Rap1GAP exacerbates myocardial infarction by regulating the AMPK/SIRT1/NF-κB signaling pathway.

Rap1 GTPase-activating protein (Rap1GAP) is an important tumor suppressor. The purpose of this study was to investigate the role of Rap1GAP in myocardial infarction (MI) and its potential mechanism. Left anterior descending coronary artery ligation was performed on cardiac-specific Rap1GAP conditional knockout (Rap1GAP-CKO) mice and control mice with MI. Seven days after MI, Rap1GAP expression in the hearts of control mice peaked, the expression of proapoptotic markers (Bax and cleaved caspase-3) increased, the expression of antiapoptotic factors (Bcl-2) decreased, and the expression of the inflammatory factors IL-6 and TNF-α increased; thus, apoptosis occurred, inflammation, infarct size, and left ventricular dysfunction increased, while the heart changes caused by MI were alleviated in Rap1GAP-CKO mice. Mouse heart tissue was obtained for transcriptome sequencing, and gene set enrichment analysis (GSEA) was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We found that Rap1GAP was associated with the AMPK and NF-κB signaling pathways and that Rap1GAP inhibited AMPK/SIRT1 and activated the NF-κB signaling pathway in model animals. Similar results were observed in primary rat myocardial cells subjected to oxygen-glucose deprivation (OGD) to induce ischemia and hypoxia. Activating AMPK with the AMPK activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) reversed the damage caused by Rap1GAP overexpression in cardiomyocytes. In addition, the coimmunoprecipitation results showed that exogenous Rap1GAP interacted with AMPK. Rap1GAP was verified to regulate the AMPK SIRT1/NF-κB signaling pathway and exacerbate the damage to myocardial cells caused by ischemia and hypoxia. In conclusion, our results suggest that Rap1GAP promotes MI by modulating the AMPK/SIRT1/NF-κB signaling pathway and that Rap1GAP may be a therapeutic target for MI treatment in the future.

Using simulated microhaplotype genotyping data to evaluate the value of machine learning algorithms for inferring DNA mixture contributor numbers.

Inferring the number of contributors (NoC) is a crucial step in interpreting DNA mixtures, as it directly affects the accuracy of the likelihood ratio calculation and the assessment of evidence strength. However, obtaining the correct NoC in complex DNA mixtures remains challenging due to the high degree of allele sharing and dropout. This study aimed to analyze the impact of allele sharing and dropout on NoC inference in complex DNA mixtures when using microhaplotypes (MH). The effectiveness and value of highly polymorphic MH for NoC inference in complex DNA mixtures were evaluated through comparing the performance of three NoC inference methods, including maximum allele count (MAC) method, maximum likelihood estimation (MLE) method, and random forest classification (RFC) algorithm. In this study, we selected the top 100 most polymorphic MH from the Southern Han Chinese (CHS) population, and simulated over 40 million complex DNA mixture profiles with the NoC ranging from 2 to 8. These profiles involve unrelated individuals (RM type) and related pairs of individuals, including parent-offspring pairs (PO type), full-sibling pairs (FS type), and second-degree kinship pairs (SE type). Our results indicated that how the number of detected alleles in DNA mixture profiles varied with the markers' polymorphism, kinship's involvement, NoC, and dropout settings. Across different types of DNA mixtures, the MAC and MLE methods performed best in the RM type, followed by SE, FS, and PO types, while RFC models showed the best performance in the PO type, followed by RM, SE, and FS types. The recall of all three methods for NoC inference were decreased as the NoC and dropout levels increased. Furthermore, the MLE method performed better at low NoC, whereas RFC models excelled at high NoC and/or high dropout levels, regardless of the availability of a priori information about related pairs of individuals in DNA mixtures. However, the RFC models which considered the aforementioned priori information and were trained specifically on each type of DNA mixture profiles, outperformed RFC_ALL model that did not consider such information. Finally, we provided recommendations for model building when applying machine learning algorithms to NoC inference.

Stimulus-responsive biomaterials for Helicobacter pylori eradication.

