Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of BIT33_RS14560 Enhances the Biofilm Formation and Virulence of Acinetobacter baumannii

Acinetobacter baumannii, a strictly aerobic, non-lactose fermented Gram-negative bacteria, is one of the important pathogens of nosocomial infection. Major facilitator superfamily (MFS) transporter membrane proteins are a class of proteins that widely exists in microbial genomes and have been revealed to be related to biofilm formation in a variety of microorganisms. However, as one of the MFS transporter membrane proteins, little is known about the role of BIT33_RS14560 in A. baumannii. To explore the effects of BIT33_RS14560 on biofilm formation of A. baumannii, the biofilm formation abilities of 62 isolates were firstly investigated and compared with their transcript levels of BIT33_RS14560. Then, this specific gene was over-expressed in a standard A. baumannii strain (ATCC 19606) and two isolates of extensively drug-resistant A. baumannii (XDR-Ab). Bacterial virulence was observed using a Galleria mellonella infection model. High-throughput transcriptome sequencing (RNA seq) was performed on ATCC 19606 over-expressed strain and its corresponding empty plasmid control strain. Spearman’s correlation analysis indicated a significant negative correlation (R = −0.569, p = 0.000) between the △CT levels of BIT33_RS1456 and biofilm grading of A. baumannii isolates. The amount of A. baumannii biofilm was relatively high within 12–48 h. Regardless of standard or clinical strains; the biofilm biomass in the BIT33_RS14560 overexpression group was significantly higher than that in the control group ( p < 0.0001). Kaplan–Meier survival curve analysis showed that the mortality of G. mellonella was significantly higher when infected with the BIT33_RS14560 overexpression strain (χ2 = 8.462, p = 0.004). RNA-Seq showed that the mRNA expression levels of three genes annotated as OprD family outer membrane porin, glycosyltransferase family 39 protein, and glycosyltransferase family 2 protein, which were related to bacterial adhesion, biofilm formation, and virulence, were significantly upregulated when BIT33_RS14560 was over-expressed. Our findings provided new insights in identifying potential drug targets for the inhibition of biofilm formation. We also developed a practical method to construct an over-expressed vector that can stably replicate in XDR-Ab isolates.
Enhanced Biosynthesis of Fatty Acids Contributes to Ciprofloxacin Resistance in Pseudomonas aeruginosa

Antibiotic-resistant Pseudomonas aeruginosa is insensitive to antibiotics and difficult to deal with. An understanding of the resistance mechanisms is required for the control of the pathogen. In this study, gas chromatography–mass spectrometer (GC-MS)-based metabolomics was performed to identify differential metabolomes in ciprofloxacin (CIP)-resistant P. aeruginosa strains that originated from P. aeruginosa ATCC 27853 and had minimum inhibitory concentrations (MICs) that were 16-, 64-, and 128-fold (PA-R16CIP, PA-R64CIP, and PA-R128CIP, respectively) higher than the original value, compared to CIP-sensitive P. aeruginosa (PA-S). Upregulation of fatty acid biosynthesis forms a characteristic feature of the CIP-resistant metabolomes and fatty acid metabolome, which was supported by elevated gene expression and enzymatic activity in the metabolic pathway. The fatty acid synthase inhibitor triclosan potentiates CIP to kill PA-R128CIP and clinically multidrug-resistant P. aeruginosa strains. The potentiated killing was companied with reduced gene expression and enzymatic activity and the returned abundance of fatty acids in the metabolic pathway. Consistently, membrane permeability was reduced in the PA-R and clinically multidrug-resistant P. aeruginosa strains, which were reverted by triclosan. Triclosan also stimulated the uptake of CIP. These findings highlight the importance of the elevated biosynthesis of fatty acids in the CIP resistance of P. aeruginosa and provide a target pathway for combating CIP-resistant P. aeruginosa.
Evaluation of a Recirculating Aquaculture System Research Facility Designed to Address Current Knowledge Needs in Atlantic Salmon Production

A better understanding of recirculating aquaculture system (RAS) biosecurity is crucial for the sustainable and ethical production of Atlantic salmon smolt and post-smolt in these systems. This study described and evaluated the performance of a RAS facility for fish infection research with Atlantic salmon as the main animal model. Fish body weight, length, water quality, and system metrics from five independent experimental trials conducted between September 2020 and July 2021 were used to analyze the variation within and between treatments. Statistical power analysis was performed to determine the minimum number of fish required. The fish parameters variability showed that the inter-class correlation coefficient was on average low (0.1) and that the variation within tanks was larger than the variation between the tanks. The power analysis showed that 15 fish were required to be sampled per tank under these study conditions. Variation of water quality and system management metrics among the five experimental trials was higher compared to the variation within the five experimental trials. Moreover, the variation of the water quality parameters controlled by sensors was relatively low, whereas the parameters depending on biofilter maturation level and performance presented a very high variation. Water exchange rate-dependent quality parameters showed a similar variation value, i.e., nitrate and water turbidity. The established baseline for variability and performance presents an important reference for the design and realization of future experiments in RAS facilities. It is foreseen that the current research facility will develop new knowledge to improve the RAS biosecurity in the Atlantic salmon aquaculture industry.
Suitability Evaluation of the Water-Energy-Food System: A Case Study in Sichuan Province, China

