Structure of the siphophage neck-Tail complex suggests that conserved tail tip proteins facilitate receptor binding and tail assembly.

Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; moreover, it serves as a channel for genome delivery during infection. However, the in situ high-resolution structure of the neck-tail complex of siphophages remains unknown. Here, we present the structure of the siphophage lambda "wild type," the most widely used, laboratory-adapted fiberless mutant. The neck-tail complex comprises a channel formed by stacked 12-fold and hexameric rings and a 3-fold symmetrical tip. The interactions among DNA and a total of 246 tail protein molecules forming the tail and neck have been characterized. Structural comparisons of the tail tips, the most diversified region across the lambda and other long-tailed phages or tail-like machines, suggest that their tail tip contains conserved domains, which facilitate tail assembly, receptor binding, cell adsorption, and DNA retaining/releasing. These domains are distributed in different tail tip proteins in different phages or tail-like machines. The side tail fibers are not required for the phage particle to orient itself vertically to the surface of the host cell during attachment.

Testing the generalizability and effectiveness of deep learning models among clinics: sperm detection as a pilot study.

BACKGROUND: Deep learning has been increasingly investigated for assisting clinical in vitro fertilization (IVF). The first technical step in many tasks is to visually detect and locate sperm, oocytes, and embryos in images. For clinical deployment of such deep learning models, different clinics use different image acquisition hardware and different sample preprocessing protocols, raising the concern over whether the reported accuracy of a deep learning model by one clinic could be reproduced in another clinic. Here we aim to investigate the effect of each imaging factor on the generalizability of object detection models, using sperm analysis as a pilot example. METHODS: Ablation studies were performed using state-of-the-art models for detecting human sperm to quantitatively assess how model precision (false-positive detection) and recall (missed detection) were affected by imaging magnification, imaging mode, and sample preprocessing protocols. The results led to the hypothesis that the richness of image acquisition conditions in a training dataset deterministically affects model generalizability. The hypothesis was tested by first enriching the training dataset with a wide range of imaging conditions, then validated through internal blind tests on new samples and external multi-center clinical validations. RESULTS: Ablation experiments revealed that removing subsets of data from the training dataset significantly reduced model precision. Removing raw sample images from the training dataset caused the largest drop in model precision, whereas removing 20x images caused the largest drop in model recall. by incorporating different imaging and sample preprocessing conditions into a rich training dataset, the model achieved an intraclass correlation coefficient (ICC) of 0.97 (95% CI: 0.94-0.99) for precision, and an ICC of 0.97 (95% CI: 0.93-0.99) for recall. Multi-center clinical validation showed no significant differences in model precision or recall across different clinics and applications. CONCLUSIONS: The results validated the hypothesis that the richness of data in the training dataset is a key factor impacting model generalizability. These findings highlight the importance of diversity in a training dataset for model evaluation and suggest that future deep learning models in andrology and reproductive medicine should incorporate comprehensive feature sets for enhanced generalizability across clinics.

Structural changes in bacteriophage T7 upon receptor-induced genome ejection.

Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane.

Structures of Mature and Urea-Treated Empty Bacteriophage T5: Insights into Siphophage Infection and DNA Ejection.

T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, we used cryo-electron microscopy (cryo-EM) to determine the structures of mature T5 (a laboratory-adapted, fiberless T5 mutant) and urea-treated empty T5 (lacking the tip complex) at near-atomic resolutions. Atomic models of the head, connector complex, tail tube, and tail tip were built for mature T5, and atomic models of the connector complex, comprising the portal protein pb7, adaptor protein p144, and tail terminator protein p142, were built for urea-treated empty T5. Our findings revealed that the aforementioned proteins did not undergo global conformational changes before and after DNA ejection, indicating that these structural features were conserved among most myophages and siphophages. The present study elucidates the underlying mechanisms of siphophage infection and DNA ejection.

Multiple states and transport properties of double-diffusive convection turbulence.

