Influence of Time-Lag Effects between Winter-Wheat Canopy Temperature and Atmospheric Temperature on the Accuracy of CWSI Inversion of Photosynthetic Parameters.

When calculating the CWSI, previous researchers usually used canopy temperature and atmospheric temperature at the same time. However, it takes some time for the canopy temperature (Tc) to respond to atmospheric temperature (Ta), suggesting the time-lag effects between Ta and Tc. In order to investigate time-lag effects between Ta and Tc on the accuracy of the CWSI inversion of photosynthetic parameters in winter wheat, we conducted an experiment. In this study, four moisture treatments were set up: T1 (95% of field water holding capacity), T2 (80% of field water holding capacity), T3 (65% of field water holding capacity), and T4 (50% of field water holding capacity). We quantified the time-lag parameter in winter wheat using time-lag peak-seeking, time-lag cross-correlation, time-lag mutual information, and gray time-lag correlation analysis. Based on the time-lag parameter, we modified the CWSI theoretical and empirical models and assessed the impact of time-lag effects on the accuracy of the CWSI inversion of photosynthesis parameters. Finally, we applied several machine learning algorithms to predict the daily variation in the CWSI after time-lag correction. The results show that: (1) The time-lag parameter calculated using time-lag peak-seeking, time-lag cross-correlation, time-lag mutual information, and gray time-lag correlation analysis are 44-70, 32-44, 42-58, and 76-97 min, respectively. (2) The CWSI empirical model corrected by the time-lag mutual information method has the highest correlation with photosynthetic parameters. (3) GA-SVM has the highest prediction accuracy for the CWSI empirical model corrected by the time-lag mutual information method. Considering time lag effects between Ta and Tc effectively enhanced the correlation between CWSI and photosynthetic parameters, which can provide theoretical support for thermal infrared remote sensing to diagnose crop water stress conditions.

Comparison of Prompt Engineering and Fine-Tuning Strategies in Large Language Models in the Classification of Clinical Notes.

The emerging large language models (LLMs) are actively evaluated in various fields including healthcare. Most studies have focused on established benchmarks and standard parameters; however, the variation and impact of prompt engineering and fine-tuning strategies have not been fully explored. This study benchmarks GPT-3.5 Turbo, GPT-4, and Llama-7B against BERT models and medical fellows' annotations in identifying patients with metastatic cancer from discharge summaries. Results revealed that clear, concise prompts incorporating reasoning steps significantly enhanced performance. GPT-4 exhibited superior performance among all models. Notably, one-shot learning and fine-tuning provided no incremental benefit. The model's accuracy sustained even when keywords for metastatic cancer were removed or when half of the input tokens were randomly discarded. These findings underscore GPT-4's potential to substitute specialized models, such as PubMedBERT, through strategic prompt engineering, and suggest opportunities to improve open-source models, which are better suited to use in clinical settings.

Clinical values of different specimen preparation methods for the diagnosis of lung cancer by EBUS-TBNA.

BACKGROUND AND OBJECTIVE: EBUS-TBNA has emerged as an important minimally invasive procedure for the diagnosis and staging of lung cancer. Our objective was to evaluate the effect of different specimen preparation from aspirates on the diagnosis of lung cancer. METHODS: 181 consecutive patients with known or suspected lung cancer accompanied by hilar / mediastinal lymphadenopathy underwent EBUS-TBNA from January 2019 to December 2022. Specimens obtained by EBUS-TBNA were processed by three methods: Traditional smear cytology of aspirates (TSC), liquid-based cytology of aspirates (LBC) and histopathology of core biopsies. RESULTS: EBUS-TBNA was performed in 181 patients on 213 lymph nodes, the total positive rate of the combination of three specimen preparation methods was 80.7%. The diagnostic positive rate of histopathology was 72.3%, TSC was 68.1%, and LBC was 65.3%, no significant differences was observed (p = 0.29); however, statistically significant difference was noted between the combination of three preparation methods and any single specimen preparation methods (p = 0.002). The diagnostic sensitivity of histopathology combined with TSC and histopathology combined with LBC were 96.5 and 94.8%, the specificity was 95.0% and 97.5%, the PPV was 98.8% and 99.4%, the NPV was 86.4% and 81.2%, the diagnostic accuracy was 96.2% and 95.3%, respectively; The sensitivity and accuracy of above methods were higher than that of single specimen preparation, but lower than that of combination of three preparation methods. CONCLUSION: When EBUS-TBNA is used for the diagnosis and staging of lung cancer, histopathology combined with TSC can achieve enough diagnostic efficiency and better cost-effectiveness.

