BioBBC: a multi-feature model that enhances the detection of biomedical entities.

The rapid increase in biomedical publications necessitates efficient systems to automatically handle Biomedical Named Entity Recognition (BioNER) tasks in unstructured text. However, accurately detecting biomedical entities is quite challenging due to the complexity of their names and the frequent use of abbreviations. In this paper, we propose BioBBC, a deep learning (DL) model that utilizes multi-feature embeddings and is constructed based on the BERT-BiLSTM-CRF to address the BioNER task. BioBBC consists of three main layers; an embedding layer, a Long Short-Term Memory (Bi-LSTM) layer, and a Conditional Random Fields (CRF) layer. BioBBC takes sentences from the biomedical domain as input and identifies the biomedical entities mentioned within the text. The embedding layer generates enriched contextual representation vectors of the input by learning the text through four types of embeddings: part-of-speech tags (POS tags) embedding, char-level embedding, BERT embedding, and data-specific embedding. The BiLSTM layer produces additional syntactic and semantic feature representations. Finally, the CRF layer identifies the best possible tag sequence for the input sentence. Our model is well-constructed and well-optimized for detecting different types of biomedical entities. Based on experimental results, our model outperformed state-of-the-art (SOTA) models with significant improvements based on six benchmark BioNER datasets.

Long-Term Outcome of Photobiomodulation Therapy for Refractory Diabetic Wound After Secretory Carcinoma of the Parotid Gland Surgery: A Case Report.

Objective: To evaluate the efficacy and safety of photobiomodulation therapy (PBMT) in the treatment of diabetic patients with refractory wound. Background: Refractory wound is one of the most challenging clinical complications of diabetes mellitus. Studies have shown that PBMT can promote wound healing in many ways. Methods: We reported a 55-year-old male patient with refractory diabetic wound after secretory carcinoma of the parotid gland surgery responding to 810 nm laser. Results: After PBMT, the refractory diabetic wound healed gradually without adverse events. During follow-up 5-years, the healed wound remained stable and showed no signs of recurrence. Conclusions: PBMT can be potentially considered as a therapeutic method in diabetic patients with refractory diabetic wound.

Genomic and biological control of Sclerotinia sclerotiorum using an extracellular extract from Bacillus velezensis 20507.

Introduction: Sclerotinia sclerotiorum is a known pathogen that harms crops and vegetables. Unfortunately, there is a lack of effective biological control measures for this pathogen. Bacillus velezensis 20507 has a strong antagonistic effect on S. Sclerotiorum; however, the biological basis of its antifungal effect is not fully understood. Methods: In this study, the broad-spectrum antagonistic microorganisms of B. velezensis 20507 were investigated, and the active antifungal ingredients in this strain were isolated, purified, identified and thermal stability experiments were carried out to explore its antifungal mechanism. Results: The B. velezensis 20507 genome comprised one circular chromosome with a length of 4,043,341 bp, including 3,879 genes, 185 tandem repeats, 87 tRNAs, and 27 rRNAs. Comparative genomic analysis revealed that our sequenced strain had the closest genetic relationship with Bacillus velezensis (GenBank ID: NC 009725.2); however, there were significant differences in the positions of genes within the two genomes. It is predicted that B. velezensis 20507 encode 12 secondary metabolites, including difficidin, macrolactin H, fengycin, surfactin, bacillibactin, bacillothiazole A-N, butirosin a/b, and bacillaene. Results showed that B. velezensis 20507 produced various antagonistic effects on six plant pathogen strains: Exserohilum turcicum, Pyricularia oryzae, Fusarium graminearum, Sclerotinia sclerotiorum, Fusarium oxysporum, and Fusarium verticillioides. Acid precipitation followed by 80% methanol leaching is an effective method for isolating the antifungal component ME80 in B. velezensis 20507, which can damage the membranes of S. sclerotiorum hyphae and has good heat resistance. Using high-performance liquid chromatography, and Mass Spectrometry analysis, it is believed that fengycin C72H110N12O20 is the main active antifungal substance. Discussion: This study provides new resources for the biological control of S. Sclerotiorum in soybeans and a theoretical basis for further clarification of the mechanism of action of B. velezensis 20507.

Kinetic Modulation of Carbon Nanotube Growth in Direct Spinning for High-Strength Carbon Nanotube Fibers.

