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Reverse osmosis (RO) membrane fouling and biological contamination problems faced by seawater desalination systems are microbiologically related. We used full-length 16S rRNA gene sequencing to assess the bacterial community structure and chlorine-resistant bacteria (CRB) associated with biofilm growth in different treatment processes under the winter mode of a chlorinated seawater desalination system in China. At the outset of the winter mode, certain CRB, such as Acinetobacter, Pseudomonas, and Bacillus held sway over the bacterial community structure, playing a pivotal role in biofouling. At the mode's end, Deinococcus and Paracoccus predominated, with Pseudomonas and Roseovarius following suit, while certain CRB genera still maintained their dominance. RO and chlorination are pivotal factors in shaping the bacterial community structure and diversity, and increases in total heterotrophic bacterial counts and community diversity in safety filters may adversely affect the effectiveness of subsequent RO systems. Besides, the bacterial diversity and culturable biomass in the water produced by the RO system remain high, and some conditionally pathogenic CRBs pose a certain microbial risk as a source of drinking water. Targeted removal of these CRBs will be an important area of research for advancing control over membrane clogging and ensuring water quality safety in the future. HIGHLIGHTS RO and chlorine disinfection of seawater desalination systems are important for the structural diversity of the bacterial community, and the composition of the bacterial community has changed significantly.; A number of CRBs typically associated with biofilm formation are important in the bacterial community structure and are present in large numbers in the RO-produced water.;

Biological nitrogen removal technology has bottlenecks such as long start-up time and low efficiency in the process of high ammonia nitrogen wastewater treatment due to the specificity of wastewater, while the screened single high-efficiency nitrogen removal strain suffers from poor stability in the actual wastewater treatment process. In this study, based on the screening of a large number of highly efficient heterotrophic nitrification- aerobic denitrification strains,the core strains 139# and 142# were identified through partial factorial experiments, and the strain combinations were optimized by combining metabolic correlation and stratified sampling methods to artificially construct an efficient nitrogen removal community. The optimum combination of strains was obtained by re-screening with sludge at pH 5.5, and the ability of the constructed community for nitrogen removal was verified by using a reactor to simulate weak acidic wastewater treatment. The results showed that the screened high-efficiency bacterial community P44-P83-A88-P94-A142 achieved 96.97% removal of NH4+-N at 48 h under the condition of initial NH4+-N mass concentration of 200 mg/L and initial pH of 5.5. Within the reactor to simulate the actual wastewater environment, the addition of the bacteria at a weakly acidic pH of 5.5 increased the removal rate of NH4+-N from 44.89% to 75.17% and the effluent pH from 6.9 to 8.3. This study can provide a theoretical basis for the application of artificially constructed bacterial community in the treatment of weakly acidic wastewater for nitrogen removal.

By collecting focal mechanism solutions of earthquakes at different depths from Northeast Japan to Northeast China during 1957 to 2022, the joint iterative stress inversion method is used to calculate the tectonic stress field in the subduction zone and the tectonic stress field state in Northeast China. The results show that the shallow area of the Japan trench is not only affected by the subduction and extrusion of the Pacific plate, but also related to the extrusion of the North American plate. The deep source earthquakes in Northeast China are closely related to the long-term action of the trench subduction zone. The formation of the Changbaishan volcanic area has a great relationship with the thrust of the subduction zone. The seismicity of the subduction zone indirectly controls the formation and activity of the volcanic area in Northeast Asia. The principal compressive stress axis distributes in the NEE-SWW direction in the Yingkou area of Liaoning, while the principal tensile stress axis distributes in the NNW-SSE direction. Based on the results of the focal mechanism of shallow earthquakes in the volcanic area and its surrounding areas, it is believed that the current tectonic stress field in the northeastern volcanic area continues the overall structure of stress in the northeastern region, with the principal compressive stress axis in the NEE-SWW direction and the principal tensile stress axis in the NNW-SSE direction.

Abstract Background Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV lineages. However, the factor of the distribution and evolution characteristics and phylodynamics of the virus was still limited. Methods To enhance comprehensive understanding of LASV, we employed phylogenetic analysis, reassortment and recombination detection, and variation evaluation utilizing publicly available viral genome sequences. Results The results showed the estimated the root of time of the most recent common ancestor (TMRCA) for large (L) segment was approximately 634 (95% HPD: [385879]), whereas the TMRCA for small (S) segment was around 1224 (95% HPD: [10301401]). LASV primarily spread from east to west in West Africa through two routes, and in route 2, the virus independently spread to surrounding countries through Liberia, resulting in a wider spread of LASV. From 1969 to 2018, the effective population size experienced two significant increased, indicating the enhanced genetic diversity of LASV. We also found the evolution rate of L segment was faster than S segment, further results showed zinc-binding protein had the fastest evolution rate. Reassortment events were detected in multiple lineages including sub-lineage IIg, while recombination events were observed within lineage V. Significant amino acid changes in the glycoprotein precursor of LASV were identified, demonstrating sequence diversity among lineages in LASV. Conclusion This study comprehensively elucidated the transmission and evolution of LASV in West Africa, providing detailed insights into reassortment events, recombination events, and amino acid variations.

PM2.5 pollution has been associated with the incidence of lung cancer, but the underlying mechanism is still unclear. PIWI-interacting RNAs (piRNAs), initially identified in germline cells, have emerged as a novel class of small non-coding RNAs (26 – 32 nucleotides) with diverse functions in various diseases, including cancer. However, the role and mechanism of piRNAs in the development of PM2.5-induced lung cancer remain to be clarified. In the presented study, we used a PM2.5-induced malignant transformation cell model to analyze the change of piRNA profiles. Among the disturbed piRNAs, piR-27222 was identified as an oncogene that inhibited cell death in a m6A-dependent manner. Mechanistically, we found that piR-27222 could deubiquitinate and stabilize eIF4B by directly binding to eIF4B and reducing its interaction with PARK2. The enhanced expression of eIF4B, in turn, promoted the expression of WTAP, leading to increased m6A modification in the Casp8 transcript. Consequently, the stability of Casp8 transcripts was reduced, rendering lung cancer cells resistant to PANoptosis. Collectively, our findings reveal that PM2.5 exposure up-regulated piR-27222 expression, which could affect EIF4B/WTAP/m6A axis, thereby inhibiting PANoptosis of cells and promoting lung cancer. Our study provides new insights into understanding the epigenetic mechanisms underlining PM2.5-induced lung cancer.

Continuous gain and loss of genes are the primary driving forces of bacterial evolution and environmental adaptation. Studying bacterial evolution in terms of protein domain, which is the fundamental function and evolutionary unit of proteins, can provide a more comprehensive understanding of bacterial differentiation and phenotypic adaptation processes. Therefore, we proposed a phylogenetic tree-based method for detecting genetic gain and loss events in terms of protein domains. Specifically, the method focuses on a single domain to trace its evolution process or on multiple domains to investigate their co-evolution principles. This novel method was validated using 122 Shigella isolates. We found that the loss of a significant number of domains was likely the main driving force behind the evolution of Shigella, which could reduce energy expenditure and preserve only the most essential functions. Additionally, we observed that simultaneously gained and lost domains were often functionally related, which can facilitate and accelerate phenotypic evolutionary adaptation to the environment. All results obtained using our method agree with those of previous studies, which validates our proposed method.

