Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.

The HADDOCK team participated in CAPRI rounds 47-55 as server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 in the server category.

The interaction of isoquinoline alkaloid crebanine with immunoglobulin G and cytotoxic effects toward MCF-7 breast cancer cell line.

In this study, the interaction of crebanine, an isoquinoline alkaloid, with immunoglobulin G (IgG) was evaluated. Subsequently, the anticancer effects of crebanine in MCF-7 breast cancer cells were assessed. The results demonstrate that static quenching plays a key role in the fluorescence quenching of the IgG by crebanine, and some embedded hydrophobic patches of the IgG are exposed upon interaction with crebanine, while the characteristic β-sheet conformation of the IgG was almost preserved.

Enhancing vaginal reconstruction through 3D bioprinted scaffolds using a novel vECM-GelMA-SF bioink.

Overcoming the low cell survival rates and insufficient neovascularization associated with tissue engineering of the vagina is crucial for advancing the vaginal reconstruction. In this research, we have developed a unique bioink composed of porcine vaginal extracellular matrix (vECM), gelatin methacrylamide (GelMA), and silk fibroin (SF) to facilitate the bioprinting of a vaginal scaffold. The vECM-GelMA-SF bioink effectively replicates themicroenvironment, supporting thecultivation of 3D bioprinted vaginal scaffolds.

A computational method to predict cerebral perfusion flow after endovascular treatment based on invasive pressure and resistance.

Background And Objective: Predicting post-operative flow is essential for assessing the risk of adverse events in cerebrovascular stenosis patients following endovascular treatment (EVT). This study aimed to evaluate the accuracy of the CFD simulation model in predicting post-operative velocity, flow and pressure distal to a stenosis, based on cerebrovascular microcirculatory resistance.

Methods: The patient-specific models of the extracranial and intracranial arteries were reconstructed.

A magnetic epitope-imprinted microsphere used for selective separation and rapid detection of SHV-type β-lactamases in bacteria: a novel strategy of antimicrobial resistance detection.

Background: The production of β-lactamases is the most prevalent resistance mechanism for β-lactam antibiotics in Gram-negative bacteria. Presently, over 4900 β-lactamases have been discovered, and they are categorized into hundreds of families. In each enzyme family, amino acid substitutions result in subtle changes to enzyme hydrolysis profiles; in contrast, certain conserved sequences retained by all of the family members can serve as important markers for enzyme family identification.

Lung Immune Cell Niches and the Discovery of New Cell Subtypes.

Immune cells in the lungs are important for maintaining lung function. The importance of immune cells in defending against lung diseases and infections is increasingly recognized. However, a primary knowledge gaps in current studies of lung immune cells is the understanding of their subtypes and functional heterogeneity.

Ce Doping Effects on the Hydrogen Sensing Properties of Graphene/SnO-Based Sensors.

The development of a sensor capable of selectively detecting hydrogen levels in the environment holds immense importance for ensuring the safer utilization of hydrogen energy. In this study, a hydrogen sensor made of Ce-doped single-layer graphene (SLG)/SnO composite material was fabricated using a hydrothermal method. The study examined the impact of varying Ce doping concentrations on the hydrogen sensing capabilities of the SLG/SnO matrix.

Pan-cancer analysis of the role of MPP7 in human tumors.

MAGUK p55 subfamily member 7, a part of the membrane palmitoylated protein subfamily, is an essential adapter that promotes epithelial cell polarity and has increasing significance in multiple cancers, including esophageal cancer, clear cell renal cell carcinoma, breast cancer, and pancreatic ductal adenocarcinoma. This paper aims to determine the effect of the MAGUK p55 subfamily member 7 in various tumor types using The Cancer Genome Atlas and Genotype-Tissue Expression database. A variety of software and web platforms, such as cBioPortal, GEPIA2, TIMER2, UALCAN, R, STRING, and DAVID, were used to obtain and analyze data.

Spatiotemporal correlation enhanced real-time 4D-CBCT imaging using convolutional LSTM networks.

Purpose: To enhance the accuracy of real-time four-dimensional cone beam CT (4D-CBCT) imaging by incorporating spatiotemporal correlation from the sequential projection image into the single projection-based 4D-CBCT estimation process.

Methods: We first derived 4D deformation vector fields (DVFs) from patient 4D-CT. Principal component analysis (PCA) was then employed to extract distinctive feature labels for each DVF, focusing on the first three PCA coefficients.

Abundance, characteristics and ecological risk assessment of microplastics in ship ballast water in ports around Liaodong Peninsula, China.

The development of the shipping industry has led to a large volume of ballast water discharge annually. This accelerates pollutants' transfer and dispersion, such as microplastics. Currently, empirical data on microplastics in ballast water are rarely available.

Spermatogenic cell-specific type 1 hexokinase (HK1S) is essential for capacitation-associated increase in tyrosine phosphorylation and male fertility in mice.

Hexokinase (HK) catalyzes the first irreversible rate-limiting step in glycolysis that converts glucose to glucose-6-phosphate. HK1 is ubiquitously expressed in the brain, erythrocytes, and other tissues where glycolysis serves as the major source of ATP production. Spermatogenic cell-specific type 1 hexokinase (HK1S) is expressed in sperm but its physiological role in male mice is still unknown.

A rare case report of Herlyn-Werner-Wunderlich syndrome: Unraveling unusual urinary anomalies and literature review.