With impressive individual properties, carbon nanotubes (CNTs) show great potential in constructing high-performance fibers. However, the tensile strength of as-prepared carbon nanotube fibers (CNTFs) by floating catalyst chemical vapor deposition (FCCVD) is plagued by the weak intertube interaction between the essential CNTs. Here, we developed a chlorine (Cl)/water (H2O)-assisted length furtherance FCCVD (CALF-FCCVD) method to modulate the intertube interaction of CNTs and enhance the mechanical strength of macroscopic fibers. The CNTs acquired by the CALF-FCCVD method show an improvement of 731% in length compared to that by the conventional iron-based FCCVD system. Moreover, CNTFs prepared by CALF-FCCVD spinning exhibit a high tensile strength of 5.27 ± 0.27 GPa (4.62 ± 0.24 N/tex) and reach up to 5.61 GPa (4.92 N/tex), which outperforms most previously reported results. Experimental measurements and density functional theory calculations show that Cl and H2O play a crucial role in the furtherance of CNT growth. Cl released from the decomposition of methylene dichloride greatly accelerates the growth of the CNTs; H2O can remove amorphous carbon on the floating catalysts to extend their lifetime, which further modulates the growth kinetics and improves the purity of the as-prepared fibers. Our design of the CALF-FCCVD platform offers a powerful way to tune CNT growth kinetics in direct spinning toward high-strength CNTFs.

Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.

Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.

MAFLD as part of systemic metabolic dysregulation.

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases worldwide. In recent years, a new terminology and definition of metabolic dysfunction-associated fatty liver disease (MAFLD) has been proposed. Compared to the NAFLD definition, MAFLD better emphasizes the pathogenic role of metabolic dysfunction in the development and progression of this highly prevalent condition. Metabolic disorders, including overweight/obesity, type 2 diabetes mellitus (T2DM), atherogenic dyslipidemia and hypertension, are often associated with systemic organ dysfunctions, thereby suggesting that multiple organ damage can occur in MAFLD. Substantial epidemiological evidence indicates that MAFLD is not only associated with an increased risk of liver-related complications, but also increases the risk of developing several extra-hepatic diseases, including new-onset T2DM, adverse cardiovascular and renal outcomes, and some common endocrine diseases. We have summarized the current literature on the adverse effect of MAFLD on the development of multiple extrahepatic (cardiometabolic and endocrine) complications and examined the role of different metabolic pathways and organ systems in the progression of MAFLD, thus providing new insights into the role of MAFLD as a multisystem metabolic disorder. Our narrative review aimed to provide insights into potential mechanisms underlying the known associations between MAFLD and extrahepatic diseases, as part of MAFLD as a multisystem disease, in order to help focus areas for future drug development targeting not only liver disease but also the risk of extrahepatic complications.

Semiautomated design and soluble expression of a chimeric antigen TbpAB01 from Glaesserella parasuis.

Pathogenic bacterial membrane proteins (MPs) are a class of vaccine and antibiotic development targets with widespread clinical application. However, the inherent hydrophobicity of MPs poses a challenge to fold correctly in living cells. Herein, we present a comprehensive method to improve the soluble form of MP antigen by rationally designing multi-epitope chimeric antigen (ChA) and screening two classes of protein-assisting folding element. The study uses a homologous protein antigen as a functional scaffold to generate a ChA possessing four epitopes from transferrin-binding protein A of Glaesserella parasuis. Our engineered strain, which co-expresses P17 tagged-ChA and endogenous chaperones groEL-ES, yields a 0.346 g/L highly soluble ChA with the property of HPS-positive serum reaction. Moreover, the protein titer of ChA reaches 4.27 g/L with >90% soluble proportion in 5-L bioreactor, which is the highest titer reported so far. The results highlight a timely approach to design and improve the soluble expression of MP antigen in industrially viable applications.

Vertically spliced tabletop light field cave display with extended depth content and separately optimized compound lens array.

Tabletop three-dimensional light field display is a kind of compelling display technology that can simultaneously provide stereoscopic vision for multiple viewers surrounding the lateral side of the device. However, if the flat panel light field display device is simply placed horizontally and displayed directly above, the visual frustum will be tilted and the 3D content outside the display panel will be invisible, the large oblique viewing angle will also lead to serious aberrations. In this paper, we demonstrate what we believe to be a new vertical spliced light field cave display system with an extended depth content. A separate optimization of different compound lens array attenuates the aberration from different oblique viewing angles, and a local heating fitting method is implemented to ensure the accuracy of fabrication process. The image coding method and the correction of the multiple viewpoints realize the correct construction of spliced voxels. In the experiment, a high-definition and precisely spliced 3D city terrain scene is demonstrated on the prototype with a correct oblique perspective in 100-degree horizontal viewing range. We envision that our research will provide more inspiration for future immersive large-scale glass-free virtual reality display technologies.