PIWI-interacting RNAs (piRNAs) is an emerging class of small non-coding RNAs that has been recently reported to have functions in infertility, tumorigenesis, and multiple diseases in humans. Previously, 5 toxicity pathways were proposed from hundreds of toxicological studies that underlie BaP-induced lung injuries, and a “Bottom-up” approach was established to identify small non-coding RNAs that drive BaP-induced pulmonary effects by investigating the activation of these pathways in vitro, and the expression of the candidate microRNAs were validated in tissues of patients with lung diseases from publications. Here in this study, we employed the “Bottom-up” approach to identifying the roles of piRNAs and further validated the mechanisms in vivo using mouse acute lung injury model. Specifically, by non-coding RNA profiling in in vitro BaP exposure, a total of 3 suppressed piRNAs that regulate 5 toxicity pathways were proposed, including piR-004153 targeting CYP1A1, FGFR1, ITGA5, IL6R, NGRF, and SDHA, piR-020326 targeting CDK6, and piR-020388 targeting RASD1. Animal experiments demonstrated that tail vein injection of respective formulated agomir-piRNAs prior to BaP exposure could all alleviate acute lung injury that was shown by histopathological and biochemical evidences. Immunohistochemical evaluation focusing on NF-kB and Bcl-2 levels showed that exogenous piRNAs protect against BaP-induced inflammation and apoptosis, which further support that the inhibition of the 3 piRNAs had an important impact on BaP-induced lung injuries. This mechanism-driven, endpoint-supported result once again confirmed the plausibility and efficiency of the approach integrating in silico, in vitro, and in vivo evidences for the purpose of identifying key molecules.

Blasting test research was conducted on iron ore specimens with variable line density charging structures. Computer tomography (CT), digital image processing, and three-dimensional model reconstruction techniques were used to analyze the damage characteristics of iron ore specimens after blasting based on the calculated number of box dimensions. The results show that increasing the variable line density section charge uncoupling coefficient reduces the overall damage to the specimen by up to 1.73%, indicating that the overall damage size negatively correlates with the size of the variable line density section charge uncoupling coefficient. The damage characteristics of iron ore specimens from different layers (uncoupled charging section, transition section, coupled charging section) have some variability; when the uncoupling coefficient of the uncoupled charging section was reduced, the uncoupled section of the center of the damaged layer increased and then reduced. In contrast, the transition section shows a trend of increase, and the coupled section shows a minor difference, fully demonstrating the change in the variable line density section of the uncoupling coefficient of the specimen blasting damage effects. This study concludes that in the actual blasting project, choosing a reasonable variable line charge density structure can make the release of explosive blast energy more uniform to efficiently and thoroughly use explosive power to improve the iron ore crushing effect.

Abstract Stretchable electronics have the unique capability of 3D (three dimensional) deformation, overcoming the brittleness of traditional inorganic electronics. However, during large deformations, different scale strains between the rigid and stretchable components lead to mismatch, causing interconnect failures. Therefore, the development of the rigidity‐programmable substrate with effective strain shielding capabilities has become a research hotspot. Furthermore, the exponential growth in electronic density presents challenges in the circuit design of stretchable electronics. The urgent need is to develop highly integrated stretchable electronic systems. In this study, a highly integrated stretchable pulse sensor with effective strain shielding capabilities using hybrid 3D printing technology is developed, which comprises electronic chips, a rigidity‐programmable substrate/encapsulation layer printed by using PSC (polydimethylsiloxane/silica‐nanoparticles composite)‐based ink, and LM (liquid metal)‐based 3D circuits. First, the PSC‐based ink is optimized to enhance the strain shielding effectiveness of the rigidity‐programmable substrate. Meanwhile, 3D printing parameters are optimized to achieve high printing precision with minimum line widths below 100 µm. The resulting stretchable pulse sensor demonstrated good mechanical and electrical stability under complex 3D deformations, including bending, twisting, and stretching. The PSC region strain of the sensor is only ≈2% when the global strain is up to ≈65%, which exhibited effective strain shielding capabilities.

This study explored the development of polyvinylpyrrolidone (PVP)–honey-gel (PHG) through 3D printing, aiming to develop a multifunctional bio-tape with adhesive and degradable properties. Based on the potential of honey to promote wound healing due to its antibacterial and anti-inflammatory properties, a PVP–honey-based 3D printing ink was developed by combining honey and PVP to create PHG through 3D printing technology that can form a film with strong adhesion and flexibility. First, the chemical–physical properties of PHG and its 3D printing performance were characterized. The line width achievable in 3D printing for the PHG line can extend to ∼100 µm. In addition, the adhesive properties of the PHG film were evaluated by using a 180° peeling test on various materials (glass, copper, wood, and pig skin), highlighting its potential for diverse applications. Finally, the application of the PHG film as a bio-tape was demonstrated through a successful animal experiment on a rabbit’s skin wound. Due to its adhesive and degradable properties, the bio-tape exhibited 3D conformability and ease of removal without residue.

Abstract CD8+ T cells are critical for host antitumor responses, whereas persistent antigenic stimulation and excessive inflammatory signals lead to T cell dysfunction or exhaustion. Increasing early memory T cells can improve T cell persistence and empower T cell‐mediated tumor eradication, especially for adoptive cancer immunotherapy. Here, it is reported that tumor‐associated monocytes (TAMos) are highly correlated with the accumulation of CD8+ memory T cells in human cancers. Further analysis identifies that TAMos selectively reprogram CD8+ T cells into T central memory‐like (TCM‐like) cells with enhanced recall responses. L‐NMMA, a pan nitric oxide synthase inhibitor, can mitigate TAMo‐mediated inhibition of T cell proliferation without affecting TCM‐like cell generation. Moreover, the modified T cells by TAMo exposure and L‐NMMA treatment exhibit long‐term persistence and elicit superior antitumor effects in vivo. Mechanistically, the transmembrane protein CD300LG is involved in TAMo‐mediated TCM‐like cell polarization in a cell‐cell contact‐dependent manner. Thus, the terminally differentiated TAMo subset (CD300LGhighACElow) mainly contributes to TCM‐like cell development. Taken together, these findings establish the significance of TAMos in boosting T‐cell antitumor immunity.

Some Brucella spp. are important pathogens. According to the latest prokaryotic taxonomy, the Brucella genus consists of facultative intracellular parasitic Brucella species and extracellular opportunistic or environmental Brucella species. Intracellular Brucella species include classical and nonclassical types, with different species generally exhibiting host preferences. Some classical intracellular Brucella species can cause zoonotic brucellosis, including B. melitensis, B. abortus, B. suis, and B. canis. Extracellular Brucella species comprise opportunistic or environmental species which belonged formerly to the genus Ochrobactrum and thus nowadays renamed as for example Brucella intermedia or Brucella anthropi, which are the most frequent opportunistic human pathogens within the recently expanded genus Brucella. The cause of the diverse phenotypic characteristics of different Brucella species is still unclear. To further investigate the genetic evolutionary characteristics of the Brucella genus and elucidate the relationship between its genomic composition and prediction of phenotypic traits, we collected the genomic data of Brucella from the NCBI Genome database and conducted a comparative genomics study. We found that classical and nonclassical intracellular Brucella species and extracellular Brucella species exhibited differences in phylogenetic relationships, horizontal gene transfer and distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes, showing the close relationship between the genetic variations and prediction of phenotypic traits of different Brucella species. Furthermore, we found significant differences in horizontal gene transfer and the distribution patterns of mobile genetic elements, virulence factor genes, and antibiotic resistance genes between the two chromosomes of Brucella, indicating that the two chromosomes had distinct dynamics and plasticity and played different roles in the survival and evolution of Brucella. These findings provide new directions for exploring the genetic evolutionary characteristics of the Brucella genus and could offer new clues to elucidate the factors influencing the phenotypic diversity of the Brucella genus.

