DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes.

Phages, the natural predators of bacteria, were discovered more than 100 years ago. However, increasing antimicrobial resistance rates have revitalized phage research. Methods that are more time-consuming and efficient than wet-laboratory experiments are needed to help screen phages quickly for therapeutic use. Traditional computational methods usually ignore the fact that phage-bacteria interactions are achieved by key genes and proteins. Methods for intraspecific prediction are rare since almost all existing methods consider only interactions at the species and genus levels. Moreover, most strains in existing databases contain only partial genome information because whole-genome information for species is difficult to obtain. Here, we propose a new approach for interaction prediction by constructing new features from key genes and proteins via the application of K-means sampling to select high-quality negative samples for prediction. Finally, we develop DeepPBI-KG, a corresponding prediction tool based on feature selection and a deep neural network. The results show that the average area under the curve for prediction reached 0.93 for each strain, and the overall AUC and area under the precision-recall curve reached 0.89 and 0.92, respectively, on the independent test set; these values are greater than those of other existing prediction tools. The forward and reverse validation results indicate that key genes and key proteins regulate and influence the interaction, which supports the reliability of the model. In addition, intraspecific prediction experiments based on Klebsiella pneumoniae data demonstrate the potential applicability of DeepPBI-KG for intraspecific prediction. In summary, the feature engineering and interaction prediction approaches proposed in this study can effectively improve the robustness and stability of interaction prediction, can achieve high generalizability, and may provide new directions and insights for rapid phage screening for therapy.

Microstructural and functional substrates underlying dispositional greed and its link with trait but not state impulsivity.

The interplay between personality traits and impulsivity has long been a central theme in psychology and psychiatry. However, the potential association between Greed Personality Traits (GPT) and impulsivity, encompassing both trait and state impulsivity and future time perspective, remains largely unexplored. To address these issues, we employed questionnaires and an inter-temporal choice task to estimate corresponding trait/state impulsivity and collected multi-modal neuroimaging data (resting-state functional imaging: n = 430; diffusion-weighted imaging: n = 426; task-related functional imaging: n = 53) to investigate the underlying microstructural and functional substrates. Behavioral analyses revealed that GPT mediated the association between time perspective (e.g., present fatalism) and trait impulsivity (e.g., motor impulsivity). Functional imaging analyses further identified that brain activation strengths and patterns related to delay length, particularly in the dorsomedial prefrontal cortex, superior parietal lobule, and cerebellum, were associated with GPT. Moreover, individuals with similar levels of greed exhibited analogous spontaneous brain activity patterns, predominantly in the Default Mode Network (DMN), Fronto-Parietal Network (FPN), and Visual Network (VIS). Diffusion imaging analysis observed specific microstructural characteristics in the spinocerebellar/pontocerebellar fasciculus, internal/external capsule, and corona radiata that support the formation of GPT. Furthermore, the corresponding neural activation pattern, spontaneous neural activity pattern, and analogous functional couplings among the aforementioned brain regions mediated the relationships between time perspective and GPT and between GPT and motor impulsivity. These findings provide novel insights into the possible pathway such as time perspective → dispositional greed → impulsivity and uncover their underlying microstructural and functional substrates.

Happy people are always similar: The evidence from brain morphological and functional inter-subject correlations.

A fundamental question in the study of happiness is whether there is neural evidence to support a well-known hypothesis that happy people are always similar while unfortunate people have their own misfortunes. To investigate this, we employed several happiness-related questionnaires to identify potential components of happiness, and further investigated and confirmed their associations with personality, mood, aggressive behaviors, and amygdala reactivity to fearful faces within a substantial sample size of college students (n = 570). Additionally, we examined the functional and morphological similarities and differences among happy individuals using the inter-subject representational similarity analysis (IS-RSA). IS-RSA emphasizes the geometric properties in a high-dimensional space constructed by brain or behavioral patterns and focuses on individual subjects. Our behavioral findings unveiled two factors of happiness: individual and social, both of which mediated the effect of personality traits on individual aggression. Subsequently, mood mediated the impact of happiness on aggressive behaviors across two subgroup splits. Functional imaging data revealed that individuals with higher levels of happiness exhibited reduced amygdala reactivity to fearful faces, as evidenced by a conventional face-matching task (n = 104). Moreover, IS-RSA demonstrated that these participants manifested similar neural activation patterns when processing fearful faces within the visual pathway, but not within the emotional network (e.g., amygdala). Morphological observations (n = 425) indicated that individuals with similar high happiness levels exhibited comparable gray matter volume patterns within several networks, including the default mode network, fronto-parietal network, visual network, and attention network. Collectively, these findings offer early neural evidence supporting the proposition that happy individuals may share common neural characteristics.