Smooth motion parallax method for 3D light-field displays with a narrow pitch based on optimizing the light beam divergence angle.

The three-dimensional (3D) light field display (LFD) with dense views can provide smooth motion parallax for the human eye. Increasing the number of views will widen the lens pitch, however, resulting in a decrease in view resolution. In this paper, an approach to smooth motion parallax based on optimizing the divergence angle of the light beam (DALB) for 3D LFD with narrow pitch is proposed. DALB is controlled by lens design. A views-fitting optimization algorithm is established based on a mathematical model between DALB and view distribution. Subsequently, the lens is reversely designed based on the optimization results. A co-designed convolutional neural network (CNN) is used to implement the algorithm. The optical experiment shows that a smooth motion parallax 3D image is achievable through the proposed method.

Advances in management of metabolic dysfunction-associated steatotic liver disease: from mechanisms to therapeutics.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease that affects over 30% of the world's population. For decades, the heterogeneity of non-alcoholic fatty liver disease (NAFLD) has impeded our understanding of the disease mechanism and the development of effective medications. However, a recent change in the nomenclature from NAFLD to MASLD emphasizes the critical role of systemic metabolic dysfunction in the pathophysiology of this disease and therefore promotes the progress in the pharmaceutical treatment of MASLD. In this review, we focus on the mechanism underlying the abnormality of hepatic lipid metabolism in patients with MASLD, and summarize the latest progress in the therapeutic medications of MASLD that target metabolic disorders.

RAAS in diabetic retinopathy: mechanisms and therapies.

Diabetic retinopathy (DR) is a complication of diabetes with a complex pathophysiology and multiple factors involved. Recently, it has been found that the upregulation of the renin-angiotensin-aldosterone system (RAAS) leads to overexpression of angiotensin II (Ang II), which induces oxidative stress, inflammation, and angiogenesis in the retina. Therefore, RAAS may be a promising therapeutic target in DR. Notably, RAAS inhibitors are often used in the treatment of hypertension. Still, the potential role and mechanism of DR must be further studied. In this review, we discuss and summarize the pathology and potential therapeutic goals of RAAS in DR.

In situ single iron atom doping on Bi2WO6 monolayers triggers efficient photo-fenton reaction.

Developing an efficient photocatalytic system for hydrogen peroxide (H2O2) activation in Fenton-like processes holds significant promise for advancing water purification technologies. However, challenges such as high carrier recombination rates, limited active sites, and suboptimal H2O2 activation efficiency impede optimal performance. Here we show that single-iron-atom dispersed Bi2WO6 monolayers (SIAD-BWOM), designed through a facile hydrothermal approach, can offer abundant active sites for H2O2 activation. The SIAD-BWOM catalyst demonstrates superior photo-Fenton degradation capabilities, particularly for the persistent pesticide dinotefuran (DNF), showcasing its potential in addressing recalcitrant organic pollutants. We reveal that the incorporation of iron atoms in place of tungsten within the electron-rich [WO4]2- layers significantly facilitates electron transfer processes and boosts the Fe(II)/Fe(III) cycle efficiency. Complementary experimental investigations and theoretical analyses further elucidate how the atomically dispersed iron induces lattice strain in the Bi2WO6 monolayer, thereby modulating the d-band center of iron to improve H2O2 adsorption and activation. Our research provides a practical framework for developing advanced photo-Fenton catalysts, which can be used to treat emerging and refractory organic pollutants more effectively.

Comparison of early patient-reported outcomes between uniportal thoracoscopic segmentectomy and wedge resection for peripheral small-sized non-small-cell lung cancer.