Abstract Herein, we fabricated a flexible semidry electrode with excellent mechanical performance, satisfactory self‐adhesiveness, and low‐contact impedance using physical/chemical crosslinked polyvinyl alcohol/polyacrylamide dual‐network hydrogels (PVA/PAM DNHs) as an efficient saline reservoir. The resultant PVA/PAM DNHs showed admirable adhesive and compliance to the hairy scalp, facilitating the establishment of a robust electrode/skin interface for biopotential signal transmission. Moreover, the PVA/PAM DNHs steadily released trace saline onto the scalp to achieve the minimized potential drift (1.47 ± 0.39 mV/min) and low electrode–scalp impedance (18.2 ± 8.9 kΩ @ 10 Hz). More importantly, the application feasibility of real‐world brain−computer interfaces (BCIs) was preliminarily validated by 10 participants using two classic BCI paradigms. The mean temporal cross‐correlation coefficients between the semidry and wet electrodes in the eyes open/closed and the N200 speller paradigms are 0.919 ± 0.054 and 0.912 ± 0.050, respectively. Both electrodes demonstrate anticipated neuroelectrophysiological responses with similar patterns. This semidry electrode could also effectively capture robust P‐QRS‐T peaks during electrocardiogram recording. Considering their outstanding advantages of fast setup, user‐friendliness, and robust signals, the proposed PVA/PAM DNH‐based electrode is a promising alternative to wet electrodes in biopotential signal acquisition.

Abstract As a red tide algal toxin with intense neurotoxicity distributed worldwide, domoic acid (DA) has attracted increasing concerns. In this work, the integrative analysis of metagenome and metabolome are applied to investigate the impact of DA on nitrogen cycling in coastal sediments. Here we show that DA can act as a stressor to induce the variation of nitrogen (N) cycling by altering the abundance of functional genes and electron supply. Moreover, microecology theory revealed that DA can increase the role of deterministic assembly in microbial dynamic succession, resulting in the shift of niches and, ultimately, the alteration in N cycling. Notably, denitrification and Anammox, the important process for sediment N removal, are markedly limited by DA. Also, variation of N cycling implies the modification in cycles of other associated elements. Overall, DA is capable of ecosystem-level effects, which require further evaluation of its potential cascading effects.

Since 3D printed structure is conducted by the style of dimension reduction, the defects typically occur between the printing layers due to the poor rheological properties, which affects the durability most. This study focuses on exploring the durability of 3D printed calcium sulphoaluminate cement-based materials (CSACMs) with slag powder based on the correlation between printed structures and rheological parameters. Experimental results show that both the static and dynamic yield stress of 3D printed CSACMs exhibits a gradual increase with the slag powder content increases, while the thixotropy improves continually until reaching a maximum content at 15%. In this case, an increase in slag powder content leads to a significant reduction for structure deformation. However, poor printability occurs when the content of slag powder exceeds 15%. Besides, the chloride migration coefficient and maximum electric flux decreases from 7.28 × 10−12 to 3.27 × 10−12 m2/s and 1347 to 711 K, respectively, when the content of slag powder increases from 0 to 10%. Meanwhile, the freezing resistance and linear shrinkage are improved. Based on the radar map correlation, structure deformation is significantly influenced by thixotropy, which is a crucial factor that can impact the durability of 3D printed CSACMs. In conclusion, the controllable rheology of 3D printed CSACMs are advantageous for improving the printed structures and durability.

This paper focuses on the IoT information data acquisition technology based on embedded systems, including the overall structure of embedded systems, hardware design and selection, software system design and data acquisition algorithm design. In the data acquisition algorithm design, the IoT approximate data acquisition and reconstruction SR algorithm are proposed, and both the time dimension curvature and the spatial dimensional curvature are used in the sampling node selection. Finally, the simulation experiment of data acquisition technology based on embedded systems is conducted to analyze the data acquisition efficiency of mobile nodes. The outcomes demonstrate that the rebuilt SR algorithm has a data collection success rate of 0.91, and the sink locations are relatively evenly distributed throughout the sensing area and cover almost the entire sensing area. The research in this paper provides some guidance and reference for the embedded system, which is applied in the field of IoT information data acquisition.

The outbreak and spread of COVID-19 remind us again of the devastating attack that human-to-human transmitted respiratory infectious diseases (H-HRIDs) bring to global economics and public health. Predicting the trend of H-HRIDs yields important suggestions for making response strategies. Existing methods predict the future trend of H-HRIDs based on the prophase epidemiological data. However, it is also crucial to predict the potential outbreak trend of H-HRIDs in regions without prophase epidemiological data based on those with epidemiological data available. This prediction can provide constructive pharmaceutical strategies and non-pharmaceutical interventions such as pre-allocating the limited preventions to regions with different potential trends, especially at the early stage of an H-HRID. In this paper, transform the problem of predicting the early-stage trend of an H-HRID in new regions without prophase epidemiological data into the problem of learning regions’ geospatial features via a Contrastive learning-based Hierarchical Graph Convolutional Neural Network (CHGCN). Specifically, CHGCN first generates training data from regions with epidemiological data available via a Relaxed Graph Edit Distance (RGED) algorithm. CHGCN then uses a constructive learning schema to learn region embeddings, where regions with similar geospatial features and H-HRID trends exhibit similar embeddings. Once trained, CHGCN searches for the region with epidemiological data available that has the highest embedding similarity to the given query region without prophase epidemiological data, so as to achieve early-stage H-HRID trend prediction for the query region. Experimental results on COVID-19 demonstrate that the proposed CHGCN achieves state-of-the-art performance in predicting the early-stage trend of H-HRIDs, compared with the baselines.

A novel type of tubular structure with negative Poisson's ratio based on gyroid-type triply periodic minimal surfaces (TPMSs) is proposed in this study. This work is an attempt to design auxetic tubular structures based on TPMS. A series of auxetic tubular structures were designed and then fabricated using laser power bed fusion. Compressive behaviours of the fabricated auxetic tubular structures were investigated using experimental and numerical methods. To obtain optimal designs of tubular structures with controllable auxetic properties, the influence of several parameters were investigated comprehensively. Subsequently, several graded auxetic tubular structures were designed based on the parametric analysis and studied numerically. The mechanical properties of the tubular structures could be controlled effectively using the proposed approach. The proposed method can be used for guiding the design and optimisation of auxetic tubular structures, showing excellent potential for various applications such as biomedical devices, vehicle crashworthiness, and protective engineering.