Water, energy, and food are the basic resources on which human beings depend for survival and development. However, these resources, ecosystem, society, and economy interact with each other in highly complex and interlinked ways, that is, the water-energy-food (WEF) nexus, which is difficult to evaluate quantitatively, particularly whether there is a harmonious, matching, and benign interaction in the WEF system for a given spatial and temporal scale, that is, the WEF system suitability. Thus, we developed a comprehensive model for the WEF system suitability evaluation, including stability, coordination, and sustainability. The model mainly contains the index system construction, weight calculation, and TOPSIS evaluation method. Specifically, we proposed an improved weight calculation method (i.e., network assignment method) based on the network analysis method and Amal’s method. A case study in Sichuan Province, China, has shown that 1) the overall level of the WEF system suitability in Sichuan Province is above medium and shows a fluctuating trend; 2) in terms of the proportion of each indicator to the total, the contribution of coordination indicators to the comprehensive evaluation decreases slightly, and the contribution of sustainability indicators is greater, but the three remain in a balanced state, as evinced by good underlying conditions and potential for future development; 3) the network assignment method can obtain more suitable statistical characteristics (standard deviation, mean, maximum, and minimum) compared with the Entropy method, Amal’s method, and analytic network process method, which are consistent with the actual conditions in the study area. In general, the evaluation results obtained by the network assignment method can better characterize the nexus at the core of complex multi-resource systems and have significant advantages in the application of comprehensive evaluation of the suitability of WEF systems.
Statistical Analysis of Multisensory and Text-Derived Representations on Concept Learning

When learning concepts, cognitive psychology research has revealed that there are two types of concept representations in the human brain: language-derived codes and sensory-derived codes. For the objective of human-like artificial intelligence, we expect to provide multisensory and text-derived representations for concepts in AI systems. Psychologists and computer scientists have published lots of datasets for the two kinds of representations, but as far as we know, no systematic work exits to analyze them together. We do a statistical study on them in this work. We want to know if multisensory vectors and text-derived vectors reflect conceptual understanding and if they are complementary in terms of cognition. Four experiments are presented in this work, all focused on multisensory representations labeled by psychologists and text-derived representations generated by computer scientists for concept learning, and the results demonstrate that (1) for the same concept, both forms of representations can properly reflect the concept, but (2) the representational similarity analysis findings reveal that the two types of representations are significantly different, (3) as the concreteness of the concept grows larger, the multisensory representation of the concept becomes closer to human beings than the text-derived representation, and (4) we verified that combining the two improves the concept representation.
Development and Validation of a Novel Hypoxia Score for Predicting Prognosis and Immune Microenvironment in Rectal Cancer

Hypoxia plays a major role in various tumor types. However, few studies have concentrated on the prognostic model of hypoxia-related genes in rectal cancer and the effect of hypoxia on neutrophil-mediated immunosuppression. We performed Kaplan–Meier analysis, random survival forest analysis, and Cox regression analysis on 342 hypoxia-related genes, constructed hypoxia score in the Gene Expression Omnibus (GEO) cohort, and verified them in the Cancer Genome Atlas (TCGA) cohort. Then the patients were divided into two groups according to the risk level. The overall survival rate of the high-risk (HRisk) group was significantly higher than that of the low-risk (LRisk) group (GEO, p < 0.001; TCGA, p = 0.016). Through receiver operating characteristic and decision curve analysis, the nomogram based on hypoxia score has excellent prediction ability. Functional enrichment analysis showed that hypoxia, metastasis, inflammation, immunity, and other related pathways were enriched. The HRisk group was associated with lower tumor purity, higher immune and stromal score, higher neutrophils, and lower activated memory CD4 + T cells. More importantly, the checkpoint of neutrophil-mediated immunosuppression increased in the HRisk group. In conclusion, a hypoxia score based on 5 hypoxia-related genes can be used to predict the prognosis of rectal cancer and ANLN with a cancer-suppressing effect and SRPX (Sushi Repeat Containing Protein X-Linked) with a cancer-promoting effect may be potential therapeutic targets for rectal cancer.
Event-Related Potentials as Markers of Efficacy for Combined Working Memory Training and Transcranial Direct Current Stimulation Regimens: A Proof-of-Concept Study

