Effectiveness of dentin pre-treatment on bond strength of two self-adhesive resin cements compared to an etch-and-rinse system: an in vitro study
Statement of problem It has been shown that selective etching improves the bond strength of some self-adhesive resin cements to enamel. The same has yet to be determined with dentin pre-treatment. Purpose To evaluate the tensile bond strength of two self-adhesive resin cements after two dentin surface pre-treatments, and also to analyze the cement/dentin interface. Material and Methods One hundred and twelve human third molars were extracted. The teeth were distributed into seven groups (n = 16). Maxcem Elite Chroma (MAX) (Kerr, Scafati, Italy) and Relyx U200 (RLX) (3M ESPE, Neuss, Germany) were used without pre-treatment or with two dentin pre-treatments (polyacrylic acid or phosphoric acid). A conventional etch-and-rinse (EAR) luting cement, NX3 Nexus (NX3) (Kerr, Scafati, Italy), was used as an external control group. Before testing, all specimens were stored in distilled water for 24 hours. Three specimens from each group were prepared for scanning electron microscopy observation (SEM). A tensile bond strength test (TBS) was performed for the remaining samples. The data were statistically analyzed using the Kruskal–Wallis test and Pairwise comparisons using the Wilcoxon rank sum test. Results MAX without pre-treatment and with phosphoric acid etching attained statistically similar bond strengths to NX3 (P > 0.05). There was a statistical difference (P = 0.00488) between RLX without pre-treatment (5.62 MPa) and NX3 (10.88 MPa). Phosphoric acid pre-treatment increases the bond strength values of RLX to a strength that is comparable to NX3 (P > 0.05). The lowest tensile bond strength (TBS) was attained after the application of polyacrylic acid with MAX (1.98 MPa). No statistical differences were found between the RLX bond strength values after polyacrylic acid treatment and RLX without pre-treatment or NX3 (P > 0.05). SEM observations disclosed an enhanced potential of the self-adhesive cements to infiltrate into dentin tubules and form resin tags when applied after phosphoric acid pre-treatment. The failure mode was dominantly adhesive. Conclusions On dentin, the self-adhesive resin cement MAX might be an effective alternative to conventional resin cement. Etching the dentin with phosphoric acid does not have a negative effect on the bond strength of MAX to dentin. On the other hand, phosphoric acid improved the bond strength of RLX when compared to EAR cement.
Hammal et al. (2021) Effectiveness of dentin pre-treatment on bond strength of two self-adhesive resin cements compared to an etch-and-rinse system: an in vitro study. PeerJ 9:e11736 https://doi.org/10.7717/peerj.11736
Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland
The rate of progression of geomorphological phenomena is greatly influenced by freeze-thaw processes. In the face of air temperature increasing over the past few decades, a question of the future impact of these processes arises, notably in the temperate and cold climate zones. Using the mean, maximum and minimum daily air temperature data in the period 1951–2018 obtained from three weather stations located in the vicinity of Jeziorsko reservoir (central Poland), we have determined the mathematical correlation, described with a polynomial function, between the mean monthly air temperature and the monthly number of freeze-thaw days (FTD). A freeze-thaw day is a day when the maximum air temperature is above 0 °C while the minimum air temperature equals or is below this threshold. The number of FTDs within the study area averaged 64–71 and demonstrated a downward trend of 2–4 FTDs/10 years. The study period (1951–2018), includes a clearly marked distinct sub-period (1991–2018), when the reservoir was in operation, which experienced 58–68 FTDs. Considering the assumed rise in temperature, one should expect a further, though slightly slower, decline in the future number of FTDs. Depending on the accepted model of the temperature increase, which for the area of Poland (Central Europe) in the perspective of 30 years oscillates between +1.1 to +1.3 °C, the number of FTDs within the study area is expected to decline by −4.5 to −5.3 FTD, i.e. 6–7% and 5.4–5.5 FTD i.e. 8–9% respectively.