Abstract In recent years, nuclear magnetic resonance (NMR) logging has become increasingly prevalent in the characterization of rock properties such as porosity, permeability, saturation, and pore size distribution. However, interpreting such properties accurately from NMR logging data is challenging for some reservoirs. In particular, the impact of salinity, viscosity, and saturation on NMR measurements is not always clear, which can lead to inaccuracies in the resulting data interpretation. Properly accounting for these factors is essential in order to obtain accurate and reliable measurements for effective characterization of subsurface formations. This study utilized a random walk technique to simulate the NMR response of homogeneous sandstones using 3D CT images and conducted a sensitivity analysis under various salinity, crude oil viscosity, and water saturation conditions. The results indicate that the T2 relaxation time slightly shifts toward the short relaxation direction as the salinity of the formation water increases. In addition, longer echo intervals result in a more significant forward shift in the T2 value than shorter intervals. Whereas, for crude oil, the T2 relaxation time becomes shorter as its viscosity increases. Furthermore, the effect of echo interval on the forward T2 shift is less pronounced for crude oil than it is for formation water. Under water wet conditions, the T2 spectrum of crude oil exhibits a peak at the volume relaxation position. As the water saturation decreases, the left two peaks in the T2 spectrum shift toward shorter relaxation times. Under oil wet conditions, the T2 spectrum exhibits a complex three-peak structure. The method provides a physical basis for interpreting NMR macroscopic responses, and the simulated NMR responses can help identify fluids in reservoirs.

Triply periodic minimal surfaces (TPMSs) have demonstrated significant potential in lattice structure design and have been successfully applied across multiple industrial fields. In this work, a novel lattice structure with tunable anisotropic properties is proposed based on two typical TPMS types, and their mechanical performances are studied both experimentally and numerically after being fabricated using a polymer 3D printing process. Initially, adjustments are made to the original TPMS lattice structures to obtain honeycomb lattice structures, which are found to possess significant anisotropy, by utilizing numerical homogenization methods. Based on this, a continuous self-twisting deformation is proposed to change the topology of the honeycomb lattice structures to largely tune the mechanical properties. Quasi-static compression experiments are conducted with different twisting angles, and the results indicate that self-twisting can affect the mechanical properties in specific directions of the structure, and also enhance the energy absorption capacity. Additionally, it mitigates the risk of structural collapse and failure during compression while diminishing structural anisotropy. The proposed self-twisting strategy, based on honeycomb lattice structures, has been proven valuable in advancing the investigation of lattice structures with largely tunable mechanical properties.

SiCp/Al composite materials are widely used in various industries such as the aerospace and the electronics industries, primarily due to their excellent material properties. However, their machinability is significantly weakened due to their unique characteristics. Consequently, efficient and precise machining technology for SiCp/Al composite materials has become a crucial research area. By conducting a comprehensive analysis of the relevant research literature from both domestic and international sources, this study examines the processing mechanism, as well as the turning, milling, drilling, grinding, special machining, and hybrid machining characteristics, of SiCp/Al composite materials. Moreover, it summarizes the latest research progress in composite material processing while identifying the existing problems and shortcomings in this area. The aim of this review is to enhance the machinability of SiCp/Al composite materials and promote high-quality and efficient processing methods.

Aristolochic acid (AA) as an emerging contaminant in herbal medicines or crops has been well-recognized for causing nephropathy since 1990s. Over the last decade, mounting evidence has linked AA to liver injury; however, the underlying mechanism is poorly elucidated. MicroRNAs respond to environmental stress and mediate multiple biological processes, thus showing biomarker potentials prognostically or diagnostically. In the present study, we investigated the role of miRNAs in AA-induced hepatotoxicity, specifically in regulating NQO1, the key enzyme responsible for AA bioactivation. In silico analysis showed that hsa-miR-766-3p and hsa-miR-671-5p were significantly associated with AAI exposure as well as NQO1 induction. A 28-day rat experiment of 20 mg/kg AA exposure demonstrated a 3-fold increase of NQO1 and an almost 50 % decrease of the homologous miR-671 that were accompanied with liver injury, which was consistent with in silico prediction. Further mechanistic investigation using Huh7 cells with IC50 of AAI at 146.5 µM showed both hsa-miR-766-3p and hsa-miR-671-5p were able to directly bind to and down-regulate NQO1 basal expression. In addition, both miRNAs were shown to suppress AAI-induced NQO1 upregulation in Huh7 cells at a cytotoxic concentration of 70 μM, and consequently alleviate AAI-induced cellular effects, including cytotoxicity and oxidative stress. Together, these data illustrate that miR-766-3p and miR-671-5p attenuate AAI-induced hepatotoxicity, and thus have monitoring and diagnostic potentials.

Hearing loss is the most common congenital sensory impairment. Mutations or deficiencies of the GJB2 gene are the most common genetic cause of congenital non-syndromic deafness. Pathological changes such as decreased potential in the cochlea, active cochlear amplification disorders, cochlear developmental disorders and macrophage activation have been observed in various GJB2 transgenic mouse models. In the past, researchers generally believed that the pathological mechanisms underlying GJB2-related hearing loss comprised a K+ circulation defect and abnormal ATP-Ca2+ signals. However, recent studies have shown that K+ circulation is rarely associated with the pathological process of GJB2-related hearing loss, while cochlear developmental disorders and oxidative stress play an important, even critical, role in the occurrence of GJB2-related hearing loss. Nevertheless, these research has not been systematically summarized. In this review, we summarize the pathological mechanisms of GJB2-related hearing loss, including aspects of K+ circulation, developmental disorders of the organ of Corti, nutrition delivery, oxidative stress and ATP-Ca2+ signals. Clarifying the pathological mechanism of GJB2-related hearing loss can help develop new prevention and treatment strategies.

Abstract Purpose Genetic testing is widely used in diagnosing genetic hearing loss in patients. Other than providing genetic etiology, the benefits of genetic testing in pediatric patients with hearing loss are less investigated. Methods From 2018–2020, pediatric patients who initially presented isolated hearing loss were enrolled. Comprehensive genetic testing, including GJB2/SLC26A4 multiplex amplicon sequencing, STRC/OTOA copy number variation analysis, and exome sequencing, were hierarchically offered. Clinical follow-up and examinations were performed. Results A total of 80 pediatric patients who initially presented isolated hearing loss were considered as nonsyndromic hearing loss and enrolled in this study. The definitive diagnosis yield was 66% (53/80) and the likely diagnosis yield was 8% (6/80) through comprehensive genetic testing. With the aid of genetic testing and further clinical follow-up and examinations, the clinical diagnoses and medical management were altered in eleven patients (19%, 11/59); five were syndromic hearing loss; six were nonsyndromic hearing loss mimics. Conclusion Syndromic hearing loss and nonsyndromic hearing loss mimics are common in pediatric patients who initially present with isolated hearing loss. The comprehensive genetic testing provides not only a high diagnostic yield but also valuable information for clinicians to uncover subclinical or pre-symptomatic phenotypes, which allows early diagnosis of SHL, and leads to precise genetic counseling and changes the medical management.

