A novel mRNA multi-epitope vaccine of Acinetobacter baumannii based on multi-target protein design in immunoinformatic approach.

Acinetobacter baumannii is a gram-negative bacillus prevalent in nature, capable of thriving under various environmental conditions. As an opportunistic pathogen, it frequently causes nosocomial infections such as urinary tract infections, bacteremia, and pneumonia, contributing to increased morbidity and mortality in clinical settings. Consequently, developing novel vaccines against Acinetobacter baumannii is of utmost importance. In our study, we identified 10 highly conserved antigenic proteins from the NCBI and UniProt databases for epitope mapping. We subsequently screened and selected 8 CTL, HTL, and LBL epitopes, integrating them into three distinct vaccines constructed with adjuvants. Following comprehensive evaluations of immunological and physicochemical parameters, we conducted molecular docking and molecular dynamics simulations to assess the efficacy and stability of these vaccines. Our findings indicate that all three multi-epitope mRNA vaccines designed against Acinetobacter baumannii are promising; however, further animal studies are required to confirm their reliability and effectiveness.

Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method.

Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.

A multi-epitope Cryptococcus neoformans vaccine covering the most common A and D phenotypes was designed using bioinformatics methods.

Predicting pragmatic functions of Chinese echo questions using prosody: evidence from acoustic analysis and data modeling.

Echo questions serve two pragmatic functions (recapitulatory and explicatory) and are subdivided into two types (yes-no echo question and wh-echo question) in verbal communication. Yet to date, most relevant studies have been conducted in European languages like English and Spanish. It remains unknown whether the different functions of echo questions can be conveyed via prosody in spoken Chinese. Additionally, no comparison was made on the diversified algorithmic models in predicting functions by the prosodity of Chinese echo questions, a novel linguistic cognition in nature. This motivated us to use different acoustic cues to predict different pragmatic functions of Chinese echo questions by virtue of acoustic experiment and data modeling. The results showed that for yes-no echo question, explicatory function exhibited higher pitch and intensity patterns than recapitulatory function whereas for wh-echo question, recapitulatory function demonstrated higher pitch and intensity patterns than explicatory function. With regard to data modeling, the algorithm Support Vector Machine (SVM) relative to Random Forest (RF) and Logistic Regression (LR) performed better when predicting different functions using prosodic cues in both yes-no and wh-echo questions. This study from a digitized perspective adds evidence to the cognition of echo questions' functions on a prosodic basis.

Detection of Verticillium infection in cotton leaves using ATR-FTIR spectroscopy coupled with machine learning algorithms.

Verticillium wilt (VW) is a soil-borne vascular disease that affects upland cotton and is caused by Verticillium dahliae Kleb. A rapid and user-friendly early diagnostic technique is essential for the preventing and controlling VW disease. In this study, Fourier transform infrared (FTIR) spectroscopy with attenuated total reflectance (ATR) technology was used to detect VW infection in cotton leaves. About 1800 FTIR spectra were obtained from 348 cotton leaves. The cotton leaves were collected from three categories: VW group, infected group and control group (non-infected). The vibrational peak of chitins at 1558 cm-1 was identified through mean and differential analysis of FTIR spectra as a criterion to differentiate the VW or infected group from the control group. Classification models were constructed using various machine learning algorithms. The support vector machines (SVM) model exhibited the highest predictive accuracy (>96 %) in each group and a total accuracy (>97 %) for the three groups. These results provide a new approach for detecting Verticillium infection in cotton leaves and shows a promising potential for the future applications of the method in plant science.

Design of a cryptococcus neoformans vaccine by subtractive proteomics combined with immunoinformatics.

The emergence of Cryptococcus neoformans has posed an undeniable burden to many regions worldwide, with its strains mainly entering the lungs through the respiratory tract and spreading throughout the body. Limitations of drug regimens, such as high costs and limited options, have directed our attention toward the promising field of vaccine development. In this study, the subtractive proteomics approach was employed to select target proteins from databases that can accurately cover serotypes A and D of the Cryptococcus neoformans. Further, two multi-epitope vaccines consisting of T and B cell epitopes were demonstrated that they have good structural stability and could bind with immune receptor to induce desired immune responses in silico. After further evaluation, these vaccines show the potential for large-scale production and applicability to the majority of the population of the world. In summary, these two vaccines have been theoretically proven to combat Cryptococcus neoformans infections, awaiting further experimental validation of their actual protective effects.

Development of a novel multi-epitope mRNA vaccine candidate to combat HMPV virus.

Human metapneumovirus (HMPV) is one of the main pathogens causing severe respiratory infections in children, as a common cause of immunodeficiency-related deaths in children and elderly individuals, the prevalence of HMPV has been showing an increasing trend during the last years. However, no vaccines or effective treatment plans are available currently. In this present, based on candidate proteins highly associated with viral virulence and has promising protective potential, we screened for immunodominant cytotoxic T cells, helper T cells, and Linear B-cell epitopes from the most promising candidate Fusion protein, together with G, SH, M, and M2. All epitopes were predicted to have strong antigenicity by Vaxijen and pose no potential toxicity, allergenicity, or hormonology to human proteins by Toxinpred, Allerpred, and Blast analysis, meanwhile, high conservancy is demanded to cover different subtypes. adjuvants ß-defensin II and Pam2Cys was attached with EAAAK linkers to improve vaccine's efficiency. Then, calculation of physicochemical properties proved the protein vaccine as a product can stably exist in the human body. Besides, we assessed the docking between the vaccine and immune receptors to evaluate its ability to stimulate immune responses, and the dynamic simulation further confirmed that the vaccine can tightly bind with immune receptors, which approved that the construction has the potential to induce strong humoral and cellular immune response. Finally, the vaccine was constructed into a multi-epitope mRNA vaccine, the immune simulations suggest that this is a vaccine candidate for controlling HMPV infection.

A review of the ESL/EFL learners' gains from online peer feedback on English writing.

Peer feedback is essential in writing English as a Second/Foreign Language (ESL/EFL). Traditionally, offline PF was more widely favored but nowadays online peer feedback (OPF) has become frequent in ESL/EFL learners' daily writing. This study is undertaken to probe into the gains of using OPF in ESL/EFL writing on the basis of 37 research articles published in core journals from 2012 till 2022. In order to accurately cover the previous researches, we capitalize on three methods to evaluate and analyze the data, i.e., database search, citation search and manual search. Results show that from the perspective of the ESL/EFL learners' gains, the OPF is basically divided into two categories (cognitive OPF and affective OPF), involving eight aspects in all: face-based strategies, revision-based comments, writing performance, learning environment, reflection/critical thinking/responsibility, writing emotion, motivation, and attitudes; and OPF can be well supported by a set of theories like Process-oriented Writing Theory, Collaborative Learning Theory, Interactionist Theory of L2 Acquisition and Vygotsky's sociocultural theory. By comparison, the gains from OPF outperform those from offline PF in many dimensions (e.g., face-based strategies), despite some overlaps (e.g., the shift of the role) that were revealed in several investigations. Based on the past studies, we propose some pedagogical implications on OPF from ESL/EFL writing, including accenting the "student-centered" teaching strategy, providing students with OPF on the basis of incremental knowledge, adopting OPF regularly in ESL/EFL writing activities to shape personalities and outlooks and putting OPF into its full play with recourse to abundant internet-based vehicles. This review is desired to provide a guideline for both the peer feedback practice and the upcoming scholarly researches with respect to EFL/ESL writing.