Bartczak et al. (2021) Measured and predicted freeze-thaw days frequencies in climate change conditions in central Poland. PeerJ 9:e12153 https://doi.org/10.7717/peerj.12153
Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction
Background In recent years, ER+ and HER2- breast cancer of adjuvant therapy has made great progress, including chemotherapy and endocrine therapy. We found that the responsiveness of breast cancer treatment was related to the prognosis of patients. However, reliable prognostic signatures based on ER+ and HER2- breast cancer and drug resistance-related prognostic markers have not been well confirmed, This study in amied to establish a drug resistance-related gene signature for risk stratification in ER+ and HER2- breast cancer. Methods We used the data from The Cancer Genoma Atlas (TCGA) breast cancer dataset and gene expression database (Gene Expression Omnibus, GEO), constructed a risk profile based on four drug resistance-related genes, and developed a nomogram to predict the survival of patients with I-III ER+ and HER2- breast cancer. At the same time, we analyzed the relationship between immune infiltration and the expression of these four genes or risk groups. Results Four drug resistance genes (AMIGO2, LGALS3BP, SCUBE2 and WLS) were found to be promising tools for ER+ and HER2- breast cancer risk stratification. Then, the nomogram, which combines genetic characteristics with known risk factors, produced better performance and net benefits in calibration and decision curve analysis. Similar results were validated in three separate GEO cohorts. All of these results showed that the model can be used as a prognostic classifier for clinical decision-making, individual prediction and treatment, as well as follow-up.
Shuai et al. (2021) Estrogen receptor—positive breast cancer survival prediction and analysis of resistance–related genes introduction. PeerJ 9:e12202 https://doi.org/10.7717/peerj.12202
Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma
Background The anti-tumor properties of curcumin have been demonstrated for many types of cancer. However, a systematic functional and biological analysis of its target proteins has yet to be fully documented. The aim of this study was to explore the underlying mechanisms of curcumin and broaden the perspective of targeted therapies. Methods Direct protein targets (DPTs) of curcumin were searched in the DrugBank database. Using the STRING database, the interactions between curcumin and DPTs and indirect protein targets (IPTs) weres documented. The protein–protein interaction (PPI) network of curcumin-mediated proteins was visualized using Cytoscape. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed for all curcumin-mediated proteins. Furthermore, the cancer targets were searched in the Comparative Toxicogenomics Database (CTD). The overlapping targets were studied using Kaplan–Meier analysis to evaluate cancer survival. Further genomic analysis of overlapping genes was conducted using the cBioPortal database. Lastly, MTT, quantitative polymerase chain reaction (qPCR), and western blot (WB) analysis were used to validate the predicted results on hepatocellular carcinoma (HCC) cells. Results A total of five DPTs and 199 IPTs were found. These protein targets were found in 121 molecular pathways analyzed via KEGG enrichment. Based on the anti-tumor properties of curcumin, two pathways were selected, including pathways in cancer (36 genes) and HCC (22 genes). Overlapping with 505 HCC-related gene sets identified in CTD, five genes (TP53, RB1, TGFB1, GSTP1, and GSTM1) were finally identified. High mRNA levels of TP53, RB1, and GSTM1 indicated a prolonged overall survival (OS) in HCC, whereas elevated mRNA levels of TGFB1 were correlated with poor prognosis. The viability of both HepG2 cells and Hep3B cells was significantly reduced by curcumin at concentrations of 20 or 30 μM after 48 or 72 h of culture. At a concentration of 20 μM curcumin cultured for 48 h, the expression of TGFB1 and GSTP1 in Hep3B cells was reduced significantly in qPCR analysis, and reduced TGFB1 protein expression was also found in Hep3B cells.
Zhao et al. (2021) Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in hepatocellular carcinoma. PeerJ 9:e12339 https://doi.org/10.7717/peerj.12339
The potential habitat of desert locusts is contracting: predictions under climate change scenarios
Desert locusts are notorious for their widespread distribution and strong destructive power. Their influence extends from the vast arid and semiarid regions of western Africa to northwestern India. Large-scale locust outbreaks can have devastating consequences for food security, and their social impact may be long-lasting. Climate change has increased the uncertainty of desert locust outbreaks, and predicting suitable habitats for this species under climate change scenarios will help humans deal with the potential threat of locust outbreaks. By comprehensively considering climate, soil, and terrain variables, the maximum entropy (MaxEnt) model was used to predict the potential habitats of solitary desert locusts in the 2050s and 2070s under the four shared socioeconomic pathways (SSP126, SSP245, SSP370, and SSP585) in the CMIP6 model. The modeling results show that the average area under the curve (AUC) and true skill statistic (TSS) reached 0.908 ± 0.002 and 0.701, respectively, indicating that the MaxEnt model performed extremely well and provided outstanding prediction results. The prediction results indicate that climate change will have an impact on the distribution of the potential habitat of solitary desert locusts. With the increase in radiative forcing overtime, the suitable areas for desert locusts will continue to contract, especially in the 2070s under the SSP585 scenario, and the moderately and highly suitable areas will decrease by 0.88 × 106 km2 and 1.55 × 106 km2, respectively. Although the potentially suitable area for desert locusts is contracting, the future threat posed by the desert locust to agricultural production and food security cannot be underestimated, given the combination of maintained breeding areas, frequent extreme weather events, pressure from population growth, and volatile sociopolitical environments. In conclusion, methods such as monitoring and early warning, financial support, regional cooperation, and scientific prevention and control of desert locust plagues should be further implemented.