Abstract Mutations in the GJB2 gene (encoding Connexin26(Cx26)) are the most common cause of hereditary deafness, accounting for about a quarter of all cases. Sensory epithelial damage is considered to be one of the main causes of deafness caused by GJB2 gene mutation. Dexamethasone (DEX) is widely used in the treatment of a variety of inner ear diseases including sudden sensorineural hearing loss (SSNHL), noise-induced hearing loss (NIHL), and deafness caused by ototoxic drugs. Whether DEX has a direct therapeutic effect on hereditary deafness, especially GJB2-related deafness, remains unclear. In this study, we revealed that DEX can effectively prevent hair cell death caused by oxidative stress in cochlear explants. Additionally, two distinct Cx26-null mouse models were established to investigate whether systemic administration of DEX alleviate the cochlear sensory epithelial injury or deafness in these models. In a specific longitudinally Cx26-null model that does not cause deafness, systemic administration of DEX prevents the degeneration of outer hair cells (OHCs) induced by Cx26 knockout. Similarly, in a targeted-Deiter’s cells (DCs) Cx26-null mouse model that causes deafness, treatment with DEX can almost completely prevent OHCs loss and alleviates auditory threshold shifts at some frequencies. Additionally, we observed that DEX inhibited the recruitment of CD45-positive cells in the targeted-DCs Cx26-null mice. Taken together, our results suggest that the protective effect of dexamethasone on cochlear sensory epithelial damage and partially rescue auditory function may be related to the regulation of inner ear immune response in Cx26 deficiency mouse models.

Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.

Rapid, non-destructive and reliable detection of the oil content of corn seeds is important for development of high-oil corn. However, determination of the oil content is difficult using traditional methods for seed composition analysis. In this study, a hand-held Raman spectrometer was used with a spectral peak decomposition algorithm to determine the oil contents of corn seeds. Mature and waxy Zhengdan 958 corn seeds and mature Jingke 968 corn seeds were analyzed. Raman spectra were obtained in four regions of interest in the embryo of the seed. After analysis of the spectra, a characteristic spectral peak for the oil content was identified. A Gaussian curve fitting spectral peak decomposition algorithm was used to decompose the characteristic spectral peak of oil at 1657 cm−1. This peak was used to determine the Raman spectral peak intensity for the oil content in the embryo and differences in the oil contents among seeds of varying maturity and different varieties. This method is feasible and effective for detection of corn seed oil.

Human health risk assessment of chemicals is essential but often relies on time-consuming and animal and labor-extensive procedures. Here, we develop a population-based, quantitative in vitro to in vivo extrapolation (QIVIVE) approach which depended on cellular effects monitored by in vitro assays, considered chemical internal concentration determined by LC-MS/MS, extrapolated into in vivo target tissue concentration through physiologically based pharmacokinetic (PBPK) modelling, and assessed populational health risk using in silico modelling. By applying this QIVIVE approach to 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA), as a representative of the emerging pollutants, we find that 6:2 Cl-PFESA disturbed lipid homeostasis in HepG2 cells through enhancement of lipid accumulation and fatty acid β-oxidation, during which miR-93-5p served as a key event towards toxicity and thus, could serve as an efficient toxicity marker for risk assessment; further, the disruption potency of lipid homeostasis of 6:2 Cl-PFESA for the most of studied populations in China might be of moderate concern. Together, our approach improved the reliability of QIVIVE during human health risk assessment, which can readily be used for other chemicals.

The evaluation of rock porosity and the mercury injection capillary pressure (MICP) curve is fundamental for oil and gas exploration and production. Digital rock (DR) technology, incorporating 3D micro-CT imaging and numerical methods, has been widely employed to predict these properties. However, analyzing the pore structure of heterogeneous rocks, such as fractured rocks or glutenite, solely through single-scale DR analysis poses challenges. Existing upscaling methods have limitations in fully representing the complete range of pore structures at different scales, with limited comparison to experimental data. To address this, we propose a novel method that upscales porosity and simulates the MICP curve from nano-scale to core scale by merging results from micro-CT (at resolutions of 35 μm and 2 μm) and SEM (at resolutions of 6.5 nm and 65 nm). We validate the developed DR model by applying it to sandstones, glutenite, and igneous rocks, and achieve excellent agreement between the experimental data and the multi-scale DR model across 67 samples. The results demonstrate that the multi-scale model effectively captures the porosity and pore structures across the entire range. In contrast, the single digital rock (DR) model underestimates the porosity measurements for both homogeneous sandstones and heterogeneous cores. While the MICP model based on a single DR proves suitable for homogeneous rock samples, it introduces noticeable discrepancies when applied to heterogeneous rock samples. The developed multi-scale method significantly enhances the confidence in using DR to assess the pore structure of complex rocks.

Perfluorooctane sulfonate (PFOS) and its alternative 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) are ubiquitous in various environmental and human samples. They have been reported to have hepatotoxicity effects, but the potential mechanisms remain unclear. Herein, we integrated metabolomics and proteomics analysis to investigate the altered profiles in metabolite and protein levels in primary human hepatocytes (PHH) exposed to 6:2 Cl-PFESA and PFOS at human exposure relevant concentrations. Our results showed that 6:2 Cl-PFESA exhibited higher perturbation effects on cell viability, metabolome and proteome than PFOS. Integration of metabolomics and proteomics revealed that the alteration of glycerophospholipid metabolism was the critical pathway of 6:2 Cl-PFESA and PFOS-induced lipid metabolism disorder in primary human hepatocytes. Interestingly, 6:2 Cl-PFESA-induced cellular metabolic process disorder was associated with the cellular membrane-bounded signaling pathway, while PFOS was associated with the intracellular transport process. Moreover, the disruption effects of 6:2 Cl-PFESA were also involved in inositol phosphate metabolism and phosphatidylinositol signaling system. Overall, this study provided comprehensive insights into the hepatic lipid toxicity mechanisms of 6:2 Cl-PFESA and PFOS in human primary hepatocytes.

Vibrio as one of the main pathogens of shellfish diseases can cause serious human seafoodborne gastroenteritis and even death. In this study, we analyzed the bacterial communities from the clam, and compared the resistance phenotypes and genotypes of Vibrio spp. from Meretrix meretrix at different growth stages. High-throughput sequencing analysis revealed the predominance of Proteobacteria (50%) in the bacterial community and Vibrio was one of the dominant genera in the clam hepatopancreas in the summer. Vibrio abundance in Meretrix meretrix positively correlated with the water temperature (p

MiRNAs are widely acknowledged as regulating gene expression and thus, being involved in broad biological functions, environmental responses, and the process of diseases. Epidemiology could provide exposure- or disease-relevant miRNAs, while toxicology could reveal the underlying mechanisms. Here, a new “Bottom-up” approach was proposed to identify miRNAs that are responsible for environmental exposure-induced adverse outcomes. In our previous study, 5 key toxicity pathways were established underlying BaP-induced lung diseases; further, genes from these 5 pathways that were responsive to BaP exposure in HBE-CYP1A1 cells were identified. In this study, we identified 26 miRNA:mRNA interactions during BaP exposure through RNA-sequencing using the same HBE-CYP1A1 cells. According to the expression alteration and regulatory mechanisms, we summarized 8 action patterns of miRNA:mRNA, which led to the induction of miRNAs that predominantly regulate target genes and responsible are for the pathway perturbations (as “drivers”), and miRNAs that subordinately regulate genes during pathway perturbations (as “symptoms”). 5 corresponding miRNAs: miR-3173-5p, miR-629-3p, miR-9-5p, miR-1343-3p and miR-219a-1-3p were identified as “drivers”, and were all validated with expression alteration in lung disease patients from published studies. In conclusion, this study offers a new approach to identification of epigenetic factors that may shed light on the causation of environment-related health outcomes.

