Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Novel Biomarkers With Diagnostic Value and Immune Infiltration in Burn Injury

Burn injury is an intractable problem in the field of surgery where screening relevant target genes and exploring pathological mechanisms through bioinformatic methods has become a necessity. Herein, we integrated three burn injury mRNA microarray datasets from the Gene Expression Omnibus database to analyze the hub differentially expressed genes (DEGs) between burn injury patient samples and healthy human samples; we conducted multiple functional enrichment analyses and constructed the protein–protein interaction (PPI) network. Finally, we evaluated the immune infiltration in the burn injury microenvironment. A total of 84 intersection DEGs (32 upregulated and 52 downregulated) were screened in burn injury patients via integrated analyses. Upregulated genes were primarily enriched in regulation of T cell activation, regulation of response to DNA damage stimulus, positive regulation of innate immune response, positive regulation of defense response. We also identified 10 hub genes from the PPI network (CCNB2, MYO10, TTK, POLQ, VASP, TIMP1, CDK16, MMP1, ZYX, and PKMYT1). Next, we found that 22 immune cells were substantially changed during the burn injury by CIBERSORT. In addition, we verified that VASP and POLQ are two novel diagnostic markers in burn processes with high diagnostic efficacy via immunohistochemistry. In summary, we identified several key genes involved in burn injury and provided a favorable basis for elucidating the molecular mechanisms of burn injury through comprehensive bioinformatic analysis.
Impact of Enrichment and Repeated Mixing on Resilience in Pigs

Resilience, the capacity of animals to be minimally affected by a disturbance or to rapidly bounce back to the state before the challenge, may be improved by enrichment, but negatively impacted by a high allostatic load from stressful management procedures in pigs. We investigated the combined effects of diverging environmental conditions from weaning and repeated mixing to create high allostatic load on resilience of pigs. Pigs were either exposed to barren housing conditions (B) from weaning onwards or provided with sawdust, extra toys, regular access to a “play arena” and daily positive human contact (E). Half of the pigs were exposed to repeated mixing (RM) and the other half to one mixing only at weaning (minimal mixing, MM). To assess their resilience, the response to and recovery from a lipopolysaccharide (LPS) sickness challenge and a Frustration challenge were studied. In addition, potential long-term resilience indicators, i.e. natural antibodies, hair cortisol and growth were measured. Some indications of more favorable responses to the challenges in E pigs were found, such as lower serum reactive oxygen metabolite (dROM) concentrations and a smaller area under the curve of dROM after LPS injection. In the Frustration challenge, E pigs showed less standing alert, escape behaviors and other negative behaviors, a tendency for a smaller area under the curve of salivary cortisol and a lower plasma cortisol level at 1 h after the challenge. Aggression did not decrease over mixings in RM pigs and was higher in B pigs than in E pigs. Repeated mixing did not seem to reduce resilience. Contrary to expectations, RM pigs showed a higher relative growth than MM pigs during the experiment, especially in the week of the challenges. Barren RM pigs showed a lower plasma cortisol concentration than barren MM pigs after the LPS challenge, which may suggest that those RM pigs responded less detrimentally than MM pigs. Enriched RM pigs showed a higher level of IgM antibodies binding keyhole limpet hemocyanin (KLH) than enriched MM and barren RM pigs, and RM pigs showed a sharper decline in IgG antibodies binding Bovine Serum Albumin (PC-BSA) over time than MM pigs. Hair cortisol concentrations were not affected by enrichment or mixing. To conclude, enrichment did not enhance the speed of recovery from challenges in pigs, although there were indications of reduced stress. Repeated as opposed to single mixing did not seem to aggravate the negative effects of barren housing on resilience and for some parameters even seemed to reduce the negative effects of barren housing.
Effect of Ferredoxin Receptor FusA on the Virulence Mechanism of Pseudomonas plecoglossicida

