Miracle-dz/UniFAR-FTUs huggingface dataset:
Native Production of Prodigiosin in the Estuarine Bacterium, Vibrio gazogenes PB1, and Identification of the Associated pig Genes

Vibrio gazogenes PB1 is an estuarine bacterium that was first isolated from saltwater mud. This bacterial species possesses the metabolic capacity to produce prodigiosin which has potential uses as an anticancer agent, antibiotic, and a fungicide. We evaluated the feasibility of employing V. gazogenes PB1 as a bacterial host for the production of prodigiosin. V. gazogenes PB1 could be grown and maintained using the well-known lysogeny broth medium when supplemented with NaCl, and revived after storage at -80°C. Under batch conditions, growth of V. gazogenes PB1 in minimal media and production of prodigiosin was observed over a wide range of NaCl concentrations from 1 to 5% (w/v). The production of prodigiosin was significantly influenced by the concentration of glucose (as the carbon source), ammonium chloride (as the nitrogen source), inorganic phosphate ions, as well as pH. The greatest titer (231 mg/L) was observed in minimal media that contained 1% (w/v) glucose, 100 mM ammonium chloride and 100 mM potassium phosphate buffer. The sequences and chromosomal locations of the pig genes associated with prodigiosin biosynthesis are revealed for the first time. PigA is an isolated gene on chromosome 2, while the remaining pig genes, from pigB to pigN, exist as a 20 kb gene cluster on chromosome 1. Given its excellent growth in a range of NaCl concentrations, wide availability from culture collections and low-risk status for experimental work, we would conclude that V. gazogenes PB1 is a promising bacterial host for the production of prodigiosin.
Comparison of perioperative outcomes with or without routine chest tube drainage after video-assisted thoracoscopic pulmonary resection: A systematic review and meta-analysis

Background In recent years, an increasing number of thoracic surgeons have attempted to apply no routine chest tube drainage (NT) strategy after thoracoscopic lung resection. However, the safety and feasibility of not routinely placing a chest tube after lung resection remain controversial. This study aimed to investigate the effect of NT strategy after thoracoscopic pulmonary resection on perioperative outcomes. Methods A comprehensive literature search of PubMed, Embase, and the Cochrane Library databases until 3 January 2022 was performed to identify the studies that implemented NT strategy after thoracoscopic pulmonary resection. Perioperative outcomes were extracted by 2 reviewers independently and then synthesized using a random-effects model. Risk ratio (RR) and standardized mean difference (SMD) with 95% confidence interval (CI) served as the summary statistics for meta-analysis. Subgroup analysis and sensitivity analysis were subsequently performed. Results A total of 12 studies with 1,381 patients were included. The meta-analysis indicated that patients in the NT group had a significantly reduced postoperative length of stay (LOS) (SMD = -0.91; 95% CI: -1.20 to -0.61; P < 0.001) and pain score on postoperative day (POD) 1 (SMD = -0.95; 95% CI: -1.54 to -0.36; P = 0.002), POD 2 (SMD = -0.37; 95% CI: -0.63 to -0.11; P = 0.005), and POD 3 (SMD = -0.39; 95% CI: -0.71 to -0.06; P = 0.02). Further subgroup analysis showed that the difference of postoperative LOS became statistically insignificant in the lobectomy or segmentectomy subgroup (SMD = -0.30; 95% CI: -0.91 to 0.32; P = 0.34). Although the risk of pneumothorax was significantly higher in the NT group (RR = 1.75; 95% CI: 1.14–2.68; P = 0.01), the reintervention rates were comparable between groups (RR = 1.04; 95% CI: 0.48–2.25; P = 0.92). No significant difference was found in pleural effusion, subcutaneous emphysema, operation time, pain score on POD 7, and wound healing satisfactory (all P > 0.05). The sensitivity analysis suggested that the results of the meta-analysis were stabilized. Conclusions This meta-analysis suggested that NT strategy is safe and feasible for selected patients scheduled for video-assisted thoracoscopic pulmonary resection. Systematic Review Registration https://inplasy.com/inplasy-2022-4-0026, identifier INPLASY202240026.
Higher order neural processing with input-adaptive dynamic weights on MoS2 memtransistor crossbars

