall spatial distribution. Areas with high–high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low–low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could directly enhance meltwater runoff from glaciers in the basin, thereby resulting in short-term improvement in the basin EEQ. Furthermore, rapid urbanization from 2015 to 2020 resulted in a decrease in the average RSEI value of the Tarim River Basin by 0.1 over this period, consequently, the EEQ level decreased slightly. Briefly, the EEQ in the Tarim River Basin showed an overall increasing trend from 2000 to 2020, further demonstrating the effectiveness of a series of implemented ecological restoration measures in the Tarim River Basin over this period.
Environmental Contamination and Remediation
Spatial and Geographic Information Science
Tang et al. (2024) Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index. PeerJ 12:e18368 https://doi.org/10.7717/peerj.18368
Development of a welfare assessment tool for tourist camp elephants in Asia
Background Approximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps. Methods Using direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (e.g., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0–2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests. Results The initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (n = 5), Environment (n = 14), Health (n = 10), and Behavior and Mental State (n = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfaction. The final tool consisted of 42 questions related to 36 measures, including 18 animal-based and 18 resource-based measures within the Nutrition (n = 5), Environment (n = 11), Health (n = 10), and Behavior and Mental State (n = 10) domains. Intraclass correlation coefficients (ICC) for inter-rater reliability (0.78–0.90, p < 0.05) and test-retest (0.77–0.91, p < 0.05) analyses conducted at two camps showed good agreement. Conclusions This new assessment tool (EWAT) is a context-specific, holistic method designed to offer a practical means of conducting individual and institutional-level assessments of elephant welfare in tourist camps. It is based on the Five Domains Model using reliable and validated animal- and resource-based measures, data collection through direct observation and interviews, and a numerical scoring system. The tool includes several criteria applicable to tourist rather than zoo venues to make it more relevant to the challenges faced by working elephants in Asia.
Ghimire et al. (2024) Development of a welfare assessment tool for tourist camp elephants in Asia. PeerJ 12:e18370 https://doi.org/10.7717/peerj.18370
Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part
Background Occupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a “service gap”. Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site. Methods This study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part. Results The results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences according to affected site or age group. This study revealed age- and body part-related relationships with chronic musculoskeletal pain in middle-aged patients and highlighted healthcare service gaps in its management in Japan.
Oka et al. (2024) Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part. PeerJ 12:e18389 https://doi.org/10.7717/peerj.18389