Vertical Cross-Alignments of 2D Semiconductors with Steered Internal Electric Field for Urea Electrooxidation via Balancing Intermediates Adsorption.

Single-component electrocatalysts generally lead to unbalanced adsorption of OH- and urea during urea oxidation reaction (UOR), thus obtaining low activity and selectivity especially when oxygen evolution reaction (OER) competes at high potentials (>1.5 V). Herein, a cross-alignment strategy of in situ vertically growing Ni(OH)2 nanosheets on 2D semiconductor g-C3N4 is reported to form a hetero-structured electrocatalyst. Various spectroscopy measurements including in situ experiments indicate the existence of enhanced internal electric field at the interfaces of vertical Ni(OH)2 and g-C3N4 nanosheets, favorable for balancing adsorption of reaction intermediates. This heterojunction electrocatalyst shows high-selectivity UOR compared to pure Ni(OH)2, even at high potentials (>1.5 V) and large current density. The computational results show the vertical heterojunction could steer the internal electric field to increase the adsorption of urea, thus efficiently avoiding poisoning of strongly adsorbed OH- on active sites. A membrane electrode assembly (MEA)-based electrolyzer with the heterojunction anode could operate at an industrial-level current density of 200 mA cm-2. This work paves an avenue for designing high-performance electrocatalysts by vertical cross-alignments of active components.

Reactivity of the ventromedial prefrontal cortex, but not the amygdala, to negative emotion faces predicts greed personality trait.

This study explored whether amygdala reactivity predicted the greed personality trait (GPT) using both task-based and resting-state functional connectivity analyses (ntotal = 452). In Cohort 1 (n = 83), task-based functional magnetic resonance imaging (t-fMRI) results from a region-of-interest (ROI) analysis revealed no direct correlation between amygdala reactivity to fearful and angry faces and GPT. Instead, whole-brain analyses revealed GPT to robustly negatively vary with activations in the right ventromedial prefrontal cortex (vmPFC), supramarginal gyrus, and angular gyrus in the contrast of fearful + angry faces > shapes. Moreover, task-based psychophysiological interaction (PPI) analyses showed that the high GPT group showed weaker functional connectivity of the vmPFC seed with a top-down control network and visual pathways when processing fearful or angry faces compared to their lower GPT counterparts. In Cohort 2, resting-state functional connectivity (rs-FC) analyses indicated stronger connectivity between the vmPFC seed and the top-down control network and visual pathways in individuals with higher GPT. Comparing the two cohorts, bilateral amygdala seeds showed weaker associations with the top-down control network in the high group via PPI analyses in Cohort 1. Yet, they exhibited distinct rs-FC patterns in Cohort 2 (e.g., positive associations of GPT with the left amygdala-top-down network FC but negative associations with the right amygdala-visual pathway FC). The study underscores the role of the vmPFC and its functional connectivity in understanding GPT, rather than amygdala reactivity.

Apple polyphenol biotransformation using probiotics in vitro and dynamic simulated digestion by bionic rats.

BACKGROUND: The present study investigated the effects of fermentation by Lactobacillus rhamnosus zrx01 (LR-zrx01), Lactobacillus acidophilus zrx02 (LA-zrx02), and Lactobacillus plantarum zrx03 (LP-zrx03), as well as dynamic simulated digestion by bionic rats, on the biotransformation and antioxidant potential of apple polyphenols. Polyphenols were determined by ultra-high-performance liquid chromatography-mass spectrometry, the dynamic simulated digestion of fermented apple pulp was determined by bionic rats, and the antibacterial and antioxidant activities were analyzed. RESULTS: The polyphenol content of apple pulp fermented using the three strains was respectively 1.41, 1.38, and 1.36 times that of non-fermented pulp. The antibacterial activity of apple pulp improved dramatically after fermentation. Moreover, the antioxidant potential of apple pulp increased after fermentation and digestion. After dynamic simulated digestion by bionic rats, the polyphenol content in unfermented and the three fermented groups increased significantly by 1.19, 1.23, 1.20, and 1.19 times compared to that before digestion, respectively. The major polyphenols in each group with obvious changes were epicatechin, rutin, kaempferol, quercetin-3 galactoside, p-coumaric acid, and two unknown substances, 1 and 2. CONCLUSION: Fermented and digested apple polyphenols showed better biotransformation effects and mostly existed in the form of small molecules, which was conducive to the improvement of polyphenol bioavailability and beneficial to the absorption of active substances by the human body. These findings build a foundation for the development of functional food beverages. © 2023 Society of Chemical Industry.

Hormone-response transcriptional landscapes of wheat seedlings and the development of a JA fluorescent reporter.