When fluid stratification is induced by the vertical gradients of two scalars with different diffusivities, double-diffusive convection (DDC) may occur and play a crucial role in mixing. Such a process exists in many natural and engineering environments. Especially in the ocean, DDC is omnipresent since the seawater density is affected by temperature and salinity. The most intriguing phenomenon caused by DDC is the thermohaline staircase, i.e., a stack of alternating well-mixed convection layers and sharp interfaces with very large gradients in both temperature and salinity. Here we investigate DDC and thermohaline staircases in the salt finger regime, which happens when warm saltier water lies above cold fresher water and is commonly observed in the (sub)tropic regions. By conducting direct numerical simulations over a large range of parameters, we reveal that multiple equilibrium states exist in fingering DDC and staircases even for the same control parameters. Different states can be established from different initial scalar distributions or different evolution histories of the flow parameters. Hysteresis appears during the transition from a staircase to a single salt finger interface. For the same local density ratio, salt finger interfaces in the single-layer state generate very different fluxes compared to those within staircases. However, the salinity flux for all salt finger interfaces follows the same dependence on the salinity Rayleigh number of the layer and can be described by an effective power law scaling. Our findings have direct applications to oceanic thermohaline staircases.

The Depression Prevalence in Chinese Patients with Rheumatoid Arthritis: A Systematic Review and Meta-analysis.

BACKGROUND: The chronic course and recurring acute episodes of rheumatoid arthritis (RA) can significantly affect the psychological and mental health of patients. This study aimed to investigate the prevalence of depression in Chinese patients with rheumatoid arthritis (RA) through a systematic review and meta-analysis. METHODS: We conducted a comprehensive literature search on electronic databases from the inception of the database to April 2023. The inclusion criteria included cross-sectional or case-control studies on depression prevalence with a sample size of at least 50 participants. The data was extracted from the included studies and analyzed to calculate the pooled depression prevalence, along with a 95% confidence interval (CI), using Review Manager 5.3 software (Version 5.3. Copenhagen: The Nordic Cochrane Centre, The Cochrane Collaboration, 2014). RESULTS: Thirteen studies (n = 29,113) were included, with females accounting for over 50% of all participants. Based on the data pooled from all 13 studies, the observed depression prevalence in Chinese individuals with RA was 37% (95% CI: 28-46%; I2 = 95%; p < 0.0001). A subsequent subgroup analysis was conducted on scale types, age, and gender. Regarding scale types, the depression prevalence was assessed using various scales included the Hospital Anxiety and Depression Scale (HAMD), Hamilton Depression Scale (HADS), Center for Epidemiologic Studies Depression (CES-D) scale, Diagnostic and Statistical Manual of Mental Disorder (fourth edition DSM.IV) diagnostic criteria, and Self-rating Depression Scale (SDS) were 50%, 35%, 58%, 39%, and 41%, respectively. Based on mean age, five studies researched RA individuals <50 years old, establishing a depression prevalence of 48% (95% CI: 32-65%). In contrast, eight studies researched RA individuals ≥50 years old, establishing a depression prevalence of 41% (95% CI: 32-51%). Gender-based analysis indicated a depression prevalence in female RA individuals of 45% (95% CI: 37-55%) and 39% (95% CI: 29-48%) among male RA patients. Depression prevalence established significant correlations with specific scales, including the HAMD scale (odds ratio (OR) 4.93, 95% CI: 1.79-10.2), CES-D scale (OR 2.83, 95% CI: 1.71-4.65), DSM.IV criteria (OR 0.75, 95% CI: 0.38-1.51), and SDS (OR 0.95, 95% CI: 0.32-2.16). Additionally, depression prevalence was associated with age categories (age ≥50: OR 1.25, 95% CI: 0.59-2.70; age <50: OR 1.99, 95% CI: 0.93-3.81), as well as gender (female: OR 1.63, 95% CI: 0.64-4.57; male: OR 1.07, 95% CI: 0.38-3.03), although some associations did not reach statistical significance. CONCLUSION: The depression prevalence was high in Chinese individuals with RA, especially in females and patients under 50 years old. These findings suggest the need for improving detection and management of depression in RA patients.

Staining-free, Automated Sperm Analysis for In Vitro Fertilization Lab Use.