Pseudomonas plecoglossicida is an aerobic Gram-negative bacterium, which is the pathogen of “Visceral white spot disease” in large yellow croaker. P. plecoglossicida is a temperature-dependent bacterial pathogen in fish, which not only reduces the yield of large yellow croaker but also causes continuous transmission of the disease, seriously endangering the healthy development of fisheries. In this study, a mutant strain of fusA was constructed using homologous recombination technology. The results showed that knockout of P. plecoglossicida fusA significantly affected the ability of growth, adhesion, and biofilm formation. Temperature, pH, H2O2, heavy metals, and the iron-chelating agent were used to treat the wild type of P. plecoglossicida; the results showed that the expression of fusA was significantly reduced at 4°C, 12°C, and 37°C. The expression of fusA was significantly increased at pH 4 and 5. Cu2+ has a significant inducing effect on the expression of fusA, but Pb2+ has no obvious effect; the expression of fusA was significantly upregulated under different concentrations of H2O2. The expression of the fusA gene was significantly upregulated in the 0.5~4-μmol/l iron-chelating agent. The expression level of the fusA gene was significantly upregulated after the logarithmic phase. It was suggested that fusA included in the TBDR family not only was involved in the transport of ferredoxin but also played important roles in the pathogenicity and environment adaptation of P. plecoglossicida.
Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways

Bioremediation has been considered as a promising method for recovering chemical polluted environments. Here Shewanella decolorationis strain Ni1-3 showed versatile abilities in bioremediation. To improve the bioremediation activity, RNA polymerase (RNAP) mutations of strain Ni1-3 were screened. Eleven mutants were obtained, of which mutant #40 showed enhanced Amaranth (AMR) degradation capacity, while mutant #21 showed defected capacity in AMR degradation but greatly enhanced capacity in cathodic metal leaching which is three to four times faster than that of the wild-type (WT) strain Ni1-3, suggesting that different pathways were involved in these two processes. Transcriptional profiling and gene co-expression networks between the mutants (i.e., #40 and #22) and the WT strain disclosed that the non-CymA-Mtr but cytochrome b- and flavin-oxidoreductase-dominated azo dye degradation pathways existed in S. decolorationis, which involved key proteins TorC, TorA, YceJ, YceI, Sye4, etc. Furthermore, the involvement of TorA was verified by trimethylamine N-oxide reduction and molybdenum enzyme inhibitory experiments. This study clearly demonstrates that RNAP mutations are effective to screen active microbial candidates in bioremediation. Meanwhile, by clarifying the novel gene co-expression network of extracellular electron transfer pathways, this study provides new insights in azo dye degradation and broadens the application of Shewanella spp. in bioremediation as well.
Polymagmatic Glaciovolcanism: Cracked Mountain Tuya, Canadian Cascades

Monogenetic volcanoes are characterized as having no temporal break in eruptive activity and are often assumed to have a simple (singular) magmatic plumbing system. However, recent studies on monogenetic systems have started to recover evidence of complexities within the magma-crustal dynamics. Here we investigate Cracked Mountain (CM), a 401 ± 38 ka glaciovolcanic basaltic landform in southwest, British Columbia, Canada. The volcano covers an area of ∼1.5 km2, has an eruptive volume of ∼0.18 km3, and comprises lapilli tuff, breccia, peperite, pillow and sheet lava, and dykes with no erosional surfaces present between the stratigraphic successions. The paleomagnetic signature of all volcanic lithofacies records a single-pole direction and, in conjunction with stratigraphic evidence, implies a monogenetic eruption. We establish that the Cracked Mountain volcano was fed by two separate crustally-stored magmas (i.e., polymagmatic), each characterized by a unique phenocryst assemblage indicative of different pre-eruptive storage conditions. The first mineral assemblage is an olivine-and-plagioclase phyric (OP) suite, and the second is an olivine-plagioclase-and-augite phyric (OPA) suite. The major-element geochemical compositions of the two petrographic suites vary slightly, with OPA samples higher in SiO2 and total-alkali contents than OP. The two magmas have similar rare earth (REE) trace element signatures, suggesting the same mantle source. We use thermodynamic modeling (Rhyolite-MELTS) to show that the OP suite derives from magma stored at depths <6 km (< 2 kbar) and temperatures of 1240–1155°C. In contrast, the OPA magmas crystallized at depths between 7–9 km (∼2–2.5 kbar) at 1,250–1,150°C prior to eruption. Both magmas are shown to be nearly “dry” having less than 0.5 H2O wt% in their respective systems. We use Pearce Element Ratios (PER) to show that the chemical variations within and between the two CM magmas are controlled solely by the crystal fractionation of two phenocryst assemblages that underwent syn-eruptive mixing. This study concludes that the polymagmatic plumbing system at Cracked Mountain shows similar complexities to other global investigations of monogenetic volcanoes. Lastly, we propose a causal link between the crustal dynamics of magma systems and the impact of crustal loading and unloading during cycles of glaciation.
A Study of Subliminal Emotion Classification Based on Entropy Features