Our brains are often under pressure to process a continuous flow of information in a short time, therefore facing a constantly increasing demand for cognitive resources. Recent studies have highlighted that a lasting improvement of cognitive functions may be achieved by exploiting plasticity, i.e., the brain’s ability to adapt to the ever-changing cognitive demands imposed by the environment. Transcranial direct current stimulation (tDCS), when combined with cognitive training, can promote plasticity, amplify training gains and their maintenance over time. The availability of low-cost wearable devices has made these approaches more feasible, albeit the effectiveness of combined training regimens is still unclear. To quantify the effectiveness of such protocols, many researchers have focused on behavioral measures such as accuracy or reaction time. These variables only return a global, non-specific picture of the underlying cognitive process. Electrophysiology instead has the finer grained resolution required to shed new light on the time course of the events underpinning processes critical to cognitive control, and if and how these processes are modulated by concurrent tDCS. To the best of our knowledge, research in this direction is still very limited. We investigate the electrophysiological correlates of combined 3-day working memory training and non-invasive brain stimulation in young adults. We focus on event-related potentials (ERPs), instead of other features such as oscillations or connectivity, because components can be measured on as little as one electrode. ERP components are, therefore, well suited for use with home devices, usually equipped with a limited number of recording channels. We consider short-, mid-, and long-latency components typically elicited by working memory tasks and assess if and how the amplitude of these components are modulated by the combined training regimen. We found no significant effects of tDCS either behaviorally or in brain activity, as measured by ERPs. We concluded that either tDCS was ineffective (because of the specific protocol or the sample under consideration, i.e., young adults) or brain-related changes, if present, were too subtle. Therefore, we suggest that other measures of brain activity may be more appropriate/sensitive to training- and/or tDCS-induced modulations, such as network connectivity, especially in young adults.
Dissecting the Effects of Aldosterone and Hypokalemia on the Epithelial Na+ Channel and the NaCl Cotransporter

Primary hyperaldosteronism (PA) is characterized by aldosterone excess and hypertension. This may be linked to increased renal Na+ reabsorption via the epithelial Na+ channel (ENaC) and the NaCl cotransporter (NCC). The majority of PA patients have normal plasma K+ levels, but a subset of cases are associated with hypokalemia. High NCC levels observed in long-term studies with aldosterone-infused rodents have been attributed to direct effects of aldosterone. Aldosterone can also increase active phosphorylated NCC (pT58-NCC) acutely. However, direct effects of aldosterone on NCC have been contested by recent studies indicating that it is rather an indirect effect of hypokalemia. We therefore set out to determine isolated long-term aldosterone and K+ effects on ENaC and NCC using various in vivo and ex vivo approaches. In mice, aldosterone-induced hypokalemia was prevented by simultaneous amiloride infusion, coupled to increased cleavage of α- and γENaC but no effect on NCC. Regression analyses of in vivo data showed a positive correlation between aldosterone/K+ and αENaC but a negative correlation with NCC and pT58-NCC. Ex vivo, exposure of kidney tubules for 21 h to aldosterone increased cleavage of αENaC and γENaC, but no effects were observed on NCC or pT58-NCC. Exposure of tubules to low K+ media reduced αENaC but increased NCC and pT58-NCC. As hypokalemia can enhance cell proliferation markers in the distal convoluted tubule (DCT), we hypothesized that aldosterone infusion would increase proliferating cell nuclear antigen (PCNA) expression. Infusion of aldosterone in mice for 6 days greatly increased PCNA expression in the DCT. Collectively, in vivo and ex vivo data suggest that both aldosterone and K+ can increase ENaC directly. In contrast, the observed increase in abundance and phosphorylation of NCC in aldosterone-infused mice is likely an indirect effect of enhanced ENaC-mediated K+ secretion and subsequent hypokalemia. Thus, it is possible that NCC may only be increased in PA when the condition is associated with hypokalemia.
Characteristics of Desalination Brine and Its Impacts on Marine Chemistry and Health, With Emphasis on the Persian/Arabian Gulf: A Review