PURPOSE: Computer-aided sperm analysis is typically used in andrology labs, not in in vitro fertilization labs, which requires staining for sperm morphology measurement. In in vitro fertilization labs, sperm analysis still relies on manual observation and suffers from subjectivity and inconsistency. We developed a system for automated measurement of sperm concentration, motility, and morphology without the need for sperm staining. The reproducibility and reliability of the system were evaluated. MATERIALS AND METHODS: Thirty-five fresh semen and 25 washed samples were obtained from male partners attending for fertility investigations. Sperm concentration, motility, and morphology were automatically measured simultaneously, leveraging robust sperm tracking for concentration and motility measurement and low contrast image segmentation for morphology measurement of live sperm. Reproducibility of sperm measurements was evaluated by intraclass correlation coefficients. Reliability of sperm measurement was evaluated by Passing and Bablok regression analysis and Bland-Altman analysis. RESULTS: Automated measurement of concentration, motility, and morphology had intraclass correlation coefficients higher than 0.97. The regression and Bland-Altman analysis indicated that automated measurement and off-line manual benchmarking with zoomed-in images were interchangeable. Further analysis on semen and washed samples and the measurement on progressive and nonprogressive motility also showed high reproducibility and reliability. CONCLUSIONS: Automated sperm analysis revealed high reproducibility and reliability. The system is designed for routine use in in vitro fertilization labs to perform quantitative sperm analysis on live samples.

Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.

Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.

Optimize the preparation of Fe3O4-modified magnetic mesoporous biochar and its removal of methyl orange in wastewater.

In this paper, Eichhornia Crassipes stems were used as biomass feedstock, and Fe2+ was used as the precursor solution to prepare Fe3O4-modified magnetic mesoporous biochar (Fe3O4@BC). By using Box-Behnken design (BBD) response surface methodology, the influences of three preparation parameters (X1 = Fe2+ concentration, X2 = pyrolysis temperature and X3 = pyrolysis time) on the adsorption of methyl orange (MO) by Fe3O4@BC were investigated, and a reliable response surface model was constructed. The results show that X1X2 and X1X3 have a significant influence on the adsorption of MO by Fe3O4@BC. The surface area and pore volume of Fe3O4@BC are controlled by all preparation parameters. The increase of pyrolysis time will significantly reduce the -OH on the surface of Fe3O4@BC and weaken its MO adsorption capacity. Through the numerical optimization of the constructed model, the optimal preparation parameters of Fe3O4@BC can be obtained as follows: Fe2+ concentration = 0.27 mol/L, pyrolysis temperature = 405 °C, and pyrolysis time = 3.2 h. The adsorption experiment shows that the adsorption of Fe3O4@BC to MO is a spontaneous exothermic process, and the adsorption capacity is maximum when pH = 4. The adsorption kinetics and adsorption isotherms of Fe3O4@BC to MO conform to the pseudo-second-order kinetics and Sips model, respectively. Mechanism analysis shows that electrostatic interaction and H bond formation are the main forces for Fe3O4@BC to adsorb MO. This research not only realizes a new way of resource utilization of Eichhornia Crassipes biomass but also enriches the preparation research of magnetic biochar.

Application of copper tailings combined with persulfate for better removing methyl orange from wastewater.

In this paper, wasted copper tailings (CT) were used to activate persulfate (PS) to degrade azo dye methyl orange (MO). The results show that a large amount of FeS2 contained in CT can slowly release Fe2+ in the aqueous solution to activate PS to generate reactive oxygen species to degrade MO. When the dosage of CT and PS was 2 g/L and 3 mM respectively, the MO degradation efficiency of 20 mg/L in the CT/PS system was 96.52% within 60 min. At the same time, it is found that CT has a certain adsorption capacity for MO, and the intra-particle diffusion model can well describe the adsorption process of MO by CT. The effects of related reaction parameters (CT dosage, PS dosage, initial MO concentration and solution pH) on MO degradation in CT/PS system were investigated. Compared with the direct addition of an equal amount of Fe2+ as in the CT/PS system, for homogeneous activated PS to degrade MO (Fe2+/PS), the results showed that the degradation efficiency of Fe2+/PS system for MO was lower than that of CT/PS system due to excessive Fe2+ consumption of SO4 ·-. By comparing the Fe2+ and Fe3+ concentrations in the two systems, it was found that the CT/PS system could maintain a low Fe2+ concentration during the reaction process, and the Fe2+ released by CT could be used by PS to degrade MO more efficiently. The free radical scavenging experiments showed that the reactive oxygen species in the CT/PS system was mainly SO4 ·-. This study not only proposed a new CT utilization approach, but also solved the problem of reduced degradation efficiency of organic pollutants caused by excessive Fe2+ in the Fenton-like reaction.