Guan et al. (2021) The potential habitat of desert locusts is contracting: predictions under climate change scenarios. PeerJ 9:e12311 https://doi.org/10.7717/peerj.12311
Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome
Background Acute respiratory distress syndrome (ARDS) is a common cause of death in ICU patients and its underlying mechanism remains unclear, which leads to its high mortality rate. This study aimed to identify candidate genes potentially implicating in the pathogenesis of ARDS and provide novel therapeutic targets. Methods Using bioinformatics tools, we searched for differentially expressed genes (DEGs) in an ARDS microarray dataset downloaded from the Gene Expression Omnibus (GEO) database. Afterwards, functional enrichment analysis of GO, KEGG, GSEA and WGCNA were carried out to investigate the potential involvement of these DEGs. Moreover, the Protein–protein interaction (PPI) network was constructed and molecular complexes and hub genes were identified, followed by prognosis analysis of the hub genes. Further, we performed qRT-PCR, Western Blot and flow cytometry analysis to detect candidate genes of CCR2 and FPR3 in macrophage model of LPS-induced ARDS and primary alveolar macrophages(AMs). Macrophage chemotaxis was evaluated using Transwell assay. Results DEGs mainly involved in myeloid leukocyte activation, cell chemotaxis, adenylate cyclase-modulating G protein-coupled receptor signaling pathway and cytokine-cytokine receptor interaction. Basing on the constructed PPI network, we identified five molecular complexes and 10 hub genes potentially participating in the pathogenesis of ARDS. It was observed that candidate genes of CCR2 and FPR3 were significantly over-expressed in primary alveolar macrophages from ARDS patients and macrophgae model of LPS-induced ARDS. Moreover, in vitro transwell assay demonstrated that CCR2 and FPR3 down-regulation, respectively, inhibited LPS-triggered macrophage chemotaxis toward CCL2. Finally, a positive correlation between FPR3 and CCR2 expression was confirmed using pearson correlation analysis and Western Blot assay. Conclusions Our study identified CCR2 and FPR3 as the candidate genes which can promote macrophage chemotaxis through a possible interaction between FPR3 and CCL2/CCR2 axis and provided novel insights into ARDS pathogenesis.
Mao et al. (2021) Identification and validation of candidate genes dysregulated in alveolar macrophages of acute respiratory distress syndrome. PeerJ 9:e12312 https://doi.org/10.7717/peerj.12312
Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was 1.3%. Among the 14 DNA methylation CpG sites, seven were related to the prognosis of HCC. HSPA4 was positively related to immune cell infiltration and immune checkpoints (PD-1 and CTLA-4) in HCC. The KEGG pathway enrichment analysis revealed HSPA4 enrichment in antigen processing and presentation together with HSPA8 and HSP90AA1. We verified the value of HSPA4 in the diagnosis and predicting prognosis of HCC. HSPA4 may not only participate in the occurrence and progression but also the immune regulation of HCC. Therefore, HSPA4 can be a potential diagnostic and prognostic biomarker and a therapeutic target for HCC.
Shang et al. (2021) Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma. PeerJ 9:e12315 https://doi.org/10.7717/peerj.12315
Removal or component reversal of local geomagnetic field affects foraging orientation preference in migratory insect brown planthopper Nilaparvata lugens
Background Migratory brown planthopper Nilaparvata lugens (N. lugens) annually migrates to Northeast Asia in spring and returns to Southeast Asia in autumn. However, mechanisms for orientation and navigation during their flight remain largely unknown. The geomagnetic field (GMF) is an important source of directional information for animals (including N. lugens), yet the magnetic compass involved has not been fully identified. Methods Here we assessed the influences of GMF on the foraging orientation preference of N. lugens by removing or component reversal of local GMF. At the same time, we examined the role of iron-sulfur cluster assembly1 (IscA1), a putative component of magnetoreceptor, in the foraging orientation preference of N. lugens under the controlled magnetic fields by RNA silencing (RNAi). Results We found that the near-zero magnetic field (NZMF) or vertical reversal of GMF could lead to N. lugens losing the foraging orientation preference, suggesting that a normal level of GMF, in the way of either intensity or inclination, was essential for the foraging orientation of N. lugens. Moreover, the gene knockdown of IscA1, also affected the foraging orientation preference of N. lugens, pointing out a potential role of IscA1 in the insects’ sensing of variation in the GMF. Discussion These results suggested a foraging orientation preference is associated with the GMF and revealed new insights into the relationship between the IscA1 and magnetosensitivity mechanism in N. lugens.