BACKGROUND: Helicobacter pylori (H. pylori), the only bacterium classified as a type I (definite) carcinogen, is strongly associated with the development of gastric inflammation and adenocarcinoma. It infects the stomach of approximately half of the global population, equivalent to nearly 4.4 billion people. However, due to physiological barriers in the stomach, microbial barriers and increased antibiotic resistance, the therapeutic efficiency of standard antibiotic therapy is limited and cannot meet the clinical needs in some areas. Combining stimulus-responsive biomaterials with certain stimuli is an emerging antibacterial strategy. Stimulus-responsive biomaterials can respond to chemical, biological or physical cues in the environment with corresponding changes in their own properties and functions, highlighting a more intelligent, targeting and efficient aspect for H. pylori therapy. AIM OF REVIEW: This review describes the critical obstacles in the current treatment of H. pylori, summarizes the recent advances in stimulus-responsive biomaterials against H. pylori by elucidating their working mechanisms and antibacterial performances under different types of stimuli (pH, enzymes, light, magnetic and ultrasound irradiations), and attempts to analyze the future prospects of such smart biomaterial for H. pylori eradication. Key Scientific Concepts of Review: Any characteristic property or change in the biomilieu at the H. pylori infected site (endogenous stimuli) or specific iatrogenic conditions in vitro (exogenous stimuli) can act as cues to activate or potentiate the antibacterial activity of responsive biomaterials. The responsiveness of these materials to endogenous stimuli enhances antimicrobial targeting, and makes physiological barriers that would otherwise hinder conventional H. pylori therapies a key factor in facilitating antibacterial effects. The responsiveness to exogenous stimuli greatly prolongs the action time of antimicrobial materials and pinpoints the site of infection, thereby reducing toxic side effects. These findings pave the way for the development of more precise and effective anti-H. pylori treatment.

Dimethylaminododecyl Methacrylate-Incorporated Dental Materials Could Be the First Line of Defense against Helicobacter pylori.

Oral cavity is an essential reservoir for H. pylori. We aimed to investigate the antibacterial effects of dimethylaminododecyl methacrylate (DMADDM) against H. pylori. Modified giomers were prepared by introducing 0%, 1.25% and 2.5% DMADDM monomers. Broth microdilution assay, spot assay, Alamer Blue assay, PMA-qPCR, crystal violet staining, scanning electron microscopy observation and live/dead bacterial staining were performed to evaluate the antibacterial and antibiofilm effects of DMADDM and modified giomers in vitro. Urease assay, qPCR, hematoxylin-eosin staining and ELISA were performed to evaluate the inflammation levels and colonization of H. pylori in vivo. In vitro experiments indicated that the minimum inhibitory concentration and minimum bactericidal concentration of DMADDM were 6.25 µg/mL and 25 µg/mL, respectively. It inhibited H. pylori in a dose- and time-dependent manner, and significantly reduced the expression of cagA, vacA, flaA and ureB. DMADDM-modified giomers inhibited the formation of H. pylori biofilm and reduced live cells within it. In vivo experiments confirmed that the pretreatment with DMADDM-modified dental resin effectively reduced the gastric colonization of oral-derived H. pylori, suppressed systemic and local gastric inflammation. DMADDM monomers and DMADDM-modified giomers possessed excellent antibacterial and antibiofilm effects on H. pylori. Pretreatment with DMADDM-modified giomers significantly inhibited the gastric infection by H. pylori.

Evaluation of large-scale highly polymorphic microhaplotypes in complex DNA mixtures analysis using RMNE method.