Electroencephalogram (EEG) has been widely utilized in emotion recognition. Psychologists have found that emotions can be divided into conscious emotion and unconscious emotion. In this article, we explore to classify subliminal emotions (happiness and anger) with EEG signals elicited by subliminal face stimulation, that is to select appropriate features to classify subliminal emotions. First, multi-scale sample entropy (MSpEn), wavelet packet energy (Ei), and wavelet packet entropy (WpEn) of EEG signals are extracted. Then, these features are fed into the decision tree and improved random forest, respectively. The classification accuracy with Ei and WpEn is higher than MSpEn, which shows that Ei and WpEn can be used as effective features to classify subliminal emotions. We compared the classification results of different features combined with the decision tree algorithm and the improved random forest algorithm. The experimental results indicate that the improved random forest algorithm attains the best classification accuracy for subliminal emotions. Finally, subliminal emotions and physiological proof of subliminal affective priming effect are discussed.
Crucial Roles of microRNA-16-5p and microRNA-27b-3p in Ameloblast Differentiation Through Regulation of Genes Associated With Amelogenesis Imperfecta

Amelogenesis imperfecta is a congenital disorder within a heterogeneous group of conditions characterized by enamel hypoplasia. Patients suffer from early tooth loss, social embarrassment, eating difficulties, and pain due to an abnormally thin, soft, fragile, and discolored enamel with poor aesthetics and functionality. The etiology of amelogenesis imperfecta is complicated by genetic interactions. To identify mouse amelogenesis imperfecta-related genes (mAIGenes) and their respective phenotypes, we conducted a systematic literature review and database search and found and curated 70 mAIGenes across all of the databases. Our pathway enrichment analysis indicated that these genes were enriched in tooth development-associated pathways, forming four distinct groups. To explore how these genes are regulated and affect the phenotype, we predicted microRNA (miRNA)-gene interaction pairs using our bioinformatics pipeline. Our miRNA regulatory network analysis pinpointed that miR-16-5p, miR-27b-3p, and miR-23a/b-3p were hub miRNAs. The function of these hub miRNAs was evaluated through ameloblast differentiation assays with/without the candidate miRNA mimics using cultured mouse ameloblast cells. Our results revealed that overexpression of miR-16-5p and miR-27b-3p, but not miR-23a/b-3p, significantly inhibited ameloblast differentiation through regulation of mAIGenes. Thus, our study shows that miR-16-5p and miR-27b-3p are candidate pathogenic miRNAs for amelogenesis imperfecta.
The Relationships of Sleep Duration and Inconsistency With the Athletic Performance of Collegiate Soft Tennis Players

We evaluated the relationships of daily sleep duration and inconsistency with soft tennis competitive performance among 15 healthy collegiate soft tennis players (13 male, 2 female, mean age = 19.7 ± 0.8 years, height = 170.8 ± 7.3 cm, weight = 60.3 ± 5.6 kg, soft tennis experience = 8.7 ± 2.0 years). Sleep duration and inconsistency were determined by a 50-day sleep diary, which recorded sleep and wake times of sleep. Soft tennis athletic performance was evaluated by a service and baseline stroke accuracy test and the spider run test. Mean sleep duration was 7.4 ± 1.7 h. No correlation was found between long-term mean sleep duration and athletic performance. But inconsistency in sleep duration (SD of sleep duration) was inversely correlated with service score after controlling for soft tennis experience and sex (r = −0.56, p = 0.046). There was no significant relationship between sleep inconsistency and other athletic performance. This result indicates that reducing the instability of sleep duration (i.e., sleep regular hours) in the long-term may have a positive effect on soft tennis players’ service performance. Although participants’ current mean sleep duration (7.4 h) was not as sufficient as the recommendation in sleep extension experiments (9–10 h), it revealed the importance for athletes to maintain regular sleep in daily life.
Induced Synthesis of Mycolactone Restores the Pathogenesis of Mycobacterium ulcerans In Vitro and In Vivo