Formation of nitroanthracene and anthraquinone from the heterogeneous reaction between NO2 and anthracene adsorbed on NaCl particles.

Oxidative derivatives of polycyclic aromatic hydrocarbons (PAHs), that is, nitro-PAHs and quinones, are classed as hazardous semivolatile organic compounds but their formation mechanism from the heterogeneous reactions of PAHs adsorbed on atmospheric particles is not well understood. The heterogeneous reaction of NO2 with anthracene adsorbed on NaCl particles under different relative humidity (RH 0-60%) was investigated under dark conditions at 298 K. The formation of the major products, 9,10-anthraquinone (9,10-AQ) and 9-nitroanthracene (9-NANT), were determined to be second-order reactions with respect to NO2 concentration. The rate of formation of 9,10-AQ under low RH (0-20%) increased as the RH increased but decreased when the RH was further increased in high RH (40-60%). In contrast, the rate of formation of 9-NANT across the whole RH range (0-60%) decreased significantly with increasing RH. Two different reaction pathways are discussed for the formation of 9,10-AQ and 9-NANT, respectively, and both are considered to be coupled to the predominant reaction of NO2 with the NaCl substrate. These results suggest that relative humidity, which controls the amount of surface adsorbed water on NaCl particles, plays an important role in the heterogeneous reaction of NO2 with adsorbed PAHs.

Railway crossing risk area detection using linear regression and terrain drop compensation techniques.

Most railway accidents happen at railway crossings. Therefore, how to detect humans or objects present in the risk area of a railway crossing and thus prevent accidents are important tasks. In this paper, three strategies are used to detect the risk area of a railway crossing: (1) we use a terrain drop compensation (TDC) technique to solve the problem of the concavity of railway crossings; (2) we use a linear regression technique to predict the position and length of an object from image processing; (3) we have developed a novel strategy called calculating local maximum Y-coordinate object points (CLMYOP) to obtain the ground points of the object. In addition, image preprocessing is also applied to filter out the noise and successfully improve the object detection. From the experimental results, it is demonstrated that our scheme is an effective and corrective method for the detection of railway crossing risk areas.

Development and Improvement of a Piezoelectrically Driven Miniature Robot.

In this paper, we proposed a miniature quadrupedal piezoelectric robot with a mass of 1.8 g and a body length of 4.6 cm. The robot adopts a novel spatial parallel mechanism as its transmission. Each leg of the robot has two degrees of freedom (DOFs): swing and lift. The trajectory necessary for walking is achieved by the appropriate phasing of these two DOFs. A new manufacturing method for piezoelectric actuators was developed. During the stacking process, discrete patterned PZT pieces are used to avoid dielectric failure caused by laser cutting. Copper-clad FR-4 is used as the solder pad instead of copper foil, making the connection between the pad and the actuator more reliable. The lift powertrain of the robot was modeled and the link length of the powertrain was optimized based on the model. The maximum output force of each leg can reach 26 mN under optimized design parameters, which is 1.38 times the required force for successful walking. The frequency response of the powertrain was measured and fitted to the second-order system, which enabled increased leg amplitudes near the powertrain resonance of approximately 70 Hz with adjusted drive signals. The maximum speed of the robot without load reached 48.66 cm/s (10.58 body lengths per second) and the payload capacity can reach 5.5 g (3.05 times its mass) near the powertrain resonance.