Proteomic Profiling of Messenger Ribonucleoproteins in Mouse Tissues Based on Formaldehyde Cross-Linking.

Messenger ribonucleoprotein particles (mRNPs) are vital for tissue-specific gene expression via mediating posttranscriptional regulations. However, proteomic profiling of proteins in mRNPs, i.e., mRNA-associated proteins (mRAPs), has been challenging at the tissue level. Herein, we report the development of formaldehyde cross-linking-based mRNA-associated protein profiling (FAXRAP), a chemical strategy that enables the identification of mRAPs in both cultured cells and intact mouse organs. Applying FAXRAP, tissue-specific mRAPs were systematically profiled in the mouse liver, kidney, heart, and brain. Furthermore, brain mRAPs in Parkinson's disease (PD) mouse model were investigated, which revealed a global decrease of mRNP assembly in the brain of mice with PD. We envision that FAXRAP will facilitate uncovering the posttranscriptional regulation networks in various biological systems.

In pursuit of feedback activation: New insights into redox-responsive hydropersulfide prodrug combating oxidative stress.

Redox-responsive hydropersulfide prodrugs are designed to enable a more controllable and efficient hydropersulfide (RSSH) supply and to thoroughly explore their biological and therapeutic applications in oxidative damage. To obtain novel activation patterns triggered by redox signaling, we focused on NAD(P)H: quinone acceptor oxidoreductase 1 (NQO1), a canonical antioxidant enzyme, and designed NQO1-activated RSSH prodrugs. We also performed a head-to-head comparison of two mainstream structural scaffolds with solid quantitative analysis of prodrugs, RSSH, and metabolic by-products by LC-MS/MS, confirming that the perthiocarbamate scaffold was more effective in intracellular prodrug uptake and RSSH production. The prodrug was highly potent in oxidative stress management against cisplatin-induced nephrotoxicity. Strikingly, this prodrug possessed potential feedback activation properties by which the delivered RSSH can further escalate the prodrug activation via NQO1 upregulation. Our strategy pushed RSSH prodrugs one step further in the pursuit of efficient release in biological matrices and improved druggability against oxidative stress.

Comparison of Prompt Engineering and Fine-Tuning Strategies in Large Language Models in the Classification of Clinical Notes.

The emerging large language models (LLMs) are actively evaluated in various fields including healthcare. Most studies have focused on established benchmarks and standard parameters; however, the variation and impact of prompt engineering and fine-tuning strategies have not been fully explored. This study benchmarks GPT-3.5 Turbo, GPT-4, and Llama-7B against BERT models and medical fellows' annotations in identifying patients with metastatic cancer from discharge summaries. Results revealed that clear, concise prompts incorporating reasoning steps significantly enhanced performance. GPT-4 exhibited superior performance among all models. Notably, one-shot learning and fine-tuning provided no incremental benefit. The model's accuracy sustained even when keywords for metastatic cancer were removed or when half of the input tokens were randomly discarded. These findings underscore GPT-4's potential to substitute specialized models, such as PubMedBERT, through strategic prompt engineering, and suggest opportunities to improve open-source models, which are better suited to use in clinical settings.

Endoscopic spraying of smectite for preventing esophageal stricture after endoscopic submucosal dissection.

Esophageal stenosis after ESD has been recorded high for large-scale esophageal lesion. Risk factors for increasing the occurrence of stenosis includes long type lesions, lesions infiltrating into the muscularis mucosa and muscular layer injury. In this case, postoperative stricture of the patient was highly likely occurred. Smectite is a mucosal protective agent that can resist external stimuli, promote wound healing, and reduce inflammatory factors. Therefore, it can effectively prevent the formation of scars on wounds. This study was carried out in humans for the first time and was successful. In conclusion, endoscopic spraying of smectite may be effective and safe in preventing esophageal stenosis after ESD with large non-circumferential lesions.

