Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of tonB Gene on the Virulence of Pseudomonas plecoglossicida and the Immune Response of Epinephelus coioides

Pseudomonas plecoglossicida is the causative agent of “visceral white spot disease” in cultured fish and has resulted in serious economic losses. tonB gene plays a crucial role in the uptake of nutrients from the outer membranes in Gram-negative bacteria. The previous results of our lab showed that the expression of tonB gene of P. plecoglossicida was significantly upregulated in the spleens of infected Epinephelus coioides. To explore the effect of tonB gene on the virulence of P. plecoglossicida and the immune response of E. coioides, tonB gene of P. plecoglossicida was knocked down by RNAi; and the differences between the wild-type strain and the tonB-RNAi strain of P. plecoglossicida were investigated. The results showed that all of the four mutants of P. plecoglossicida exhibited significant decreases in mRNA of tonB gene, and the best knockdown efficiency was 94.0%; the survival rate of E. coioides infected with the tonB-RNAi strain was 20% higher than of the counterpart infected with the wild strain of P. plecoglossicida. Meanwhile, the E. coioides infected with the tonB-RNAi strain of P. plecoglossicida carried less pathogens in the spleen and less white spots on the surface of the spleen; compared with the wild-type strain, the motility, chemotaxis, adhesion, and biofilm formation of the tonB-RNAi strain were significantly attenuated; the transcriptome data of E. coioides infected with the tonB-RNAi strain were different from the counterpart infected with the wild strain of P. plecoglossicida; the antigen processing and presentation pathway and the complement and coagulation cascade pathway were the most enriched immune pathways. The results indicated that tonB was a virulence gene of P. plecoglossicida; tonB gene was involved in the regulation of motility, chemotaxis, adhesion, and biofilm formation; tonB gene affected the immune response of E. coioides to P. plecoglossicida infection.
Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113

According to the sit-and-wait hypothesis, long-term environmental survival is positively correlated with increased bacterial pathogenicity because high durability reduces the dependence of transmission on host mobility. Many indirectly transmitted bacterial pathogens, such as Mycobacterium tuberculosis and Burkhoderia pseudomallei, have high durability in the external environment and are highly virulent. It is possible that abiotic stresses may activate certain pathways or the expressions of certain genes, which might contribute to bacterial durability and virulence, synergistically. Therefore, exploring how bacterial phenotypes change in response to environmental stresses is important for understanding their potentials in host infections. In this study, we investigated the effects of different concentrations of salt (sodium chloride, NaCl), on survival ability, phenotypes associated with virulence, and energy metabolism of the lab strain Escherichia coli BW25113. In particular, we investigated how NaCl concentrations influenced growth patterns, biofilm formation, oxidative stress resistance, and motile ability. In terms of energy metabolism that is central to bacterial survival, glucose consumption, glycogen accumulation, and trehalose content were measured in order to understand their roles in dealing with the fluctuation of osmolarity. According to the results, trehalose is preferred than glycogen at high NaCl concentration. In order to dissect the molecular mechanisms of NaCl effects on trehalose metabolism, we further checked how the impairment of trehalose synthesis pathway (otsBA operon) via single-gene mutants influenced E. coli durability and virulence under salt stress. After that, we compared the transcriptomes of E. coli cultured at different NaCl concentrations, through which differentially expressed genes (DEGs) and differential pathways with statistical significance were identified, which provided molecular insights into E. coli responses to NaCl concentrations. In sum, this study explored the in vitro effects of NaCl concentrations on E. coli from a variety of aspects and aimed to facilitate our understanding of bacterial physiological changes under salt stress, which might help clarify the linkages between bacterial durability and virulence outside hosts under environmental stresses.
Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity

Complex diseases, such as breast cancer, are often caused by mutations of multiple functional genes. Identifying disease-related genes is a critical and challenging task for unveiling the biological mechanisms behind these diseases. In this study, we develop a novel computational framework to analyze the network properties of the known breast cancer–associated genes, based on which we develop a random-walk-with-restart (RCRWR) algorithm to predict novel disease genes. Specifically, we first curated a set of breast cancer–associated genes from the Genome-Wide Association Studies catalog and Online Mendelian Inheritance in Man database and then studied the distribution of these genes on an integrated protein–protein interaction (PPI) network. We found that the breast cancer–associated genes are significantly closer to each other than random, which confirms the modularity property of disease genes in a PPI network as revealed by previous studies. We then retrieved PPI subnetworks spanning top breast cancer–associated KEGG pathways and found that the distribution of these genes on the subnetworks are non-random, suggesting that these KEGG pathways are activated non-uniformly. Taking advantage of the non-random distribution of breast cancer–associated genes, we developed an improved RCRWR algorithm to predict novel cancer genes, which integrates network reconstruction based on local random walk dynamics and subnetworks spanning KEGG pathways. Compared with the disease gene prediction without using the information from the KEGG pathways, this method has a better prediction performance on inferring breast cancer–associated genes, and the top predicted genes are better enriched on known breast cancer–associated gene ontologies. Finally, we performed a literature search on top predicted novel genes and found that most of them are supported by at least wet-lab experiments on cell lines. In summary, we propose a robust computational framework to prioritize novel breast cancer–associated genes, which could be used for further in vitro and in vivo experimental validation.
Using Interpersonal Dimensions of Personality and Personality Pathology to Examine Momentary and Idiographic Patterns of Alliance Rupture

The Alternative Model of Personality Disorders (AMPD) integrates several theoretical models of personality functioning, including interpersonal theory. The interpersonal circumplex dimensions of warmth and dominance can be conceptualized as traits similar to those in AMPD Criterion B, but interpersonal theory also offers dynamic hypotheses about how these variables that change from moment to moment, which help to operationalize some of the processes alluded to in AMPD Criterion A. In the psychotherapy literature, dynamic interpersonal behaviors are thought to be critical for identifying therapeutic alliance ruptures, yet few studies have examined moment-to-moment interpersonal behaviors that are associated with alliance ruptures at an idiographic level. The current study examined the concurrent and cross-lagged relationships between interpersonal behaviors and alliance ruptures within each session in the famous Gloria films (“Three Approaches to Psychotherapy”). Interpersonal behaviors (warmth and dominance) as well as alliance ruptures (i.e., withdrawal and confrontation) were calculated at half minute intervals for each dyad. We identified distinct interpersonal patterns associated with alliance ruptures for each session: Gloria (patient)’s warmth was positively related with withdrawal ruptures concurrently in the session with Carl Rogers; Gloria’s dominance and coldness were related with increased confrontation ruptures in the session with Fritz Perls concurrently, while her coldness was also predicted by confrontation ruptures at previous moments; lastly, both Gloria’s dominance and Albert Ellis’s submissiveness were positively related with withdrawal ruptures. These interpersonal patterns demonstrated the promise of using AMPD dimensions to conceptualize momentary interpersonal processes related to therapy ruptures, as well as the clinical importance of attuning to repetitive, dyad-specific interpersonal cues of ruptures within each session.
Whiplash-Associated Disorders. Biopsychosocial Profiles of Pain Perception in Forensic Cases of Victims of Motor Vehicle Accidents

In order to make a complete diagnosis of all the factors influencing whiplash associated disorders (WAD), the evidence suggests that the condition evaluation should follow an integrated biopsychosocial model. This perspective would offer a fuller view of it, recognizing the interplay between the medical, biomechanical, social, and psychological factors. Despite the progress made in the subject, evidence of which psychosocial factors influence the experience of pain in litigant WAD patients is limited. A cross-sectional design and a cluster analysis was used to study the experience of pain and the psychosocial factors included therein in 249 patients with WAD assessed after suffering a motor vehicle accident. Three clusters were obtained: C1, with low scores of pain and a slight-moderate alteration of the Health-Related Quality of Life (HRQoL); C2, with medium scores of pain, alteration of HRQoL and a perception of moderate disability; and C3, with medium-high scores of pain, alteration of the HQoL, perception of moderate disability, presence of anxious-depressive symptomatology, poorer comprehension of the condition suffered, and the belief that it will extend over a long period of time. The results show a heterogeneous experience of pain in WAD, compatible with the biopsychosocial model of disease and the multidimensional approach to pain. The role of the psychologist in the evaluation of the condition could be useful to obtain a complete view of the condition, thus ensuring that the treatment is adapted to the needs of the patient.
Recent Advances in Model Predictive and Sliding Mode Current Control Techniques of Multiphase Induction Machines