Based on network pharmacology, molecular docking and experimental verification to reveal the mechanism of Andrographis paniculata against solar dermatitis.

BACKGROUND: Solar dermatitis (SD) is an acute, damaging inflammation of the skin caused by UV exposure, especially UVB. Therefore, the discovery of novel anti-SD therapeutic agents is crucial. Andrographis paniculata (AP) is a medicinal plant with a wide range of pharmacological effects. Increased evidence shows that AP has potential therapeutic effects on SD. However, the therapeutic mechanisms of AP against SD have not yet been completely elucidated, which is an unexplored field. PURPOSE: This study employed network pharmacology, molecular docking and experimental verification to ascertain the active constituents, possible targets, and biological pathways associated with AP in the treatment of SD. METHODS: AP-related active ingredients and their potential targets were screened from TCMSP and Swiss Target Prediction database, respectively. Potential therapeutic targets of SD were collected using the GeneCards, DrugBank and OMIM databases. Then, we established protein-protein interaction (PPI), compound-target-disease (D-C-T-D) through Cytoscape to identify the major components, core targets of AP against SD. Next, the GO and KEGG pathway was identified by the David database of AP in the treatment of SD. Molecular docking techniques were used to estimate the binding force between the components and the hub genes. In this paper, we used UVB-irradiated HaCaT keratinocytes as an in vitro model and established the dorsal skin of UVB-irradiated ICR mice as an in vivo model to explore the mechanism for further verification. RESULTS: There were 24 active components and 63 related target genes in AP against SD. PPI analysis showed that AKT-1, TNF-α, IL6, MMP9, EGFR, and PTGS2 shared the highest centrality among all target genes. KEGG pathway analysis revealed that the PI3K-Akt signaling pathway may be central in the anti-SD system. The molecular docking results showed that the main active components of AP have strong binding affinity with hub genes. In vitro results showed that WG had a protective effect on UVB-intervened HaCat cells. Western blot analysis showed that WG intervention achieved anti-inflammation by reducing the phosphorylated expression of AKT, PI3K proteins in the PI3K-AKT signaling pathway and downregulating the expression of TNF-α, IL-6, EGFR. Furthermore, Histological analysis confirmed that administration of WG to ICR mice significantly ameliorated UVB-induced skin roughness, epidermal thickening, disturbed collagen fiber alignment and wrinkles. Meanwhile, immunohistochemistry showed that administration of WG to ICR mice significantly reduced UVB-induced expression of MMP9, MPO, F4/80 in the skin. These results provide new insights into the contribution of WG to the development of clinical treatment modalities for UVB-induced SD. CONCLUSION: The crucial element in the fight against SD is WG, with the primary route being PI3K/Akt. The main components and hub genes had robust binding abilities. In vitro and vivo experiments showed that WG could inhibit the expression level of the hub genes by inhibiting the PI3K/Akt pathway. In summary, the information presented in this study indicates that WG might be utilised as a treatment for UVB-induced SD.

CP-Net: Instance-aware part segmentation network for biological cell parsing.

Instance segmentation of biological cells is important in medical image analysis for identifying and segmenting individual cells, and quantitative measurement of subcellular structures requires further cell-level subcellular part segmentation. Subcellular structure measurements are critical for cell phenotyping and quality analysis. For these purposes, instance-aware part segmentation network is first introduced to distinguish individual cells and segment subcellular structures for each detected cell. This approach is demonstrated on human sperm cells since the World Health Organization has established quantitative standards for sperm quality assessment. Specifically, a novel Cell Parsing Net (CP-Net) is proposed for accurate instance-level cell parsing. An attention-based feature fusion module is designed to alleviate contour misalignments for cells with an irregular shape by using instance masks as spatial cues instead of as strict constraints to differentiate various instances. A coarse-to-fine segmentation module is developed to effectively segment tiny subcellular structures within a cell through hierarchical segmentation from whole to part instead of directly segmenting each cell part. Moreover, a sperm parsing dataset is built including 320 annotated sperm images with five semantic subcellular part labels. Extensive experiments on the collected dataset demonstrate that the proposed CP-Net outperforms state-of-the-art instance-aware part segmentation networks.