The main defense response to Soybean mosaic virus (SMV) infection in soybean [Glycine max (L.) Merr.] is thought to be blockage of intercellular virus transport by callose deposition on plasmodesmata. But the specific regulatory mechanism remains largely unknown. In this study, we found that hydrogen peroxide (H2O2) signal downstream of NO was associated with the regulation of callose accumulation. Abundant H2O2 was produced on the cell membrane and cell wall in the incompatible combination of soybean cultivar Jidou 7 and SMV strain N3, whereas no obvious H2O2 was observed in the compatible combination of Jidou 7 and strain SC-8. When H2O2 production was inhibited, callose accumulation induced by SMV infection decreased to a level insufficient to restrict virus transport in the incompatible combination. The H2O2-associated transcriptome dynamics of soybean during SMV infection was investigated. Transcriptome and functional analysis using virus-induced gene silencing showed that GmSEOB and GmPAP27, two genes regulated by H2O2, functioned in resistance by positively regulating the accumulation of callose in response to SMV infection. These results lay a foundation for further research on the signal transduction and molecular regulation of callose deposition during soybean resistance to SMV infection.

Abstract Background For the past decades, benefitting from the rapid growth of protein sequence data in public databases, a lot of machine learning methods have been developed to predict physicochemical properties or functions of proteins using amino acid sequence features. However, the prediction performance often suffers from the lack of labeled data. In recent years, pre-training methods have been widely studied to address the small-sample issue in computer vision and natural language processing fields, while specific pre-training techniques for protein sequences are few. Results In this paper, we propose a pre-training platform for representing protein sequences, called ProtPlat, which uses the Pfam database to train a three-layer neural network, and then uses specific training data from downstream tasks to fine-tune the model. ProtPlat can learn good representations for amino acids, and at the same time achieve efficient classification. We conduct experiments on three protein classification tasks, including the identification of type III secreted effectors, the prediction of subcellular localization, and the recognition of signal peptides. The experimental results show that the pre-training can enhance model performance effectively and ProtPlat is competitive to the state-of-the-art predictors, especially for small datasets. We implement the ProtPlat platform as a web service ( https://compbio.sjtu.edu.cn/protplat ) that is accessible to the public. Conclusions To enhance the feature representation of protein amino acid sequences and improve the performance of sequence-based classification tasks, we develop ProtPlat, a general platform for the pre-training of protein sequences, which is featured by a large-scale supervised training based on Pfam database and an efficient learning model, FastText. The experimental results of three downstream classification tasks demonstrate the efficacy of ProtPlat.

Introduction: The objective of this paper is to identify the prognostic risk factors of secondary adult hemophagocytic syndrome (HLH) in hospitalized patients and establish a simple and convenient prognostic scoring system. Method:We reviewed 162 adult patients secondary with HLH treated in Zhejiang Cancer Hospital and the First Affiliated Hospital of Medical College of Zhejiang University from January 2014 to December 2018 were enrolled to form the test group; from January 2019 to February 2021, 162 adult patients in the hospitals constituted the validation group. The HLH prognosis scoring system was constructed according to the risk factors, and the patients were divided into three risk groups: low risk, medium risk, and high risk. The scoring system was verified by Kaplan–Meier method and log rank test survival analysis. The discrimination ability was evaluated according to the receiver operating characteristic (ROC) curve. Results: Univariate and multivariate analysis showed that the independent risk factors for the prognosis of HLH were male sex, activated partial prothrombin time (APTT) greater than 36 s, lactate dehydrogenase (LDH) greater than 1000 U/L, and C-reactive protein (CRP) greater than 100 mg/L. The area under the ROC curve was 0.754 (95% Cl: 0.678–0.829). The patients were divided into a low-risk group (0–1), a medium-risk group (2–4), and a high-risk group (5–6). The 5-year overall survival (OS) rate were 87.5%, 41.8% and 12.8%, respectively (p < 0.001). The area under ROC curve was 0.736 (95% Cl: 0.660–0.813) in the validation group, and the 2-year OS of patients in low-risk, medium-risk and high-risk groups were 88.0%, 45.1% and 16.7%, respectively (p < 0.001). Conclusion:The new prognostic scoring system can accurately predict the prognosis of secondary adult HLH and can further provide basis for the accurate treatment of secondary adult HLH.

Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line (RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the T1 stage, and the six-leaf stage as the flowering critical stage was designated as the T2 stage. In total, 200 single nucleotide polymorphism (SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the T1 stage, and 109 detected at the T2 stage. Among these SNP loci, one SNP cluster (s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the T1 stage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster (ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the T2 stage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci (ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the T1 and T2 stages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by qRT-PCR. Thus, these genetic loci and candidate genes could be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

Blasting quality is a key factor in determining the productivity and total cost of the shaft blasting excavation construction, so it is of great engineering and theoretical importance to evaluate blasting quality rationally. The existing evaluation methods rely more on previous experience and the knowledge level of technicians, which are more subjective and cannot be judged by quantitative or unified standards, so the evaluation results have limitations. This paper proposes the Analytic Hierarchy Process (AHP) based on Particle Swarm Optimization (PSO) to obtain the weights of each index for evaluating the blasting quality of shafts, then combine expert knowledge, field engineering experience and statistical data for a comprehensive analysis to determine the quantitative interval of blasting quality evaluation index levels and construct a blasting quality evaluation index system, which makes the evaluation indexes more accurate and more in line with reality. The PSO-AHP combined with fuzzy comprehensive evaluation technique has constructed a blasting quality evaluation matrix more in line with the engineering reality and established a shaft blasting quality evaluation model adapted to different geological conditions. Finally, the established blasting quality evaluation model is combined with computer programming and artificial intelligence technology to develop a visualized shaft blasting quality intelligent evaluation system, which meets the practical needs of front-line operators in the field to evaluate the blasting quality objectively and reasonably, and achieves the accuracy, objectivity and intelligence of shaft blasting quality evaluation.