The increasing complexity of deep learning systems has pushed conventional computing technologies to their limits. While the memristor is one of the prevailing technologies for deep learning acceleration, it is only suited for classical learning layers where only two operands, namely weights and inputs, are processed simultaneously. Meanwhile, to improve the computational efficiency of deep learning for emerging applications, a variety of non-traditional layers requiring concurrent processing of many operands are becoming popular. For example, hypernetworks improve their predictive robustness by simultaneously processing weights and inputs against the application context. Two-electrode memristor grids cannot directly map emerging layers’ higher-order multiplicative neural interactions. Addressing this unmet need, we present crossbar processing using dual-gated memtransistors based on two-dimensional semiconductor MoS2. Unlike the memristor, the resistance states of memtransistors can be persistently programmed and can be actively controlled by multiple gate electrodes. Thus, the discussed memtransistor crossbar enables several advanced inference architectures beyond a conventional passive crossbar. For example, we show that sneak paths can be effectively suppressed in memtransistor crossbars, whereas they limit size scalability in a passive memristor crossbar. Similarly, exploiting gate terminals to suppress crossbar weights dynamically reduces biasing power by ∼20% in memtransistor crossbars for a fully connected layer of AlexNet. On emerging layers such as hypernetworks, collocating multiple operations within the same crossbar cells reduces operating power by ∼ 15 × on the considered network cases.
Korean university students’ significant learning experiences and associated generic skills: A qualitative essay review

The purpose of the present study was to explore significant learning experiences of Korean university students and examine associated generic skills. The study implemented a document analysis approach to investigate essays collected from 33 students in a 4-year university in Seoul, South Korea. A total of 102 excerpts were coded, forming 14 sub-themes which were categorized into five themes that describe students’ significant learning experiences. The five themes are interacting with others, learning by oneself and about oneself, realizing applicability to real-life, venturing into advanced learning, and experiencing a respectful learning atmosphere. Also, 18 generic skills were identified which were categorized into four clusters, namely comprehensive thinking skills, information utilization skills, interpersonal skills, and personal attributes. The results of the present study provide the groundwork for understanding students’ perceptions of significant learning experiences and associated generic skills.
Pan-Cancer Analysis of the Immunological Role of PDIA5: A Potential Target for Immunotherapy

The aberrant protein disulfide isomerase A5 (PDIA5) expression was relevant to the poor prognosis of patients with human cancers. However, its relationship with the epigenetic and genetic alterations and its effect on tumor immunity is still lacking. In the present study, we comprehensively analyzed the immune infiltration role of PDIA5 in human cancers based on large-scale bioinformatics analyses and in vitro experiments. Obvious DNA methylation and moderate alteration frequency of PDIA5 were observed in human cancers. The expression level of PDIA5 was significantly correlated with infiltrated immune cells, immune pathways, and other immune signatures. We found that cancer cells and macrophages exhibited high PDIA5 expression in human cancers using the single-cell RNA sequencing analysis. We also demonstrated the interaction between PDIA5 and immune cells in glioblastoma multiforme (GBM). Multiplex immunofluorescence staining showed the upregulated expression level of PDIA5 and the increased number of M2 macrophage markers-CD163 positive cells in pan-cancer samples. Notably, PDIA5 silencing resulted in upregulated expression of PD-L1 and SPP1 in U251 cells. Silencing of PDIA5 in hepG2 cells, U251 cells, and PC3 cells contributed to a decline in their ability of proliferation, clone formation, and invasion and inhibited the migration of cocultured M2 macrophages. Additionally, PDIA5 also displayed predictive value in the immunotherapy response of both murine and human cancer cohorts. Overall, our findings indicated that PDIA5 might be a potential target for immunotherapies in cancers.
Expanding the chemical diversity of M13 bacteriophage