The impact of SLC10A3 on prognosis and immune microenvironment in colorectal adenocarcinoma.

BACKGROUND: SLC10A3, a gene upregulated in pan-cancer, lacks full understanding regarding its prognostic implications and association with immune infiltration in colorectal cancer (CRC). This study comprehensively analyzed SLC10A3 in CRC, evaluating its prognostic significance and influence on the tumor's immune microenvironment. METHODS: Transcriptomic data from TCGA were obtained to compare SLC10A3 expression in both colorectal cancer (CRC) and normal tissues. Prognostic value was assessed for overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). DNA methylation patterns of SLC10A3 and correlation with DNA mismatch repair (MMR) were explored. Genetic alterations in SLC10A3 were scrutinized. The study also delved into the influence of SLC10A3 on the immune microenvironment of CRC, including immune cell infiltration and chemokines. Involvement of cancer-associated fibroblasts (CAFs) was explored. Methylation status of specific CpG islands in the SLC10A3 gene correlated with CRC patient prognosis. CRC tissue microarray was performed to verify the expression of SLC10A3 and its relationship with prognosis. RESULTS: The research revealed that SLC10A3 is significantly upregulated in CRC and holds promise as a potential diagnostic marker. Elevated SLC10A3 expression was linked to poorer OS, DSS, and PFI. Methylation patterns of SLC10A3 displayed prognostic relevance, and genetic alterations in the gene were identified. SLC10A3 was shown to impact the immune microenvironment, with significant correlations observed between its expression and various immune cell types, chemokines, and markers associated with CAFs. Furthermore, an inverse relationship between SLC10A3 and MMR molecules was established. Methylation status of specific CpG islands within the SLC10A3 gene was associated with CRC patient prognosis. Tissue microarray showed that SLC10A3 was highly expressed in CRC and significantly correlated with poor prognosis. CONCLUSION: The study underscores the importance of elevated SLC10A3 in CRC, associating it with decreased survival and immune infiltration, proposing it as a diagnostic biomarker and appealing immunotherapy target, given its significant overexpression and influence on the immune microenvironment and prognosis through methylation patterns.

Phenotypic variations induced emergence of orientation order and morphology in Bacillus subtilis biofilm growth.

During the Bacillus subtilis biofilm growth on the solid MSgg substrate, the biofilm exhibits highly ordered structures such as matrix-producing-cell chains and Van Gogh bundles due to bacterial orientation order. These structures make the biofilm have strong mobility and environmental adaptability, thus making bacteria easier to survive and thrive in biofilms comparing to planktonic bacteria. We tested the behaviors of different phenotypes as well as their impacts on bacterial clusters: motile cells arrange disorderly, the biofilm made up of motile cells tends to be circular and isotropic; matrix-producing cells form cellular chains that guide motile cells along the chain to form a locally nematic phase, the morphology of the biofilm made up of both motile cells and matrix-producing cells is rendered irregular. Combining the results of a coarse-grained and individual-based model, we can control the biofilm growth through regulating environmental friction, bacterial growth rate and adhesion between cells.

Super-wetting and self-cleaning polyvinyl alcohol/sodium alginate nanofiber membrane decorated with MIL-88A(Fe) for efficient oil/water emulsion separation and dye degradation.

Membrane separation is considered an effective approach to water purification. Nevertheless, membrane fouling dramatically decreases the separation efficiency and lifetime of membranes, thus limiting its further development and application. Herein, a multifunctional self-cleaning MIL-88A(Fe) decorated polyvinyl alcohol/sodium alginate (MIL-88A(Fe)@PVA-SA) nanofiber membrane was prepared by electrospinning and in-situ growth methods for the separation of oil/water emulsions and photo-Fenton degradation of dyes. The membrane possesses superhydrophilicity with a water contact angle (WCA) of 0° and superoleophobicity with underwater oil contact angle (UCA) of 161.7°, and exhibits superior separation efficiency (>99.5 %) and permeation flux (1140-2455 L/m2/h) for different oil/water emulsions. Moreover, the membrane exhibited an outstanding photo-Fenton performance under visible light, with degradation efficiencies (~99.9 %) towards methylene blue (MB) and reactive red 24 (RR24) within 90 min. Importantly, the membrane can be easily regenerated by simple rinsing and photo-Fenton self-cleaning treatment. In this study, MIL-88A(Fe)@PVA-SA nanofiber membrane has a promising application in dye removal and oil/water separation, providing a new idea to develop novel membrane materials.