DNA mixture interpretation is one of the most challenging problems in forensics. Complex DNA mixtures are more difficult to analyze when there are more than two contributors or related contributors. Microhaplotypes (MHs) are polymorphic genetic markers recently discovered and employed in DNA mixture analysis. However, the evidentiary interpretation of the MH genotyping data needs more debate. The Random Man Not Excluded (RMNE) method analyzes DNA mixtures without using allelic peak height data or the number of contributors (NoC) assumptions. This study aimed to assess how well RMNE interpreted mixed MH genotyping data. We classified the MH loci from the 1000 Genomes Project database into groups based on their Ae values. Then we performed simulations of DNA mixtures with 2-10 unrelated contributors and DNA mixtures with a pair of sibling contributors. For each simulated DNA mixture, incorrectly included ratios were estimated for three types of non-contributors: random men, parents of contributors, and siblings of contributors. Meanwhile, RMNE probability was calculated for contributors and three types of non-contributors, allowing loci mismatch. The results showed that the MH number, the MH Ae values, and the NoC affected the RMNE probability of the mixture and the incorrectly included ratio of non-contributors. When there were more MHs, MHs with higher Ae values, and a mixture with less NoC, the RMNE probability, and the incorrectly included ratio decreased. The existence of kinship in mixtures complicated the mixture interpretation. Contributors' relatives as non-contributors and related contributors in the mixture increased the demands on the genetic markers to identify the contributors correctly. When 500 highly polymorphic MHs with Ae values higher than 5 were used, the four individual types could be distinguished according to the RMNE probabilities. This study reveals the promising potential of MH as a genetic marker for mixed DNA interpretation and the broadening of RMNE as a parameter indicating the relationship of a specific individual with a DNA mixture in the DNA database search.

FST estimates of 94 populations in China based on STR markers.

The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the FST values. Thus, FST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific FST values of each population, the overall FST values of each province, each region, and the whole country, and the locus-specific FST values of different loci were calculated. The LRs using different allele frequencies and different FST values were compared based on the combination of simulated genotypes. As a result, the FST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after FST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding FST values can make the LRs more accurate and reasonable.

Characterizing the amplification of STR markers in multiplex polymerase chain displacement reaction using massively parallel sequencing.

Polymerase chain displacement reaction (PCDR) showed advantages in forensic low-template DNA analysis with improved amplification efficiency, higher allele detection capacity, and lower stutter artifact than PCR. However, characteristics of STR markers after PCDR amplification remain unclarified for the limited resolving power of capillary electrophoresis (CE). This issue can be addressed by massively parallel sequencing (MPS) technology with higher throughput and discriminability. Here, we developed a multiplex PCDR system including 24 STRs and amelogenin. In addition, a PCR reference was established for comparison. After amplification, products were subjected to PCR-free library construction and sequenced on the Illumina NovaSeq system. We implemented a sequence-matching pipeline to separate different amplicon types of PCDR products from the combination of primers. In the sensitivity test, the PCDR multiplex obtained full STR profiles with as low as 125 pg 2800M control DNA. Based on that, single-source DNA samples were tested. First, highly concordant genotypes were observed among the PCDR multiplex, the PCR reference, and CE-based STR kits. Next, read counts of different PCDR amplicon types were investigated, showing a relative abundance of 78:12:12:1 for the shortest amplicon S, the two medium amplicons M1 and M2, and the longest amplicon L. We also analyzed the stutter artifacts for distinct amplicon types, and the results revealed the reduction of N - 1 and N - 2 contraction stutters, and the increase of N + 1 and N + 2 elongation stutters in PCDR samples. Moreover, we confirmed the feasibility of PCDR for amplifying degraded DNA samples and unbalanced DNA mixtures. Compared to the previous proof of principle study, our work took a further step to characterize the complete profile of STR markers in the PCDR context. Our results suggested that the PCDR-MPS workflow is an effective approach for forensic STR analysis. Corresponding findings in this study may help the development of PCDR-based assays and probabilistic methods in future studies.

Pulmonary Embolism After in vitro Fertilization and Cesarean Section: Two Case Reports and Brief Review of the Literature.

This paper reports two cases of postpartum pulmonary embolism in Taicang First People's Hospital affiliated to Soochow University. They share many similarities in age, fertilization way, birthing method, incidence of pulmonary embolism, treatment and prognosis. The main purpose is to inspire the current maternal PTE risk assessment, diagnosis and treatment, as well as to explore the existing limitations and problems.

Evaluation of Prognosis and Risk of Death by Neutrophil/Lymphocyte Ratio, C-Reactive Protein/Albumin Ratio and Plasma D-Dimer in Patients with Pulmonary Thromboembolism.