Using extracorporeal membrane oxygenation in donations after cardiac death or brain death: A single-center experience and long-term outcome.

Aims: The use of extended criteria donors is a routine practice that sometimes involves extracorporeal membrane oxygenation (ECMO) in donations after cardiac death or brain death. Methods: We performed a retrospective study in a single center from January 2006 to December 2019. The study included 90 deceased donor liver transplants. The patients were divided into three groups: the donation after brain death (DBD) group (n = 58, 64.4%), the DBD with ECMO group (n = 11, 12.2%) and the donation after cardiac death (DCD) with ECMO group (n = 21, 23.3%). Results: There were no significant differences between the DBD with ECMO group and the DBD group. When comparing the DCD with ECMO group and the DBD group, there were statistically significant differences for total warm ischemia time (p < 0.001), total cold ischemia time (p = 0.023), and split liver transplantation (p < 0.001), and there was significantly poor recovery in regard to total bilirubin level (p = 0.027) for the DCD with ECMO group by repeated measures ANOVA. The 5-year survival rates of the DBD, DBD with ECMO, and DCD with ECMO groups were 78.1%, 90.9%, and 75.6%, respectively. The survival rate was not significantly different when comparing the DBD group to either the DBD with ECMO group (p = 0.435) or the DCD with ECMO group (p = 0.310). Conclusions: Using ECMO in donations after cardiac death or brain death is a good technology, and it contributed to 35.6% of the liver graft pool.

Apoptosis related genes mediated molecular subtypes depict the hallmarks of the tumor microenvironment and guide immunotherapy in bladder cancer.

Apoptosis has been discovered as a mechanism of cell death. The purpose of this study is to identify the diagnostic signature factors related to bladder cancer (BLCA) through apoptosis related genes (ARGs). Clinicopathological parameters and transcriptomics data of 1,440 BLCA patients were obtained from 7 datasets (GSE13507, GSE31684, GSE32548, GSE32894, GSE48075, TCGA-BLCA, and IMvigor210). We first identified prognosis-related ARGs in BLCA and used them to construct two ARGs molecular subtypes by using consensus clustering algorithm. By using principal component analysis algorithms, a ARGscore was constructed to quantify the index of individualized patient. High ARGscore correlated with progressive malignancy and poor outcomes in BLCA patients. High ARGscore was associated with higher immune cell, higher estimate scores, higher stromal scores, higher immune scores, higher immune checkpoint, and lower tumor purity, which was consistent with the "immunity tidal model theory". Preclinically, BLCA immunotherapy cohorts confirmed patients with low ARGscore demonstrated significant therapeutic advantages and clinical benefits. These findings contribute to our understanding of ARGs and immunotherapy in BLCA. The ARGscore is a potentially useful tool to predict the prognosis and immunotherapy in BLCA.

Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures.

The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation.

Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers.

Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.

Remarkable Wear Resistance in a Complex Concentrated Alloy with Nanohierarchical Architecture and Composition Undulation.

Sustained wear damages on the sliding surfaces of alloys are generally the culprit responsible for the failure of various mechanical systems. Inspired by high-entropy effects, here we deliberately deploy nanohierarchical architecture with composition undulation in a Ni50(AlNbTiV)50 complex concentrated alloy, which yields ultralow wear rate within the order of 10-7 to 10-6 mm3/Nm between room temperature and 800 °C. Such remarkable wear resistance heretofore represents one of the highest wear resistance reported for the bulk alloys or composites, and originates from the multi-type adaptive friction interface protection governed by intrinsically nano-coupled grains and nanoprecipitates. This cooperative heterostructure releases gradient frictional stress in stages upon wear at room temperature through the coexistence of multiple deformation pathways while activating a dense nanocrystalline glaze layer upon wear at 800 °C to minimize adhesive and oxidative wear. Our work uncovers a practical avenue for tailoring wear properties with multicomponent heterostructures over a wide temperature range.