At a time when worldwide water shortage is increasing, seawater is being viewed as an inexhaustible supply of freshwater via the process of seawater desalination. As a result, seawater desalination is becoming more popular, especially in areas where freshwater is scarce, such as the Middle East and North Africa (MENA), which accounts for half of all global saltwater desalination activities. To enhance the efficiency of saltwater desalination, thermal and membrane-based desalination technologies are continually being developed and hybridized systems established. Brine is an unavoidable product of seawater desalination and is commonly disposed of in oceans and seas, where it has negative effects on the surrounding marine environment and its biodiversity due to the resultant increased salinity and temperature, as well as the presence of chemicals. Furthermore, the quality and amount of brine are influenced by several parameters, including the input quality and quantity, the desalination process, and the discharge method. The intensity of brine’s influence on the marine biota is determined by a number of factors; nevertheless, marine species differ in their tolerance to brine’s effects. Desalination technology is improving to maximize water recovery and reduce the volume of brine produced, with the objective of eventually reaching zero liquid discharge and limiting harmful effects on the marine environment. Meanwhile, proper systems for analyzing the effects of seawater desalination facilities on the marine ecology must be implemented. This review study will look at all of the factors that determine the physicochemical features of desalination brine, with a focus on its impact on marine chemistry and biodiversity. More crucially, the most cutting-edge brine management methods will be investigated for long-term desalination and a healthy marine ecosystem.
Addition of In‐Play Cooling Breaks During Intermittent Exercise While Wearing Lacrosse Uniforms in The Heat Attenuates Increases in Rectal Temperature

Abstract To reduce the risk of heat-related illness, appropriate body cooling strategies are needed during men’s lacrosse competitions in hot-humid environments. The current study investigated whether additional in-play cooling breaks would attenuate the core (rectal) body temperature rise during exercise designed to mimic the activity patterns of a men’s lacrosse match while wearing uniform in hot-humid environments. In randomized and counterbalanced order, ten physically active men completed two experimental trials comprising four quarters of 15-min intermittent cycling exercises separated by a 10-min simulated half-time break and two 2-min quarter breaks in a climate chamber (35°C, 50% relative humidity). The two trials included a regular simulated match condition (REG) and a water break time out condition (WBTO) that included additional 2-min breaks 7.5-min into each quarter. Rectal temperature was significantly lower (p=0.017) in the WBTO condition (38.23±0.23°C) compared with the REG condition (38.50±0.46°C) at the end of the 4th quarter. In addition, ratings of perceived exertion, thermal sensation, heart rate and the physiological strain index were significantly lower (all p<0.05) in the WBTO condition compared with the REG condition. The current results indicated that, even when wearing lacrosse uniforms, the implementation of WBTO attenuated the core body temperature elevation only in the latter stages of an intermittent cycling exercise protocol designed to mimic the exercise pattern of a men’s lacrosse match. Therefore, WBTO may provide a feasible and effective cooling strategy for lacrosse players to reduce the risk of heat-illness.
Integrated Transcriptomic and Metabolomic Analyses Reveal the Mechanisms Underlying Anthocyanin Coloration and Aroma Formation in Purple Fennel

The color and aroma are the significant traits of vegetables and fruits, but the metabolic and molecular mechanisms underlying anthocyanin accumulation and aroma formation remain almost unknown in fennel (Anethum foeniculum L.), which is a crucial vegetable crop and grown widely for aromatic leaves and bulbs. Here, ten major anthocyanins identified and quantified by ultra-high performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) were mainly responsible for the coloration of purple fennel leaf. With the application of GC-MS, it was found that the reduced volatile phenylpropanoids including isoeugenol, trans-isoeugenol, and apiol chiefly account for the characteristic aroma changes of the purple fennel. Moreover, the characteristic anthocyanin coloration and aroma formation in purple fennel were systematically studied with the integrated transcriptomics and metabolomics. The critical genes associated with the biosynthesis and regulation of anthocyanins and volatile phenylpropanoids were isolated and studied carefully in transiently transfected tobacco cells and transgenic tomato plants. Together with the results of UHPLC-Q-Orbitrap HRMS, RT-qPCR, and yeast two hybrid (Y2H), it is proved that the metabolic flux redirection of phenylpropanoid pathway primarily regulated by a functional MYB-bHLH-WD40 complex consisting of AfTT8, AfMYB7, and AfTTG1 accounts for the characteristic anthocyanin coloration and aroma formation in purple fennel leaf. The systematic understanding of the anthocyanin accumulation and aroma formation will assist in the improvement of fennel resource utilization and breeding.
Verbal or Written? The Impact of Apology on the Repair of Trust: Based on Competence- vs. Integrity-Based Trust Violation

This study examined the effect of verbal and written apologies on trust repair based on competence and integrity after a trust violation. Through three experiments, the empirical results showed that the written apology was more effective than verbal ones a restoring trust for integrity-based trust violations. However, the verbal apology was more effective against competency-based trust violations than a written one. Moreover, the results also showed that perceived trustworthiness played a mediating role between trust violation and trust repair, while positive emotions played a moderating role. Finally, this study provided a general discussion, implications, and suggestions for future research.