Bacteriophage M13 virions are very stable nanoparticles that can be modified by chemical and genetic methods. The capsid proteins can be functionalized in a variety of chemical reactions without loss of particle integrity. In addition, Genetic Code Expansion (GCE) permits the introduction of non-canonical amino acids (ncAAs) into displayed peptides and proteins. The incorporation of ncAAs into phage libraries has led to the discovery of high-affinity binders with low nanomolar dissociation constant (KD) values that can potentially serve as inhibitors. This article reviews how bioconjugation and the incorporation of ncAAs during translation have expanded the chemistry of peptides and proteins displayed by M13 virions for a variety of purposes.
Electroacupuncture attenuates surgical pain-induced delirium-like behavior in mice via remodeling gut microbiota and dendritic spine

Surgical pain is associated with delirium in patients, and acupuncture can treat pain. However, whether electroacupuncture can attenuate the surgical pain-associated delirium via the gut–brain axis remains unknown. Leveraging a mouse model of foot incision-induced surgical pain and delirium-like behavior, we found that electroacupuncture stimulation at specific acupoints (e.g., DU20+KI1) attenuated both surgical pain and delirium-like behavior in mice. Mechanistically, mice with incision-induced surgical pain and delirium-like behavior showed gut microbiota imbalance, microglia activation in the spinal cord, somatosensory cortex, and hippocampus, as well as an enhanced dendritic spine elimination in cortex revealed by two-photon imaging. The electroacupuncture regimen that alleviated surgical pain and delirium-like behavior in mice also effectively restored the gut microbiota balance, prevented the microglia activation, and reversed the dendritic spine elimination. These data demonstrated a potentially important gut–brain interactive mechanism underlying the surgical pain-induced delirium in mice. Pending further studies, these findings revealed a possible therapeutic approach in preventing and/or treating postoperative delirium by using perioperative electroacupuncture stimulation in patients.
Recent progress of catalytic methane combustion over transition metal oxide catalysts

Methane (CH4) is one of the cleanest fossil fuel resources and is playing an increasingly indispensable role in our way to carbon neutrality, by providing less carbon-intensive heat and electricity worldwide. On the other hand, the atmospheric concentration of CH4 has raced past 1,900 ppb in 2021, almost triple its pre-industrial levels. As a greenhouse gas at least 86 times as potent as carbon dioxide (CO2) over 20 years, CH4 is becoming a major threat to the global goal of deviating Earth temperature from the +2°C scenario. Consequently, all CH4-powered facilities must be strictly coupled with remediation plans for unburned CH4 in the exhaust to avoid further exacerbating the environmental stress, among which catalytic CH4 combustion (CMC) is one of the most effective strategies to solve this issue. Most current CMC catalysts are noble-metal-based owing to their outstanding C–H bond activation capability, while their high cost and poor thermal stability have driven the search for alternative options, among which transition metal oxide (TMO) catalysts have attracted extensive attention due to their Earth abundance, high thermal stability, variable oxidation states, rich acidic and basic sites, etc. To date, many TMO catalysts have shown comparable catalytic performance with that of noble metals, while their fundamental reaction mechanisms are explored to a much less extent and remain to be controversial, which hinders the further optimization of the TMO catalytic systems. Therefore, in this review, we provide a systematic compilation of the recent research advances in TMO-based CMC reactions, together with their detailed reaction mechanisms. We start with introducing the scientific fundamentals of the CMC reaction itself as well as the unique and desirable features of TMOs applied in CMC, followed by a detailed introduction of four different kinetic reaction models proposed for the reactions. Next, we categorize the TMOs of interests into single and hybrid systems, summarizing their specific morphology characterization, catalytic performance, kinetic properties, with special emphasis on the reaction mechanisms and interfacial properties. Finally, we conclude the review with a summary and outlook on the TMOs for practical CMC applications. In addition, we also further prospect the enormous potentials of TMOs in producing value-added chemicals beyond combustion, such as direct partial oxidation to methanol.
MiR-202-3p determines embryo viability during mid-blastula transition