Development and validation for bioanalysis of VK2809, its active metabolite VK2809A and glutathione-conjugated metabolite MB06588 in rat liver using LC-MS/MS.

VK2809 is a promising drug candidate in Phase II clinical trials for the treatment of non-alcoholic steatohepatitis (NASH). It is a prodrug with a HepDirect strategy, which can achieve selective hepatic metabolic activation, generating an active metabolite VK2809A as a potent and selective agonist for thyroid hormone receptor beta (TRß), a concomitant reactive metabolite VK2809B, and a glutathione (GSH) conjugate MB06588. Currently, there is no convenient and sensitive bioanalytical method for the simultaneous determination of the above three metabolites. Herein, we established an LC-MS/MS method to separate VK2809 and its metabolites on the XSelect HSS T3 column and quantified them in negative electrospray ionization mode. Subsequently, several factors were investigated such as the use of 60% acetonitrile for homogenization to stabilize the analytes, the addition of 20 mM glutathione for the derivation of VK2809B, and the protein precipitation with methanol containing Sobetirome as the internal standard (IS). The method exhibited good linearity for all compounds (19.4-388.4 nM for VK2809; 27.4-2744.4 nM for VK2809A and 10.6-211.0 nM for MB06588) with great correlation coefficients (r > 0.996). The method validation also demonstrated acceptable precision (RSD < 13.0% for VK2809, RSD < 7.9% for VK2809A, RSD < 14.4% for MB06588) and accuracy (92.7%-103% for VK2809, 91.2%-107.3% for VK2809A, 96%-106.7% for MB06588). The matrix effect, recovery, and stability were also suitable to determine all the analytes. This method is suitable for the bioanalysis of VK2809 and its metabolites and has been successfully applied to the study of intrahepatic exposure in rats. It is expected to be further practiced in drug design, optimization, and metabolism study in the following research.

Click-iG: Simultaneous Enrichment and Profiling of Intact N-linked, O-GalNAc, and O-GlcNAcylated Glycopeptides.

Proteins are ubiquitously modified with glycans of varied chemical structures through distinct glycosidic linkages, making the landscape of protein glycosylation challenging to map. Profiling of intact glycopeptides with mass spectrometry (MS) has recently emerged as a powerful tool for revealing matched information of the glycosylation sites and attached glycans (i.e., intact glycosites), but is largely limited to individual glycosylation types. Herein, we describe Click-iG, which integrates metabolic labeling of glycans with clickable unnatural sugars, an optimized MS method, and a tailored version of pGlyco3 software to enable simultaneous enrichment and profiling of three types of intact glycopeptides: N-linked, mucin-type O-linked, and O-GlcNAcylated glycopeptides. We demonstrate the utility of Click-iG by the identification of thousands of intact glycosites in cell lines and living mice. From the mouse lung, heart, and spleen, a total of 2053 intact N-glycosites, 262 intact O-GalNAc glycosites, and 1947 O-GlcNAcylation sites were identified. Click-iG-enabled comprehensive coverage of the protein glycosylation landscape lays the foundation for interrogating crosstalk between different glycosylation pathways.

Analysis of biofilm expansion rate of Bacillus subtilis (MTC871) on agar substrates with different stiffness.

The surface morphology of mature biofilms is heterogeneous and can be divided into concentric rings wrinkles (I), labyrinthine networks wrinkles (II), radial ridges wrinkles (III), and branches wrinkles (IV), according to surface wrinkle structure and distribution characteristics. Due to the wrinkle structures, channels are formed between the biofilm and substrate and transport nutrients, water, metabolic products, etc. We find that expansion rate variations of biofilms growing on substrates with high and low agar concentrations (1.5, 2.0, 2.5 wt.%) are not in the same phase. In the first 3 days' growth, the interaction stress between biofilm and each agar substrate increases, which makes the biofilm expansion rate decreases before wrinkle pattern IV (branches) comes up. After 3 days, in the later growth stage after wrinkle pattern IV appears, the biofilm has larger expansion rate growing on 2.0 wt.% agar concentration, which has the larger wrinkle distance in wrinkle pattern IV reducing energy consumption. Our study shows that the stiff substrate does not always inhibit the biofilm expansion, although it does in the earlier stage; after that, mature biofilms acquire larger expansion rate by adjusting the growth mode through the wrinkle evolution even in nutrient extremely depletion.