Mycobacterium ulcerans is the causative agent of Buruli ulcer (BU), the third most common mycobacterial infection. Virulent M. ulcerans secretes mycolactone, a polyketide toxin. Most observations of M. ulcerans infection are described as an extracellular milieu in the form of a necrotic ulcer. While some evidence exists of an intracellular life cycle for M. ulcerans during infection, the exact role that mycolactone plays in this process is poorly understood. Many previous studies have relied upon the addition of purified mycolactone to cell-culture systems to study its role in M. ulcerans pathogenesis and host-response modulation. However, this sterile system drastically simplifies the M. ulcerans infection model and assumes that mycolactone is the only relevant virulence factor expressed by M. ulcerans. Here we show that the addition of purified mycolactone to macrophages during M. ulcerans infection overcomes the bacterial activation of the mechanistic target of rapamycin (mTOR) signaling pathway that plays a substantial role in regulating different cellular processes, including autophagy and apoptosis. To further study the role of mycolactone during M. ulcerans infection, we have developed an inducible mycolactone expression system. Utilizing the mycolactone-deficient Mul::Tn118 strain that contains a transposon insertion in the putative beta-ketoacyl transferase (mup045), we have successfully restored mycolactone production by expressing mup045 in a tetracycline-inducible vector system, which overcomes in-vitro growth defects associated with constitutive complementation. The inducible mycolactone-expressing bacteria resulted in the establishment of infection in a murine footpad model of BU similar to that observed during the infection with wild-type M. ulcerans. This mycolactone inducible system will allow for further analysis of the roles and functions of mycolactone during M. ulcerans infection.
ERBB2 Mutations as Potential Predictors for Recurrence in Colorectal Serrated Polyps by Targeted Next-Generation Sequencing

Background Follow-up guidelines for serrated polyps (SPs) are mainly based on factors such as histology and size with limited evidence. The underlying genomic mechanism of SPs in relation to recurrence risks is utterly unknown. Methods We applied targeted next-generation sequencing (NGS) approach on two groups of SPs [polyp-relapsed SPs (PRSPs) vs. polyp-free SPs (PFSPs)] based on the surveillance outcomes to compare differences of DNA variants in 71 colorectal cancer-associated genes. A multicenter validation cohort was established longitudinally from 2016 to 2019 to confirm the relevant results. Results Among the 96 NGS samples, at least one mutant after filtration was detected in 90 samples (94%). Molecular profiling presented BRAF, KRAS, and APC as top 3 mutated genes. FBXW7, MSH2, and ERBB2 might be recurrence-relevant, while DMD, BRCA1, and BRCA2 might be negatively correlated with recurrence. Notably, ERBB2 mutants (R678Q and V842I) (n = 5) had higher risks of polyp recurrence than the wild types (n = 85), with a median polyp-free interval of 15 months compared to 26 months [P < 0.001; hazard ratio (HR) = 4.9; 95% confidence interval (CI) = 1.9–12.8]. Furthermore, a multicenter cohort composed by 321 SPs verified that ERBB2-mutated SPs had increased risks of polyp recurrence (P < 0.001; HR = 3.7; 95% CI = 2.3–6.0) and advanced neoplastic lesion (ANL) recurrence (P < 0.001; HR = 10.0; 95% CI = 2.7–36.9) compared with wild-type SPs, respectively. Conclusions Our results are emphasizing that SP individuals with ERBB2 mutants are at higher risks of subsequent colorectal neoplasms. ERBB2 mutants might work as facilitated markers for prediction of high-risk SPs and might implicate a potential mechanism in the serrated pathway to colorectal carcinoma (CRC).
Fatigue Modeling as Related to Flexible Pavement Design