Multiphase machines have attracted the attention of the research and industrial communities due to their advantages, namely better power distribution and fault-tolerant capabilities without extra hardware. However, the multiphase machine requires high-performance control strategies to take advantage of these features. From this perspective, the field-oriented control with the inner current control loop that uses using an explicit modulation stage has been considered the benchmark solution thanks to the reduced harmonic distortion obtained with this regulation strategy. Nevertheless, nonlinear controllers, thanks to their inherent nature, allow exploiting the extra multiphase capabilities in a simplified manner. Consequently, this paper aims to concentrate and discuss the latest developments on nonlinear current control of two of the most popular multiphase electric drive configurations, five-phase and six-phase. Then, this paper covers mainly finite-control-set model predictive control and their variations. Moreover, sliding-mode control is also explained. Finally, this paper includes experimental assessments of the most recent nonlinear current control techniques considering steady-state and transient conditions, stability and performance analysis.
Nasal High-Frequency Oscillatory Ventilation vs. Nasal Continuous Positive Airway Pressure as Therapy for Postextubation Respiratory Failure in Infants After Congenital Heart Surgery

Objective: This study aimed to evaluate the effects of nasal high-frequency oscillatory ventilation (NHFOV) vs. nasal continuous positive airway pressure (NCPAP) on postextubation respiratory failure (PRF) in infants after congenital heart surgery (CHS). Method: Eighty infants underwent postoperative invasive mechanical ventilation for more than 12 h and planned extubation. The infants were randomized to undergo either NHFOV or NCPAP after extubation. Primary outcomes were the incidence of PRF and reintubation, the average PaCO2 level, the average oxygenation index (OI), and pulmonary recruitment in the early extubation phase. Secondary outcomes included the NCPAP/NHFOV time, length of hospital stay, treatment intolerance, signs of discomfort, pneumothorax, adverse hemodynamic effects, nasal trauma, and mortality. Results: Except for PaCO2 within 12 after extubation (39.3 ± 5.8 vs. 43.6 ± 7.3 mmHg, p = 0.05), there was no statistically significant difference for any of the primary outcome measure (PRF, reintubation within 12 h after extubation, oxygenation index within 12 h after extubation, or lung volumes on X-ray after extubation) or secondary outcome measures (duration of non-invasive ventilation, duration of hospital stay, ventilation intolerance, signs of discomfort, pneumothorax, nasal trauma, adverse hemodynamic effects, or death prior to discharge), p > 0.1 for each comparison. Conclusion: NHFOV therapy after extubation in infants after CHS was more efficient in improving CO2 cleaning than NCPAP therapy, but there was no difference in other outcomes (PRF, reintubation, oxygenation index, and pulmonary recruitment).
Delayed Disease in Cynomolgus Macaques Exposed to Ebola Virus by an Intranasal Route