Wheat is an essential energy and protein source for humans. Climate change brings daunting challenges to wheat yield through environmental stresses, in which phytohormones play critical roles. Nevertheless, the comprehensive understanding of wheat phytohormone responses remains elusive. Here, we investigated the transcriptome response of wheat seedlings to five phytohormones, cytokinin (6-BA), abscisic acid (ABA), gibberellic acid (GA), jasmonate (JA) and salicylic acid (SA). We further selected two JA marker genes and cloned their promoters to drive the expression of 3XEGFP (tandem trimeric enhanced green fluorescent protein) in transgenic lines. The JA fluorescent reporter displayed a fast and stable response to JA treatment as an ideal tool to follow JA dynamics during fungal and cold stresses at a cellular resolution. Overall, this study provided a transcriptional landscape and facilitated generating fluorescent reporters to monitor the dynamics of phytohormones in food crops.

Highly Efficient Ag3PO4/g-C3N4 Z-Scheme Photocatalyst for Its Enhanced Photocatalytic Performance in Degradation of Rhodamine B and Phenol.

Ag3PO4/g-C3N4 heterojunctions, with different g-C3N4 dosages, were synthesized using an in situ deposition method, and the photocatalytic performance of g-C3N4/Ag3PO4 heterojunctions was studied under simulated sunlight conditions. The results revealed that Ag3PO4/g-C3N4 exhibited excellent photocatalytic degradation activity for rhodamine B (Rh B) and phenol under the same light conditions. When the dosage of g-C3N4 was 30%, the degradation rate of Rh B at 9 min and phenol at 30 min was found to be 99.4% and 97.3%, respectively. After five cycles of the degradation experiment for Rh B, g-C3N4/Ag3PO4 still demonstrated stable photodegradation characteristics. The significant improvement in the photocatalytic activity and stability of g-C3N4/Ag3PO4 was attributed to the rapid charge separation between g-C3N4 and Ag3PO4 during the Z-scheme charge transfer and recombination process.

Change of Flavonoid Content in Wheatgrass in a Historic Collection of Wheat Cultivars.

Wheatgrass is recognized for its nutritional and medicinal properties, partly attributed to its flavonoid content. The objective of this study was to assess the flavonoid content and antioxidant properties of wheatgrass obtained from a wide range of 145 wheat cultivars, which included Chinese landraces (CL), modern Chinese cultivars (MCC), and introduced modern cultivars (IMC). The flavonoids were extracted using a solution of 80% methanol, and their content was evaluated using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). The results revealed the assessed cultivars showed significant variation in their total flavonoid content (TFC), with MCCs generally having higher amounts compared to CLs. PCA analysis demonstrated clear variations in flavonoid profiles between different cultivar groups, emphasizing the evolutionary inconsistencies in wheat breeding. The antioxidant assays, ABTS, DPPH, and FRAP, exhibited robust abilities for eliminating radicals, which were found to be directly associated with the amounts of flavonoids. In addition, this study investigated the correlation between the content of flavonoids and the ability to resist powdery mildew in a collection of mutated wheat plants. Mutants exhibiting heightened flavonoid accumulation demonstrated a decreased severity of powdery mildew, suggesting that flavonoids play a protective role against fungal infections. The results highlight the potential of wheatgrass as a valuable source of flavonoids that have antioxidant and protective effects. This potential is influenced by the genetic diversity and breeding history of wheatgrass. Gaining insight into these connections can guide future wheat breeding endeavors aimed at improving nutritional value and in strengthening disease resistance. The current finding provides critical information for developing wheatgrass with high flavonoid content and antioxidant activity.

Study on The Concentration of Acrylic Acid and Acetic Acid by Reverse Osmosis.

In the production of acrylic acid, the concentration of acrylic acid solution from the adsorption tower was low, which would lead to significant energy consumption in the distillation process to purify acrylic acid, along with the production of a large amount of wastewater. Reverse osmosis (RO) was proposed to concentrate the acrylic acid aqueous solution taken from a specific tray in the absorption tower. The effects of operating conditions on the permeate flux and acid retention were studied with two commercial RO membranes (SWC5 and SWC6). When the operating pressure was 4 MPa and the temperature was 25 °C, the permeate fluxes of two membranes were about 20 L·m-2·h-1. The acrylic acid and acetic acid retentions were about 80% and 78%, respectively. After being immersed in the acid solutions for several months, the characteristics of the two membranes were tested to evaluate their acid resistance. After six months of exposure to the acid solution containing 2.5% acrylic acid and 2.5% acetic acid, the retentions of acrylic acid and acetic acid were decreased by 5.7% and 4.1% for SWC5 and 4.9% and 2.2% for SWC6, respectively. The changes of membrane surface morphology and chemical composition showed the hydrolysis of some amide bonds.