Abstract Background Neonatal hypoxic-ischemic encephalopathy (HIE) refers to the perinatal asphyxia caused by the cerebral hypoxic-ischemic injury. The current study was aimed at investigating the therapeutic efficacy of Scutellarin (Scu) administration on neurological impairments induced by hypoxic-ischemic injury and exploring the underlying mechanisms. Methods Primary cortical neurons were cultured and subjected to oxygen–glucose deprivation (OGD), and then treated with Scu administration. The growth status of neurons was observed by immunofluorescence staining of TUJ1 and TUNEL. Besides, the mRNA level of growth-associated protein 43 (GAP43) in OGD neurons with Scu treatment was detected by quantitative real-time polymerase chain reaction (qRT-PCR). To further verify the role of GAP43 in Scu treatment, GAP43 siRNA and knockout were applied in vitro and in vivo. Moreover, behavioral evaluations were performed to elucidate the function of GAP43 in the Scu-ameliorated long-term neurological impairments caused by HI insult. The underlying biological mechanism of Scu treatment was further elucidated via network pharmacological analysis. Finally, the interactive genes with GAP43 were identified by Gene MANIA and further validated by qRT-PCR. Results Our data demonstrated that Scu treatment increased the number of neurons and axon growth, and suppressed cell apoptosis in vitro. And the expression of GAP43 was downregulated after OGD, but reversed by Scu administration. Besides, GAP43 silencing aggravated the Scu-ameliorated neuronal death and axonal damage. Meanwhile, GAP43 knockout enlarged brain infarct area and deteriorated the cognitive and motor dysfunctions of HI rats. Further, network pharmacological analysis revealed the drug targets of Scu participated in such biological processes as neuronal death and regulation of neuronal death, and apoptosis-related pathways. GAP43 exhibited close relationship with PTN, JAK2 and STAT3, and GAP43 silencing upregulated the levels of PTN, JAK2 and STAT3. Conclusions Collectively, our findings revealed Scu treatment attenuated long-term neurological impairments after HI by suppressing neuronal death and enhancing neurite elongation through GAP43-dependent pathway. The crucial role of Scutellarin in neuroprotection provided a novel possible therapeutic agent for the treatment of neonatal HIE. Graphic abstract

ObjectiveElemene emulsion injection (EEI) has been approved for interventional and intracavitary chemotherapy in treating malignant ascites in China, but few studies have focused on the effects of EEI on gut microbiota and metabolites. In this study, we investigated the effects of EEI on the fecal microbiota and metabolites in healthy Sprague-Dawley (SD) rats.MethodsWe randomly assigned 18 male SD rats to three groups (n = 6 in each group): the sham group (group S), the low-concentration EEI group (L-EEI), and the high-concentration EEI group (H-EEI). The L-EEI and H-EEI rats were administered 14 days of consecutive EEI, 20 mg/kg, and 40 mg/kg intraperitoneally (IP). Group S rats were administered the same volume of normal saline. On day 14, each animal's feces were collected for metagenomic sequencing and metabolomic analysis, and the colonic contents were collected for 16S rRNA sequencing.ResultsEEI could alter the β-diversity but not the α-diversity of the fecal microbiota and induce structural changes in the fecal microbiota. Different concentrations of EEI affect the fecal microbiota differently. The effects of different EEI concentrations on the top 20 bacteria with significant differences at the species level among the three groups were roughly divided into three categories: (1) A positive or negative correlation with the different EEI concentrations. The abundance of Ileibacterium Valens increased as the EEI concentration increased, while the abundance of Firmicutes bacteria and Clostridium sp. CAC: 273 decreased. (2) The microbiota showed a tendency to increase first, then decrease or decrease first, and then increase as EEI concentration increased—the abundance of Prevotella sp. PCHR, Escherichia coli, and Candidatus Amulumruptor caecigallinarius tended to decrease with L-EEI but significantly increased with H-EEI. In contrast, L-EEI significantly increased Ruminococcus bromii and Dorea sp. 5–2 abundance, and Oscillibacter sp. 1–3 abundance tended to increase, while H-EEI significantly decreased them. (3) L-EEI and H-EEI decreased the abundance of bacteria (Ruminococcaceae bacterium, Romboutsia ilealis, and Staphylococcus xylosus). Fecal metabolites, like microbiota, were sensitive to different EEI concentrations and correlated with fecal microbiota and potential biomarkers.ConclusionThis study shows that intraperitoneal EEI modulates the composition of rat fecal microbiota and metabolites, particularly the gut microbiota's sensitivity to different concentrations of EEI. The impact of changes in the microbiota on human health remains unknown, particularly EEI's efficacy in treating tumors.

Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.

ABSTRACT Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious and urgent threat for hospitalized patients. This study aims to describe the clinical and molecular characteristics of CRKP causing BSI in a tertiary-care hospital in Beijing, China. A total of 146 CRKP strains and 39 carbapenem-susceptible K. pneumoniae (CSKP) strains collected in the hospital from 2017 to 2020 were sent for whole-genome sequencing. Univariate and multivariate analyses were used to evaluate risk factors for in-hospital mortality of CRKP-BSI cases. Thirty (20.5%) of 146 CRKP-BSI patients and three (7.7%) of 39 CSKP-BSI patients died at discharge (χ2 = 3.471, P = 0.062). Multivariate logistic regression analysis indicated that age and use of urinary catheters were independent risk factors for the death of CRKP-BSI. The 146 CRKP isolates belonged to 9 sequence types (STs) and 11 serotypes, while the 39 CSKP isolates belonged to 23 STs and 27 serotypes. The mechanism of carbapenem resistance for all the CRKP strains was the acquisition of carbapenemase, mainly KPC-2 (n = 127). There were 2 predominant serotypes for ST11 CRKP, namely, KL47 (n = 82) and KL64 (n = 42). Some virulent genes, including rmpA2, iucABCD and iutA, and repB gene, which was involved in plasmid replication, were detected in all ST11-KL64 strains. Evolutionary transmission analysis suggested that ST11 CRKP strains might have evolved from KL47 into KL64 and were accompanied by multiple outbreak events. This study poses an urgent need for enhancing infection control measures in the hospital, especially in the intensive care unit where the patients are at high-risk for acquiring CRKP-BSI. IMPORTANCE CRKP-BSI is demonstrated to cause high mortality. In this study, we demonstrated that ST11 CRKP strains might carry many virulent genes. Meanwhile, outbreak events occurred several times in the strains collected. Carbapenemase acquisition (mainly KPC-2 carbapenemase) was responsible for carbapenem resistance of all the 146 CRKP strains. As 2 predominant strains, all ST11-KL64 strains, but not ST11-KL47 strains, carried rmpA2, iucABCD, iutA, as well as a plasmid replication initiator (repB). Our study suggested that the occurrence of region-specific recombination events manifested by the acquisition of some virulence genes might contribute to serotype switching from ST11-KL47 to ST11-KL64. The accumulation of virulent genes in epidemic resistant strains poses a great challenge for the prevention and treatment of BSI caused by K. pneumoniae in high-risk patients.

In hydrogel-based tissue engineering, channel network is an efficient structure for transporting nutrients/oxygen to support cell survival and construct living tissues in vitro. 3D printing can create complex hydrogel-based tissue constructs, however, due to the weak mechanical properties of hydrogel bioinks, cell-laden hydrogel constructs with effective channel networks are difficult to be directly printed. Here, an easy sacrificial 3D printing method based on commercial desktop 3D printer and water-soluble polyvinyl alcohol (PVA) to construct effective hydrogel channel networks is introduced. Specifically, i) commercial PVA consumables are printed to be sacrificial templates; ii) gelatin methacryloyl (GelMA) solution is cast to encapsulate the sacrificial template; iii) the sacrificial template is dissolved to form channel networks. PVA is a water-soluble sacrificial material with sufficient dissolution time and high mechanical strength, which can avoid the disadvantages of classic sacrificial materials (sugar and Pluronic F127). High roundness of printed PVA filaments results in high roundness of the channel networks. The interconnected channel networks accelerate the supply of oxygen/nutrients and promote cell growth. And with a period of culture, the higher the channel networks density, the better the cell growth. Additionally, PVA sacrificial templates have high stability and long-term preservation, facilitating transportation, circulation and use, which is conducive to the manufacturing and promotion of hydrogel-based constructs with channel networks. Taken together, our easy strategy of manufacturing hydrogel constructs with channel networks has broad application prospects, such as 3D cell culture, construction of functional tissue in vitro or tissue repair in vivo etc.