Ebola virus remains a significant public health concern due to high morbidity and mortality rates during recurrent outbreaks in endemic areas. Therefore, the development of countermeasures against Ebola virus remains a high priority, and requires the availability of appropriate animal models for efficacy evaluations. The most commonly used nonhuman primate models for efficacy evaluations against Ebola virus utilize the intramuscular or aerosol route of exposure. Although clinical disease signs are similar to human cases, disease progression in these models is much more rapid, and this can pose significant hurdles for countermeasure evaluations. The objective of the present study was to evaluate the Ebola virus disease course that arises after cynomolgus macaques are exposed to Ebola virus by a mucosal route (the intranasal route). Two different doses (10 pfu and 100 pfu) and delivery methodologies (drop-wise and mucosal atomization device) were evaluated on this study. Differences in clinical disease between dose and delivery groups were not noted. However, a delayed disease course was identified for approximately half of the animals on study, and this delayed disease was dose and administration method independent. Therefore, it appears that mucosal exposure with Ebola virus results in a disease course in cynomolgus macaques that more accurately replicates that which is documented for human cases. In summary, the data presented support the need for further development of this model as a possible alternative to parenteral and small-particle aerosol models for the study of human Ebola virus disease and for countermeasure evaluations.
Mobile Phone Use “on the Road”: A Self-Report Study on Young Drivers

Background Extensive research showed that multitasking negatively affects driving performance. Multitasking activities can range from talking and texting to listening to music; particularly among young drivers, multitasking behavior is caused mainly from mobile phone use while driving which is one of the main causes of road accidents. Objective The main purpose of this study was to investigate whether some variables (e.g., Sensation-Seeking, preferences of Multitasking) could affect mobile phone use while driving in young drivers and whether any gender differences were present among the examined variables. Setting and participants The sample consists of 424 Italian students (56% males) with an age range of 18–21 years. A self-report questionnaire was specifically developed to assess variables such as: Attitude toward Multitasking, Perceived Self-efficacy in Multitasking, Accident Risk Perception, General Multitasking Habits, and Sensation Seeking. Results Through SEM modeling, we found the attitude to multitasking while driving to be largely explained by the considered variables. Using multigroup analysis (MGSEM), the model we developed appears to be suitable for explaining the behaviors of both male and female young drivers. Furthermore, data comparison showed that females were more likely to risk perception toward multitasking, and risk perception when using a mobile phone while driving, while males obtained higher mean scores in Sensation Seeking, Perceived Self-Efficacy in Multitasking, and in Multitasking caused by mobile phone use while driving. Conclusion Our research showed how some variables may influence the inclination of some subjects to engage in multitasking while driving. Furthermore, we discussed the importance of considering these variables in the implementation of effective road safety education projects on driving multitasking.
rGO/Silk Fibroin-Modified Nanofibrous Patches Prevent Ventricular Remodeling via Yap/Taz-TGFβ1/Smads Signaling After Myocardial Infarction in Rats

Objective: After acute myocardial infarction (AMI), the loss of cardiomyocytes and dysregulation of extracellular matrix homeostasis results in impaired cardiac function and eventually heart failure. Cardiac patches have emerged as a potential therapeutic strategy for AMI. In this study, we fabricated and produced reduced graphene oxide (rGO)/silk fibroin-modified nanofibrous biomaterials as a cardiac patch to repair rat heart tissue after AMI and investigated the potential role of rGO/silk patch on reducing myocardial fibrosis and improving cardiac function in the infarcted rats. Method: rGO/silk nanofibrous biomaterial was prepared by electrospinning and vacuum filtration. A rat model of AMI was used to investigate the ability of patches with rGO/silk to repair the injured heart in vivo. Echocardiography and stress–strain analysis of the left ventricular papillary muscles was used to assess the cardiac function and mechanical property of injured hearts treated with this cardiac patch. Masson's trichrome staining and immunohistochemical staining for Col1A1 was used to observe the degree of myocardial fibrosis at 28 days after patch implantation. The potential direct mechanism of the new patch to reduce myocardial fibrosis was explored in vitro and in vivo. Results: Both echocardiography and histopathological staining demonstrated improved cardiac systolic function and ventricular remodeling after implantation of the rGO/silk patch. Additionally, cardiac fibrosis and myocardial stiffness of the infarcted area were improved with rGO/silk. On RNA-sequencing, the gene expression of matrix-regulated genes was altered in cardiofibroblasts treated with rGO. Western blot analysis revealed decreased expression of the Yap/Taz-TGFβ1/Smads signaling pathway in heart tissue of the rGO/silk patch group as compared with controls. Furthermore, the rGO directly effect on Col I and Col III expression and Yap/Taz-TGFβ1/Smads signaling was confirmed in isolated cardiofibroblasts in vitro. Conclusion: This study suggested that rGO/silk improved cardiac function and reduced cardiac fibrosis in heart tissue after AMI. The mechanism of the anti-fibrosis effect may involve a direct regulation of rGO on Yap/Taz-TGFβ1/Smads signaling in cardiofibroblasts.
Bespoke Biomolecular Wires for Transmembrane Electron Transfer: Spontaneous Assembly of a Functionalized Multiheme Electron Conduit