Developmental growth is an intricate process involving the coordinated regulation of the expression of various genes, and microRNAs (miRNAs) play crucial roles in diverse processes throughout animal development. The mid-blastula transition (MBT) is a developmental milestone when maternal RNAs are cleared and the zygotic genome programmed asynchronous cell division begins to drive embryogenesis. While mechanisms underlying MBT have been intensively revealed, factors regulating cell proliferation at the transition remain largely unknown. We report here a microRNA, miR-202-3p to be a key factor that determines embryonic fate during MBT in zebrafish. A miR-202-3p antagomir specifically terminated embryo development at the mid-blastula stage. In vivo deletion of the miR-202 locus recapitulated the fatal phenotypes, which were rescued only by miR-202-3p or its precursor. Transcriptome comparison revealed >250 RNAs including both maternal and zygotic origins were dysregulated at MBT in the miR-202−/− embryos, corresponding with arrays of homeostatic disorders leading to massive apoptosis. A trio of genes: nfkbiaa, perp and mgll, known to be intimately involved with cell proliferation and survival, were identified as direct targets of miR-202-3p. Importantly, over- or under-expression of any of the trio led to developmental delay or termination at the blastula or gastrula stages. Furthermore, nfkbiaa and perp were shown to inter-regulate each other. Thus, miR-202-3p mediates a regulatory network whose components interact closely during MBT to determine embryonic viability and development.
Comparison of hook-wire and medical glue for CT-guided preoperative localization of pulmonary nodules

Background Preoperative localization is challenging due to the small diameter of pulmonary nodules or their deep location in the lung parenchyma during VATS surgery. The purpose of this study was to compare the efficacy and safety of both hook-wire and medical glue for pre-operative localization of pulmonary nodules. Methods In the current study, 158 patients were retrospectively analyzed (January 2019 and January 2020). The patients underwent hook-wire or medical glue for pre-operative localization of pulmonary nodules. Among them, 74 patients in the hook-wire group and 84 patients in the medical glue group underwent VATS anatomic segmentectomy or wedge resection after localization of pulmonary nodules. Pre-operative localization data from all patients were compiled. Moreover, the efficacy and safety of the two methods were evaluated according to localization success rates and localization-related complications. Results The success rate of localization in the medical glue group was 100% while 97.3% in the hook-wire group. After localization of the pulmonary nodules, the incidence of minor pneumothorax in the medical glue group (11.9%) was lower than that in the hook-wire group (37.8%) (p=0.01). The incidence of mild pulmonary parenchymal hemorrhage in the medical glue group (13.1%) was also lower than that in the hook-wire group (24.3%) (p=0.000). The mean time from the completion of localization to the start of surgery was also longer in the medical glue group than in the hook-wire group (p=0.000). The mean visual analog scale (VAS) scores after localization were higher in the hook-wire group than in the medical glue group (p=0.02). In both groups, parenchymal hemorrhage was significantly associated with the needle length in hook-wire localization and the depth of the medical glue in the lung parenchyma (p = 0.009 and 0.001, respectively). Conclusion These two localization methods are safe and effective in pre-operative pulmonary nodule localization. The medical glue localization method had a lower risk of complications, a higher localization success rate, less pain after localization and more flexibility in the arrangement of operation time.
Wenshenyang recipe treats infertility through hormonal regulation and inflammatory responses revealed by transcriptome analysis and network pharmacology

The Wenshenyang recipe (WSYR) has the effect of treating infertility, but the mechanisms underlying this activity have not been fully elucidated. In this study, network pharmacology and RNA sequencing were combined, with database-based “dry” experiments and transcriptome analysis-based “wet” experiments used conjointly to analyse the mechanism of WSYR in the treatment of infertility. In the dry analysis, 43 active compounds in WSYR and 44 therapeutic targets were obtained through a database search, 15 infertility pathways were significantly enriched, and key targets, such as ESR1, TP53, AKT1, IL-6, and IL-10 were identified. Then the wet experiments were performed to detect the expression changes of the 412 genes from 15 infertility pathways identified by dry analysis. HK-2 cells were treated with the three herbs of WSYR and subjected to targeted RNA sequencing. Based on the results, 92 of the 412 genes in 15 infertility pathways were identified as DEGs. Additionally, key targets, such as ESR2, STAT1, STAT3, and IL6, were also identified in the wet experiments. RT-qPCR experiments further verified that WSYR played an anti-inflammatory role by upregulating IL-4 and IL-10 and Epimedium brevicornu Maxim (Yinyanghuo) showed broader effect than Drynaria fortunei (Kunze) J. Sm (Gusuibu) and Cistanche deserticola Y.C. Ma (Roucongrong). By screening compounds of WSYR using molecular docking models of ESR1 and ESR2, it was further found that xanthogalenol in Gusuibu, arachidonate in Roucongrong, and anhydroicaritin in Yinyanghuo had good affinity for estrogen receptors. These findings provide evidence for an estrogen-regulating role of the three herbs in WSYR.
Exploring the concept of pedagogical resilience during the COVID-19 pandemic: Teachers’ perspectives from Thailand and the Philippines