ABSTRACT A literature study of rheological and fatigue modeling of asphalt mixtures is presented. Theoretical aspects on structural modeling, rheological behavior and the fatigue integration in design procedures are reviewed. In principle, pavement design methods can be categorized in three broad groups: empirical, semi-mechanistic and fully mechanistic methods. Pavement design is generally performed using semi-mechanistic methods comprising analytical or numerical structural response models and deterioration modeling based on transfer functions and shift factors. In the case of fatigue deterioration, several approaches have been elaborated e.g. classical models, fracture mechanics and damage mechanics. The approaches differ regarding theoretical foundation and evaluation methods used. Recognizing significant limitations concerning theoretical basis as well as lack of empirical support for current design methods, a shift in paradigm from semi-empirical methods towards more advanced fully mechanistic methods have been initiated. According to this approach, improved pavements are achieved by appropriate design methods which are capable of predicting fatigue resistance in the actual pavement environment, and thus taking into account complex stress conditions, influence of temperature and material characteristics, such as aging and healing.
BOLD Monitoring in the Neural Simulator ANNarchy

Multi-scale network models that simultaneously simulate different measurable signals at different spatial and temporal scales, such as membrane potentials of single neurons, population firing rates, local field potentials, and blood-oxygen-level-dependent (BOLD) signals, are becoming increasingly popular in computational neuroscience. The transformation of the underlying simulated neuronal activity of these models to simulated non-invasive measurements, such as BOLD signals, is particularly relevant. The present work describes the implementation of a BOLD monitor within the neural simulator ANNarchy to allow an on-line computation of simulated BOLD signals from neural network models. An active research topic regarding the simulation of BOLD signals is the coupling of neural processes to cerebral blood flow (CBF) and cerebral metabolic rate of oxygen (CMRO2). The flexibility of ANNarchy allows users to define this coupling with a high degree of freedom and thus, not only allows to relate mesoscopic network models of populations of spiking neurons to experimental BOLD data, but also to investigate different hypotheses regarding the coupling between neural processes, CBF and CMRO2 with these models. In this study, we demonstrate how simulated BOLD signals can be obtained from a network model consisting of multiple spiking neuron populations. We first demonstrate the use of the Balloon model, the predominant model for simulating BOLD signals, as well as the possibility of using novel user-defined models, such as a variant of the Balloon model with separately driven CBF and CMRO2 signals. We emphasize how different hypotheses about the coupling between neural processes, CBF and CMRO2 can be implemented and how these different couplings affect the simulated BOLD signals. With the BOLD monitor presented here, ANNarchy provides a tool for modelers who want to relate their network models to experimental MRI data and for scientists who want to extend their studies of the coupling between neural processes and the BOLD signal by using modeling approaches. This facilitates the investigation and model-based analysis of experimental BOLD data and thus improves multi-scale understanding of neural processes in humans.
Ag-Incorporated Polydopamine/Tannic Acid Coating on Titanium With Enhanced Cytocompatible and Antibacterial Properties

Titanium (Ti) and its alloys are the most commonly used materials for bone implants. However, implant failure often happens due to bacterial infection. Developing antibacterial coatings on Ti implants is an effective strategy. Dopamine and tannic acid were cross-linked to form coating on Ti through Michael addition and Schiff base reaction. In addition, the Ag ions were grafted on the coating by the redox reaction of phenolic hydroxyl groups. Thus, an Ag-incorporated polydopamine/tannic acid coating was prepared on Ti substrate. SEM, EDS, water contact angle, FTIR, and XRD results demonstrated that the coating was formed on Ti successfully. The antibacterial activity of the coating against Gram-negative E. coli was examined, and the cytotoxicity of the coating was investigated by mouse fibroblast cells. The improvement of hydrophilicity, good cytocompatibility, and antibacterial effectiveness indicates that the coating has potential to surface modification of Ti implants.