Shewanella oneidensis exchanges electrons between cellular metabolism and external redox partners in a process that attracts much attention for production of green electricity (microbial fuel cells) and chemicals (microbial electrosynthesis). A critical component of this pathway is the outer membrane spanning MTR complex, a biomolecular wire formed of the MtrA, MtrB, and MtrC proteins. MtrA and MtrC are decaheme cytochromes that form a chain of close-packed hemes to define an electron transfer pathway of 185 Å. MtrA is wrapped inside MtrB for solubility across the outer membrane lipid bilayer; MtrC sits outside the cell for electron exchange with external redox partners. Here, we demonstrate tight and spontaneous in vitro association of MtrAB with separately purified MtrC. The resulting complex is comparable with the MTR complex naturally assembled by Shewanella in terms of both its structure and rates of electron transfer across a lipid bilayer. Our findings reveal the potential for building bespoke electron conduits where MtrAB combines with chemically modified MtrC, in this case, labeled with a Ru-dye that enables light-triggered electron injection into the MtrC heme chain.
Facial Cartilaginous Reconstruction—A Historical Perspective, State-of-the-Art, and Future Directions

Importance: Reconstruction of facial deformity poses a significant surgical challenge due to the psychological, functional, and aesthetic importance of this anatomical area. There is a need to provide not only an excellent colour and contour match for skin defects, but also a durable cartilaginous structural replacement for nasal or auricular defects. The purpose of this review is to describe the history of, and state-of-the-art techniques within, facial cartilaginous surgery, whilst highlighting recent advances and future directions for this continually advancing specialty. Observations: Limitations of synthetic implants for nasal and auricular reconstruction, such as silicone and porous polyethylene, have meant that autologous cartilage tissue for such cases remains the current gold standard. Similarly, tissue engineering approaches using unrelated cells and synthetic scaffolds have shown limited in vivo success. There is increasing recognition that both the intrinsic and extrinsic microenvironment are important for tissue engineering and synthetic scaffolds fail to provide the necessary cues for cartilage matrix secretion. Conclusions and Relevance: We discuss the first-in-man studies in the context of biomimetic and developmental approaches to engineering durable cartilage for clinical translation. Implementation of engineered autologous tissue into clinical practise could eliminate donor site morbidity and represent the next phase of the facial reconstruction evolution.
The Embodied Crossmodal Self Forms Language and Interaction: A Computational Cognitive Review

Human language is inherently embodied and grounded in sensorimotor representations of the self and the world around it. This suggests that the body schema and ideomotor action-effect associations play an important role in language understanding, language generation, and verbal/physical interaction with others. There are computational models that focus purely on non-verbal interaction between humans and robots, and there are computational models for dialog systems that focus only on verbal interaction. However, there is a lack of research that integrates these approaches. We hypothesize that the development of computational models of the self is very appropriate for considering joint verbal and physical interaction. Therefore, they provide the substantial potential to foster the psychological and cognitive understanding of language grounding, and they have significant potential to improve human-robot interaction methods and applications. This review is a first step toward developing models of the self that integrate verbal and non-verbal communication. To this end, we first analyze the relevant findings and mechanisms for language grounding in the psychological and cognitive literature on ideomotor theory. Second, we identify the existing computational methods that implement physical decision-making and verbal interaction. As a result, we outline how the current computational methods can be used to create advanced computational interaction models that integrate language grounding with body schemas and self-representations.