OBJECTIVE: To investigate the relationship between neutrophil/lymphocyte ratio, C-reactive protein/albumin ratio, plasma D-dimer and prognosis in patients with pulmonary thromboembolism, and to evaluate the risk of death. METHODS: We retrospectively analyzed peripheral hematology and coagulation-related indicators of 362 pulmonary thromboembolism patients and 32 normal people, and the differences between the patients and control group and between good and poor prognosis groups were compared. And we analyzed and compared separate detection and combined detection of neutrophil/lymphocyte ratio, C-reactive protein/albumin ratio and D-dimer on the efficiency of risk of death in patients. RESULTS: ① Neutrophil/lymphocyte ratio of pulmonary thromboembolism patients was 8.96±1.94, significantly higher than that of control group 1.76±0.53 (t=2.4281, P<0.05). C-reactive protein/albumin ratio was 2.13±2.08, significantly higher than 0.03±0.01 in control group (t=20.7736, P<0.01). D-dimer was 9.69±8.61mg/L, significantly higher than 0.20±0.11mg/L in control group (t=3.0066, P<0.01). ② Hemoglobin, lymphocyte, albumin and lymphocyte/monocyte ratio in patients with good prognosis were significantly lower than those in poor prognosis group, while white blood cell, C-creative protein, neutrophil, C-reactive protein/albumin ratio, neutrophil/lymphocyte ratio and D-dimer were significantly lower than those in poor prognosis group (P all <0.05). ③ Regression analysis showed that neutrophil/lymphocyte ratio (P=0.007), C-reactive protein/albumin ratio (P=0.010) and D-dimer (P=0.003) were independent prognostic factors for pulmonary thromboembolism. ④ In assessing the risk of death of patients, D-dimer alone had the highest sensitivity (93.1%), and C-reactive protein/albumin ratio alone had the highest specificity (68.8%). The combined detection of these three indicators had higher sensitivity (86.2%) and higher specificity (67.6%) at the same time. ⑤ The area under receiver operating characteristic curve for combined detection of neutrophil/lymphocyte ratio, C-reactive protein/albumin ratio and D-dimer was the largest (up to 0.821). CONCLUSION: Patients with pulmonary thromboembolism highly expressed in neutrophil/lymphocyte ratio, C-reactive protein/albumin ratio and D-dimer. The combined detection of these three indicators can improve the assessment efficacy of the risk of death in patients with pulmonary thromboembolism.

Cone beam computed tomography analysis of accessory canals of the canalis sinuosus: A prevalent but often overlooked anatomical variation in the anterior maxilla.

STATEMENT OF PROBLEM: Accessory canals of the canalis sinuosus, a bony canal carrying the anterior superior alveolar nerve and vessels, can often be present but overlooked in the anterior maxilla. Dental implant placement in this area may damage neurovascular branches if this anatomic variation is not carefully identified, resulting in unexpected complications. PURPOSE: The purpose of this retrospective study was to identify accessory canals of the canalis sinuosus and analyze their relationship to the terminal canalis sinuosus and anterior maxilla in Chinese patients to provide a warning for surgeons operating in the anterior maxilla. MATERIAL AND METHODS: Cone beam computed tomography (CBCT) scans of 1007 Chinese patients were examined to identify the prevalence and size of accessory canals with at least 1.0-mm diameter. Axial position of this canal was classified referring to the nasal cavity and adjacent teeth. Its sagittal position was determined by the distance from the bifurcation site of canalis sinuosus to the buccal alveolar crest and the distance from the canal opening to the palatal alveolar crest. Diameter of the terminal canalis sinuosus, distance from the terminal canalis sinuosus to the buccal alveolar crest, and anterior maxillary volume were measured on all scans. Binary logistic regression and the Spearman rank correlation coefficient were used for prevalence and diameter analysis. RESULTS: The prevalence of the accessory canal was 36.9%, positively correlated the anterior maxillary volume (OR 1.408) and negatively correlated with the distance from the terminal canalis sinuosus to the buccal alveolar crest (OR 0.921). Average diameter of such canal was 1.1 ±0.1 mm, significantly higher in men, positively correlated with the diameter of terminal canalis sinuosus (rs=0.163) and the distance from the canal opening to the palatal alveolar crest (rs=0.192). All accessory canals started below the buccal cortical bone, 19.3 ±2.7 mm away from the buccal alveolar crest. There were 61.9% accessory canals opened between the central and the lateral incisors. Openings here and in the central incisor region were closer to the alveolar crest than that between the lateral incisor and the canine (P<.05). CONCLUSIONS: Accessory canals of the canalis sinuosus have high prevalence in the anterior maxilla in a Chinese population. Large anterior maxillary volume has been demonstrated as a risk factor associated with the presence of such canals. The region between the central and the lateral incisors was a predominant location. Openings in this region were closer to the alveolar crest than those between the lateral incisor and the canine.