BACKGROUND: Analysis of patient-reported outcomes (PROs) offers valuable insights into distinguishing the effects of closely related medical procedures from the patient's perspective. In this study we compared symptom burden in patients undergoing uniportal thoracoscopic segmentectomy and wedge resection for peripheral small-sized non-small cell lung cancer (NSCLC). METHODS: This study included patients with peripheral NSCLC from an ongoing longitudinal prospective cohort study (CN-PRO-Lung 3) who underwent segmentectomy or wedge resection with tumor diameter ≤ 2 cm and consolidation tumor ratio (CTR) ≤ 0.5. PROs data were collected using the Perioperative Symptom Assessment for Lung Surgery questionnaire pre-operatively, daily post-surgery up to the fourth hospitalization day, and weekly post-discharge up to the fourth week. Propensity score matching and a generalized estimation equation model were employed to compare symptom severity. In addition, short-term clinical outcomes were compared. RESULTS: In total, data of 286 patients (82.4%) undergoing segmentectomy and 61 patients (17.6%) undergoing wedge resection were extracted from the cohort. No statistically significant differences were found in the proportion of moderate-to-severe symptoms and mean scores for pain, cough, shortness of breath, disturbed sleep, fatigue, drowsiness, and distress during the 4-day postoperative hospitalization or the 4-week post-discharge period before or after matching (all p > 0.05). Compared with segmentectomy, wedge resection showed better short-term clinical outcomes, including shorter operative time (p = 0.001), less intraoperative bleeding (p = 0.046), and lower total hospital costs (p = 0.002). CONCLUSIONS: The study findings indicate that uniportal thoracoscopic segmentectomy and wedge resection exert similar early postoperative symptom burden in patients with peripheral NSCLC (tumor diameter ≤ 2 cm and CTR ≤ 0.5). CLINICAL TRIAL REGISTRATION: Not applicable.

DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins.

MOTIVATION: Understanding the intermolecular interactions of ligand-target pairs is key to guiding the optimization of drug research on cancers, which can greatly mitigate overburden workloads for wet labs. Several improved computational methods have been introduced and exhibit promising performance for these identification tasks, but some pitfalls restrict their practical applications: (i) first, existing methods do not sufficiently consider how multigranular molecule representations influence interaction patterns between proteins and compounds; and (ii) second, existing methods seldom explicitly model the binding sites when an interaction occurs to enable better prediction and interpretation, which may lead to unexpected obstacles to biological researchers. RESULTS: To address these issues, we here present DrugMGR, a deep multigranular drug representation model capable of predicting binding affinities and regions for each ligand-target pair. We conduct consistent experiments on three benchmark datasets using existing methods and introduce a new specific dataset to better validate the prediction of binding sites. For practical application, target-specific compound identification tasks are also carried out to validate the capability of real-world compound screen. Moreover, the visualization of some practical interaction scenarios provides interpretable insights from the results of the predictions. The proposed DrugMGR achieves excellent overall performance in these datasets, exhibiting its advantages and merits against state-of-the-art methods. Thus, the downstream task of DrugMGR can be fine-tuned for identifying the potential compounds that target proteins for clinical treatment. AVAILABILITY AND IMPLEMENTATION: https://github.com/lixiaokun2020/DrugMGR.

Micromorphology reformation of regenerated cellulose nanofibers from corn (Zea Mays) stalk pith in urea solution with high-speed shear induced.

Nanocellulose is a kind of renewable natural polymer material with high specific surface area, high crystallinity, and strong mechanical properties. RC nanofibers (RCNFs) have attracted an increasing attention in various applications due to their high aspect ratio and good flexibility. Herein, a novel and facile strategy for RCNFs preparation with high-speed shear induced in urea solution through "bottom-up" approach was proposed in this work. Results indicated that the average diameter and yield of RCNF was approach to 136.67 nm and 53.3 %, respectively. Meanwhile, due to the regular orientation RC chains and arrangement micro-morphology, RCNFs exhibited high crystallinity, strong mechanical properties, stable thermal degradation performance, and excellent UV resistance. In this study, a novel regeneration process with high-speed shear induced was developed to produce RCNFs with excellent properties. This study paved a strategy for future low-energy production of nanofibers and high value-added conversion applications of agricultural waste.

Patient privacy in AI-driven omics methods.

Artificial intelligence (AI) in omics analysis raises privacy threats to patients. Here, we briefly discuss risk factors to patient privacy in data sharing, model training, and release, as well as methods to safeguard and evaluate patient privacy in AI-driven omics methods.

Potassium Chloride as an Effective Alternative to Sodium Chloride in Delaying the Thermal Aggregation of Liquid Whole Egg.

The potential of potassium chloride (KCl) to be used as a substitute for sodium chloride (NaCl) was studied by monitoring the effects of salt treatment on thermal behavior, aggregation kinetics, rheological properties, and protein conformational changes. The results show that the addition of KCl can improve solubility, reduce turbidity and particle size, and positively influence rheological parameters such as apparent viscosity, consistency coefficient (K value), and fluidity index (n). These changes indicate delayed thermal denaturation. In addition, KCl decreased the content of ß-sheet and random coil structures and increased the content of α-helix and ß-turn structures. The optimal results were obtained with 2% KCl addition, leading to an increase in Tp up to 85.09 °C. The correlation results showed that Tp was positively correlated with solubility, α-helix and ß-turn but negatively correlated with ΔH, turbidity, ß-sheet and random coil. Overall, compared to NaCl, 2% KCl is more effective in delaying the thermal aggregation of LWE, and these findings lay a solid theoretical foundation for the study of sodium substitutes in heat-resistant liquid egg products.

ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles.

The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures poses a significant challenge for computational biology in leveraging structural information and accurate representation of protein surface properties. Recently, AlphaFold2 released the comprehensive proteomes of various species, and protein surface property representation plays a crucial role in protein-molecule interaction predictions, including those involving proteins, nucleic acids and compounds. Here, we proposed the first extensive database, namely ProNet DB, that integrates multiple protein surface representations and RNA-binding landscape for 326 175 protein structures. This collection encompasses the 16 model organism proteomes from the AlphaFold Protein Structure Database and experimentally validated structures from the Protein Data Bank. For each protein, ProNet DB provides access to the original protein structures along with the detailed surface property representations encompassing hydrophobicity, charge distribution and hydrogen bonding potential as well as interactive features such as the interacting face and RNA-binding sites and preferences. To facilitate an intuitive interpretation of these properties and the RNA-binding landscape, ProNet DB incorporates visualization tools like Mol* and an Online 3D Viewer, allowing for the direct observation and analysis of these representations on protein surfaces. The availability of pre-computed features enables instantaneous access for users, significantly advancing computational biology research in areas such as molecular mechanism elucidation, geometry-based drug discovery and the development of novel therapeutic approaches. Database URL:  https://proj.cse.cuhk.edu.hk/aihlab/pronet/.

Molecular characterization of vascular endothelial growth factor b from spotted sea bass (Lateolabrax maculatus) and its potential roles in decreasing lipid deposition.

Vascular endothelial growth factor B (VEGFB), a member of the VEGF family, exhibits limited angiogenic activity in mammals but plays an unexpected role in targeting lipids to peripheral tissues. However, its role in lipid metabolism in fish is unknown. In this study, the vegfb gene was cloned and characterized from spotted sea bass (Lateolabrax maculatus). It encodes 254 amino acids and possesses the typical characteristics of the Vegfb family, demonstrating high homology with those from other vertebrate species. The vegfb gene exhibits the highest expression levels in the liver, followed by the gills, intestine, and adipose tissues in spotted sea bass. In vivo, high-lipid diets decreased vegfb expression and increased lipid deposition in liver of fish. In vitro, palmitic acid + oleic acid treatment or vegfb knockdown significantly increased TG and TC contents, promoting lipid droplet deposition in hepatocytes. Vegfb overexpression has the opposite effects, inhibiting lipid deposition and downregulating fatty acid transport and adipogenesis genes. In contrast, the vegfb knockdown significantly upregulated the expression levels of c/ebpα, plin2, and dgat1 (P < 0.05). These results demonstrate that Vegfb may play an important role in reducing lipid deposition by regulating fatty acid transport and adipogenesis in the hepatocytes of spotted sea bass.

Gene expression prognostic of early relapse risk in low-risk B-cell acute lymphoblastic leukaemia in children.

ETV6::RUNX1 is the most common fusion gene in childhood acute lymphoblastic leukaemia (ALL) and is associated with favorable outcomes, especially in low-risk children. However, as many as 10% of children relapse within 3 years, and such early relapses have poor survival. Identifying children at risk for early relapse is an important challenge. We interrogated data from 87 children with low-risk ETV6::RUNX1-positive B-cell ALL and with available preserved bone marrow samples (discovery cohort). We profiled somatic point mutations in a panel of 559 genes and genome-wide transcriptome and single-nucleotide variants. We found high TIMD4 expression (> 85th-percentile value) at diagnosis was the most important independent prognostic factor of early relapse (hazard ratio [HR] = 5.07 [1.76, 14.62]; p = 0.03). In an independent validation cohort of low-risk ETV6::RUNX1-positive B-cell ALL (N = 68) high TIMD4 expression at diagnosis had an HR = 4.78 [1.07, 21.36] (p = 0.04) for early relapse. In another validation cohort including 78 children with low-risk ETV6::RUNX1-negative B-cell ALL, high TIMD4 expression at diagnosis had an HR = 3.93 [1.31, 11.79] (p = 0.01). Our results suggest high TIMD4 expression at diagnosis in low-risk B-cell ALL in children might be associated with high risk for early relapse.