This brief research report aimed to explore the concept of pedagogical resilience and how teachers in Thailand and the Philippines build resilience in pedagogy during the COVID-19 pandemic. Employing the qualitative research design, the data were obtained from the focus group discussion (FGD) and semi-structured interviews with 12 teachers, 8 of whom were from 1 of the universities in the Philippines and another four teachers from a university in Thailand. The thematic analysis revealed that pedagogical resilience is influenced by teachers’ personal, professional, and social attitudes toward teaching and learning during the COVID-19 pandemic. Although teachers acknowledged that they had no experience in remote and online teaching, they demonstrated resiliency by being flexible and adaptive to the situation. Such an attitude allowed them to build a relationship with their colleagues and design teaching and learning pedagogy that addresses the issues in their online and remote teaching. The findings provide a clear understanding of the conceptualization of pedagogical resilience from the perspectives of teachers in the Philippines and Thailand.
Functional characterization of MEKK3 in the intestinal immune response to bacterial challenges in grass carp (Ctenopharyngodon idella)

Mitogen-activated protein kinase kinase kinase 3 (MEKK3) is an evolutionarily conserved Ser/Thr protein kinase of the MEKK family that is essential for the host immune response to pathogen challenges in mammals. However, the immune function of MEKK3s in lower vertebrate species, especially in bony fish, remains largely unknown. In this study, a fish MEKK3 (designated CiMEKK3) gene was cloned and identified from grass carp (Ctenopharyngodon idella). The present CiMEKK3 cDNA encoded a 620 amino acid polypeptide containing a conserved S-TKc domain and a typical PB1 domain. Several potential immune-related transcription factor-binding sites, including activating protein 1 (AP-1), nuclear factor kappa B (NF-κB) and signal transducer and activator of downstream transcription 3 (STAT3), were observed in the 5’ upstream DNA sequence of CiMEKK3. A phylogenetic tree showed that CiMEKK3 exhibits a close evolutionary relationship with MEKK3s from Cyprinus carpio and Carassius auratus. Quantitative real-time PCR analysis revealed that CiMEKK3 transcripts were widely distributed in all selected tissues of healthy grass carp, with a relatively high levels observed in the gill, head kidney and intestine. Upon in vitro challenge with bacterial pathogens (Aeromonas hydrophila and Aeromonas veronii) and pathogen-associated molecular patterns (PAMPs) (lipopolysaccharide (LPS), peptidoglycan (PGN), L-Ala-γ-D-Glu-mDAP (Tri-DAP) and muramyl dipeptide (MDP)), the expression levels of CiMEKK3 in the intestinal cells of grass carp were shown to be significantly upregulated in a time-dependent manner. In vivo injection experiments revealed that CiMEKK3 transcripts were significantly induced by MDP challenge in the intestine; however, these effects could be inhibited by the nutritional dipeptides carnosine and Ala-Gln. Moreover, subcellular localization analysis and luciferase reporter assays indicated that CiMEKK3 could act as a cytoplasmic signal-transducing activator involved in the regulation of NF-κB and MAPK/AP-1 signaling cascades in HEK293T cells. Taken together, these findings strongly suggest that CiMEKK3 plays vital roles in the intestinal immune response to bacterial challenges, which will aid in understanding the pathogenesis of inflammatory bowel disease in bony fish.