The Antibacterial Effect of Graphene Oxide on Streptococcus mutans.

To select the optimal graphene oxide (GO) for anticaries dental applications, aqueous dispersions containing GO nanosheets with various oxygen-containing functional groups were prepared and characterized using atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. The antibacterial effect towards Streptococcus mutans (S. mutans) in both planktonic and biofilm forms was studied by colony forming units (CFU) counting, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reduction assay, live/dead fluorescent staining, and confocal laser scanning microscopy (CLSM) observation. The oxidation capacity of different GO nanosheets was examined by 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) assay and in vitro glutathione (GSH) oxidation assay. The results indicated that GO exerted strong antibacterial activities in a concentration-dependent manner towards S. mutans in both planktonic and biofilm forms. The minimum bactericidal concentration (MBC) was 40 µg/mL for planktonic S. mutans. When the concentration was higher than 80 µg/mL, 80% of the bacteria in the biofilms were devitalized. GO nanosheets with more oxygen-containing functional groups exerted higher toxicity at low concentrations. The functional groups of GO played a crucial role in its antibacterial outcome.

The inhibitory effect of carboxyl-terminated polyamidoamine dendrimers on dentine host-derived matrix metalloproteinases in vitro in an etch-and-rinse adhesive system.

The biomimetic remineralization of collagen fibrils has increased interest in restoring the demineralized dentine generated by dental caries. Carboxyl-terminated polyamidoamine dendrimers (PAMAM-COOH), hyperbranched polymeric macromolecules, can act as non-collagenous proteins to induce biomimetic remineralization on a dentine organic matrix. However, in vivo remineralization is an extremely time-consuming process; before complete remineralization, demineralized dentine collagen fibrils are susceptible to degradation by host-derived matrix metalloproteinases (MMPs). Therefore, we examined the effect of fourth-generation PAMAM-COOH (G4-PAMAM-COOH) on the collagenolytic activities of endogenous MMPs, the interaction between G4-PAMAM-COOH and demineralized dentine collagen and the influence of G4-PAMAM-COOH pre-treatment on resin-dentine bonding. G4-PAMAN-COOH not only inhibited exogenous soluble rhMMP9 but also hampered the proteolytic activities of dentine collagen-bound MMPs. Cooperated with the results of G4-PAMAM-COOH absorption and desorption, FTIR spectroscopy provided evidence for the exclusive electrostatic interaction rather than hydrogen or covalent bonding between G4-PAMAM-COOH and dentine collagen. Furthermore, G4-PAMAM-COOH pre-treatment showed no damage to resin-dentine bonding because it did not significantly decrease the elastic modulus of the demineralized dentine, degree of conversion, penetration of the adhesive into the dentinal tubules or ultimate tensile strength. Thus, G4-PAMAM-COOH can effectively inactivate MMPs, retard the enzymolysis of collagen by MMPs and scarcely influence the application of resin-dentine bonding.

Novel Biomedical Applications of Crosslinked Collagen.

Collagen is one of the most useful biopolymers because of its low immunogenicity and biocompatibility. The biomedical potential of natural collagen is limited by its poor mechanical strength, thermal stability, and enzyme resistance, but exogenous chemical, physical, or biological crosslinks have been used to modify the molecular structure of collagen to minimize degradation and enhance mechanical stability. Although crosslinked collagen-based materials have been widely used in biomedicine, there is no standard crosslinking protocol that can achieve a perfect balance between stability and functional remodeling of collagen. Understanding the role of crosslinking agents in the modification of collagen performance and their potential biomedical applications are crucial for developing novel collagen-based biopolymers for therapeutic gain.