Zhang et al. (2021) Removal or component reversal of local geomagnetic field affects foraging orientation preference in migratory insect brown planthopper Nilaparvata lugens. PeerJ 9:e12351 https://doi.org/10.7717/peerj.12351
Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury
Background Renal ischemia-reperfusion injury (IRI) is a disease with high incidence rate in kidney related surgery. Micro RNA (miRNA) and transcription factors (TFs) are widely involved in the process of renal IRI through regulation of their target genes. However, the regulatory relationships and functional roles of TFs, miRNAs and mRNAs in the progression of renal IRI are insufficiently understood. The present study aimed to clarify the underlying mechanism of regulatory relationships in renal IRI. Methods Six gene expression profiles were downloaded from Gene Expression Omnibus (GEO). Differently expressed genes (DEGs) and differently expressed miRNAs (DEMs) were identified through RRA integrated analysis of mRNA datasets (GSE39548, GSE87025, GSE52004, GSE71647, and GSE131288) and miRNA datasets (GSE29495). miRDB and TransmiR v2.0 database were applied to predict target genes of miRNA and TFs, respectively. DEGs were applied for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, followed with construction of protein-protein interaction (PPI) network. Then, the TF-miRNA-mRNA network was constructed. Correlation coefficient and ROC analysis were used to verify regulatory relationship between genes and their diagnostic value in GSE52004. Furthermore, in independent mouse RNA-seq datasets GSE98622, human RNA-seq GSE134386 and in vitro, the expression of hub genes and genes from the network were observed and correlation coefficient and ROC analysis were validated. Results A total of 21 DEMs and 187 DEGs were identified in renal IRI group compared to control group. The results of PPI analysis showed 15 hub genes. The TF-miRNA-mRNA regulatory network was constructed and several important pathways were identified and further verified, including Junb-miR-223-Ranbp3l, Cebpb-miR-223-Ranbp3l, Cebpb-miR-21-Ranbp3l and Cebpb-miR-181b-Bsnd. Four regulatory loops were identified, including Fosl2-miR-155, Fosl2-miR-146a, Cebpb-miR-155 and Mafk-miR-25. The hub genes and genes in the network showed good diagnostic value in mice and human. Conclusions In this study, we found 15 hub genes and several TF-miRNA-mRNA pathways, which are helpful for understanding the molecular and regulatory mechanisms in renal IRI. Junb-miR-223-Ranbp3l, Cebpb-miR-223-Ranbp3l, Cebpb-miR-21-Ranbp3l and Cebpb-miR-181b-Bsnd were the most important pathways, while Spp1, Fos, Timp1, Tnc, Fosl2 and Junb were the most important hub genes. Fosl2-miR-155, Fosl2-miR-146a, Cebpb-miR-155 and Mafk-miR-25 might be the negative feedback loops in renal IRI.
Ke et al. (2021) Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury. PeerJ 9:e12375 https://doi.org/10.7717/peerj.12375
Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)
Dispersal flights by the mountain pine beetle have allowed range expansion and major damage to pine stands in western Canada. We asked what the genetic and transcriptional basis of mountain pine beetle dispersal capacity is. Using flight mills, RNA-seq and a targeted association study, we compared strong-flying, weak-flying, and non-flying female beetles from the recently colonized northern end of their range. Nearly 3,000 genes were differentially expressed between strong and weak flying beetles, while weak fliers and nonfliers did not significantly differ. The differentially expressed genes were mainly associated with lipid metabolism, muscle maintenance, oxidative stress response, detoxification, endocrine function, and flight behavior. Three variant loci, two in the coding region of genes, were significantly associated with flight capacity but these genes had no known functional link to flight. Several differentially expressed gene systems may be important for sustained flight, while other systems are downregulated during dispersal and likely to conserve energy before host colonization. The candidate genes and SNPs identified here will inform further studies and management of mountain pine beetle, as well as contribute to understanding the mechanisms of insect dispersal flights.
Shegelski et al. (2021) Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). PeerJ 9:e12382 https://doi.org/10.7717/peerj.12382