Herlyn-Werner-Wunderlich syndrome (HWWS) is a rare congenital genitourinary abnormality defined by uterine didelphys, obstructed hemivagina, and ipsilateral urological anomalies. Accurate diagnosis and prompt commencement of therapy can be difficult owing to heterogeneous genitourinary malformation among different patients. This is a case report of a patient with rare HWWS with uterine didelphys, obstructed hemivagina, vagina-ureteral remnant fistula (Gartner's duct cyst), and ipsilateral kidney dysgenesis who complained of intermittent abdominal pain during menstruation.

A novel prediction approach driven by graph representation learning for heavy metal concentrations.

The potential risk of heavy metals (HMs) to public health is an issue of great concern. Early prediction is an effective means to reduce the accumulation of HMs. The current prediction methods rarely take internal correlations between environmental factors into consideration, which negatively affects the accuracy of the prediction model and the interpretability of intrinsic mechanisms.

Jiawei Duhuo Jisheng Mixture Mitigates Osteoarthritis Progression in Rabbits by Inhibiting Inflammation: A Network Pharmacology and Experimental Approach.

Background: Knee osteoarthritis (KOA) is a common degenerative joint disease characterized by cartilage degradation, inflammation, and pain. Traditional Chinese Medicine, including JDJM (a herbal formula derived from the renowned Du Huo Ji Sheng Tang), has been used to alleviate symptoms of KOA, but its underlying mechanisms remain unclear.

Objective: This study aims to elucidate the potential therapeutic mechanisms of JDJM in treating KOA through network pharmacology, weighted gene co-expression network analysis (WGCNA), molecular docking, and experimental validation in animal models.

Halotolerant Bacillus sp. strain RA coordinates myo-inositol metabolism to confer salt tolerance to tomato.

Soil salinity is a worldwide problem threatening crop yields. Some plant growth-promoting rhizobacteria (PGPR) could survive in high salt environment and assist plant adaptation to stress. Nevertheless, the genomic and metabolic features, as well as the regulatory mechanisms promoting salt tolerance in plants by these bacteria remain largely unknown.

No Evidence of an Association between Genetic Factors Affecting Response to Vitamin A Supplementation and Myopia: A Mendelian Randomization Study and Meta-Analysis.

The relationship between vitamin A supplementation and myopia has been a topic of debate, with conflicting and inconclusive findings. We aimed to determine whether there is a causal relationship between vitamin A supplementation and the risk of myopia using Mendelian randomization (MR) and meta-analytical methods. Genetic variants from the UK Biobank and FinnGen studies associated with the response to vitamin A supplementation were employed as instrumental variables to evaluate the causal relationship between vitamin A supplementation and myopia.

Self-Assembly of Strain-Adaptable Surface-Enhanced Raman Scattering Substrate on Polydimethylsiloxane Nanowrinkles.

Flexible surface-enhanced Raman scattering (SERS) substrates adaptable to strains enable effective sampling from irregular surfaces, but the preparation of highly stable and sensitive flexible SERS substrates is still challenging. This paper reports a method to fabricate a high-performance strain-adaptable SERS substrate by self-assembly of Au nanoparticles (AuNPs) on polydimethylsiloxane (PDMS) nanowrinkles. Nanowrinkles are created on prestrained PDMS slabs by plasma-induced oxidation followed by the release of the prestrain, and self-assembled AuNPs are transferred onto the nanowrinkles to construct the high-performance SERS substrate.

Longitudinal changes in sarcopenia was associated with survival among cirrhotic patients.

Background: Sarcopenia is common in patients with liver cirrhosis and is an independent predictor of multiple clinical outcomes. Most studies to date have used a static assessment of sarcopenia. However, there is very limited data evaluating the temporal course of muscle area in cirrhosis.

A brain subcortical segmentation tool based on anatomy attentional fusion network for developing macaques.

Magnetic Resonance Imaging (MRI) plays a pivotal role in the accurate measurement of brain subcortical structures in macaques, which is crucial for unraveling the complexities of brain structure and function, thereby enhancing our understanding of neurodegenerative diseases and brain development. However, due to significant differences in brain size, structure, and imaging characteristics between humans and macaques, computational tools developed for human neuroimaging studies often encounter obstacles when applied to macaques. In this context, we propose an Anatomy Attentional Fusion Network (AAF-Net), which integrates multimodal MRI data with anatomical constraints in a multi-scale framework to address the challenges posed by the dynamic development, regional heterogeneity, and age-related size variations of the juvenile macaque brain, thus achieving precise subcortical segmentation.

Biomimetic Nano-Regulator that Induces Cuproptosis and Lactate-Depletion Mediated ROS Storm for Metalloimmunotherapy of Clear Cell Renal Cell Carcinoma.

Herein, a ccRCC targeting nanodrug is designed to enhance chemodynamic therapy (CDT) as well as activate cuproptosis and tumor immunotherapy via ccRCC cell membrane modifying CuO@GdO yolk-like particles (CGYL) loaded with lactate oxidase (LOx) (mCGYL-LOx). Benefiting from the homologous targeting effect of Renca cell membranes, the mCGYS-LOx can be effectively internalized by Renca cells, open the "gate", and then release LOx and copper (Cu) ions. LOx can catalyze excessive lactate in Renca cells into HO, following that the produced HO is further converted by Cu ions to the highly toxic ·OH, contributing to tumor CDT.