Triply periodic minimal surfaces (TPMS) - based porous structures have been universally adopted for mimicking the properties of bone scaffolds due to their interconnected geometries with smooth surfaces and controllable pores. To further increase the versatility and controllability, an enhanced porous scaffold based on TPMS is proposed. The enhanced pores with different sizes are designed onto three types of TPMS-based scaffolds and then additively manufactured through laser powder bed fusion (LPBF). To investigate the manufacturability, various approaches are used and the results confirm that morphological features of printed samples are identical to the designed ones. As for mechanical properties, the results from the compression tests show that the elastic modulus and compressive strength of enhanced porous scaffolds are 2.0 GPa to 5.1 GPa and 86.7 MPa to 264.2 MPa respectively, which are all in the range of human bones. In terms of permeability, both experiments and simulation indicate that the designed scaffolds have 40%−150% improvement compared to scaffolds without enhanced pores. The biocompatibility of the scaffolds is further verified by in vitro studies. The results demonstrate the suitability of the proposed enhanced porous scaffolds for bone implants, and it will facilitate the design of more effective porous materials.

Hearing loss is among the most common congenital sensory impairments. Genetic causes account for more than 50% of the cases of congenital hearing loss. The PTPRQ gene, encoding protein tyrosine phosphatase receptor Q, plays an important role in maintaining the stereocilia structure and function of hair cells. Mutations in the PTPRQ gene have been reported to cause hereditary sensorineural hearing loss. By using next-generation sequencing and Sanger sequencing, we identified a novel compound heterozygous mutation (c.997 G > A and c.6603-3 T > G) of the PTPRQ gene in a Chinese consanguineous family. This is the first report linking these two mutations to recessive hereditary sensorineural hearing loss. These findings contribute to the understanding of the relationship between genotype and hearing phenotype of PTPRQ-related hearing loss, which may be helpful to clinical management and genetic counseling.

Klebsiella pneumoniae is a common human commensal and opportunistic pathogen. In recent years, the clinical isolation and resistance rates of K. pneumoniae have shown a yearly increase, leading to a special interest in mobile genetic elements. Prophages are a representative class of mobile genetic elements that can carry host-friendly genes, transfer horizontally between strains, and coevolve with the host’s genome. In this study, we identified 15,946 prophages from the genomes of 1437 fully assembled K. pneumoniae deposited in the NCBI database, with 9755 prophages on chromosomes and 6191 prophages on plasmids. We found prophages to be notably diverse and widely disseminated in the K. pneumoniae genomes. The K. pneumoniae prophages encoded multiple putative virulence factors and antibiotic resistance genes. The comparison of strain types with prophage types suggests that the two may be related. The differences in GC content between the same type of prophages and the genomic region in which they were located indicates the alien properties of the prophages. The overall distribution of GC content suggests that prophages integrated on chromosomes and plasmids may have different evolutionary characteristics. These results suggest a high prevalence of prophages in the K. pneumoniae genome and highlight the effect of prophages on strain characterization.

Background Hypoxic‐ischemic encephalopathy (HIE) could induce exacerbated changes and unpredictable effects in brain cells, and the mechanism remains unclear. Methods HIE model was established in neonatal rats, Zea‐Longa score and TTC staining were used to observe the neurobehavior and brain infarct volume in rats subjected to cerebral hypoxia‐ischemia (HI). Primary cortical neurons were then cultured in vitro to establish an oxygen and glucose deprivation model. To determine the role of synaptosomal‐associated protein‐25 (SNAP25) in HIE, PC12 cells were cultured and effective siRNA fragments were screened, and SNAP25 was transfected into primary neurons. Then, quantitative real‐time polymerase chain reaction was used to detect the mRNA expression level and immunofluorescence staining was used to observe the morphological changes of neurons before and after the injury. Finally, the abundance values of SNAP25 and its associated genes were filtered using the NCBI and GeneMANIA, respectively. Results HI leads to a decrease in neuronal number and an increase in SNAP25 expression. Whereas, the interference of SNAP25 caused marked decrease in neuronal number and the length of neurite. Moreover, the expression levels of CREB and SYP were significantly decreased after interference of SNAP25. Conclusion SNAP25 exhibited several neuroprotective effects to neuronal protection in neonatal cerebral HI by regulating CREB and SYP.

Abstract Extracellular vesicles (EVs) are single‐membrane vesicles that play an essential role in long‐range intercellular communications. EV investigation has been explored largely through cell‐culture systems, but it remains unclear how physiological EVs exert homeostatic or pathological functions in vivo. Here, we report that lung EVs promote chemotaxis of neutrophils in bone marrow through delivery of double stranded DNA (dsDNA). We have identified and characterized EVs containing dsDNA collected from both human and murine lung tissues using newly developed approaches. Our analysis of EV proteomics together with single‐cell RNA sequencing data reveals that type II alveolar epithelial cells are the main source of the lung EVs. Furthermore, we demonstrate that the lung EVs accumulate in bone marrow and enhance neutrophil recruitment under inflammation conditions. Moreover, lung EV‐DNA stimulates neutrophils to release the chemokines CXCL1 and CXCL2 via DNA‐TLR9 signalling. Our findings establish a molecular basis of lung EVs in enhancement of host immune response to bacterial infection and provide new insights into understanding of vesicle‐mediated systematic communications.

Mutations in the GJB2 gene encoding connexin26 (Cx26) protein are one of the most common causes of hereditary deafness. Previous studies have found that different Cx26-null mouse models have severe hearing loss and deformity of the organ of Corti (OC) as well as a reduction in microtubules in pillar cells (PCs). To explore the underlying mechanism of OC deformity caused by Cx26 downregulation further, we established Cx26 knockdown (KD) mouse models at postnatal days (P)0 and P8. The actin filaments contained in the pillar cells of mice in the P0 KD group were reduced by 54.85% and vinculin was increased by 22%, while the outer hair cells (OHCs) showed normal F-actin content. In the P8 KD group, PCs and OHCs of mice also showed almost normal F-actin content. The G-actin/F-actin ratio increased by 38% in the P0 KD group. No significant change was found in the mRNA or protein expression level of G-actin or the cadherin–catenin core complex in the P0 KD group at P6. Moreover, immunofluorescence showed that the intensity of LRRK2 was reduced by 97% in the P0 KD group at P6. Our results indicate that Cx26 is involved in the maturation of the cytoskeleton during the development of the OC at the early postnatal stage. The polymerization of G-actin into F-actin is prevented in Cx26 KD mice.