Matrix Producing Cells Induce the Morphological Difference in the Bacillus subtilis Biofilm.

There is a 'coffee ring' in the Bacillus subtilis biofilm center, and the colony biofilm morphologies are distinct inside and outside the 'coffee ring'. In this paper, we study this morphological difference and explain the reasons of the 'coffee ring' formation and further the causes to the morphological variation. We developed a quantitative method to characterize the surface morphology, the outer area is thicker than the inner area of the 'coffee ring', and the thickness amplitude in outer area is larger than inner area of the 'coffee ring'. We adopt a logistic growth model to obtain how the environmental resistance influence the colony biofilm thickness. Dead cells provide gaps for stress release and make folds formation in colony biofilm. we developed a technique for optical imaging and matching cells with the BRISK algorithm to capture the distribution and movement of motile cells and matrix producing cells in the colony biofilm. Matrix producing cells are mainly distribute in the outside of the 'coffee ring', and the extracellular matrix (ECM) prevents the motile cells moving outward from center. Motile cells mainly locate inside the ring, a small amount of dead motile cells outside the 'coffee ring' give rise to radial folds formation. There are no ECM blocking cell movements inside the ring, which result in uniform folds formation. The distribution of ECM and different phenotypes lead to the formation of the 'coffee ring', which is verified by using eps and flagellar mutants.

Rapid on-site evaluation of touch imprints of medical thoracoscopy biopsy tissue for the management of pleural disease.

Background and objective: Medical thoracoscopy (MT) plays an important role in the diagnosis and treatment of pleural diseases, and rapid on-site evaluation (ROSE) has long been used for transbronchial needle aspiration or fine-needle aspiration to evaluate the adequacy of biopsy materials for the diagnosis of peripheral lung lesions. However, research on ROSE combined with MT for the management of pleural disease has been rarely reported. We aimed to evaluate the diagnostic performance of ROSE for pleura biopsies and visual diagnosis by thoracoscopists for gross thoracoscopic appearance. The secondary objective was to assess the intermodality agreement between ROSE and the final histopathologic diagnosis. Methods: A total of 579 patients with exudative pleural effusion (EPE) who underwent MT combined with ROSE from February 2017 to December 2020 at Taihe Hospital were included in the study. Thoracoscopists' visual diagnosis of gross thoracoscopic appearance, ROSE results, histopathologic findings, and the final diagnosis was recorded. Results: Thoracoscopic pleural biopsies were performed in 565 patients (97.6%); 183 patients were confirmed to have malignant pleural effusion (MPE), and 382 patients were confirmed to have benign pleural effusion (BPE). The area under the curve of ROSE for the diagnosis of MPE was 0.96 (95% CI: 0.94-0.98, p < 0.001), with a sensitivity of 98.7%, a specificity of 97.2%, a diagnostic accuracy of 97.1%, a positive predictive value of 97.2%, and a negative predictive value of 97.2%. Diagnostic consistency between ROSE and histopathology was good (κ ± SE = 0.93 ± 0.02, p < 0.001). The area under the curve of the thoracoscopists' visual diagnosis of gross thoracoscopic appearance was 0.79 (95% CI: 0.75-0.83, p < 0.01), with a sensitivity of 76.7%, a specificity of 80.9%, a positive predictive value of 62.4%, and a negative predictive value of 89.3%. Conclusion: ROSE of touch imprints of MT biopsy tissue during MT showed high accuracy for distinguishing between benign and malignant lesions. In addition, ROSE was in good agreement with the histopathological diagnosis, which may help thoracoscopists perform pleurodesis (talc poudrage) directly during the procedure, especially in patients with malignant results.

Simulation of various biofilm fractal morphologies by agent-based model.

Biofilms are clusters of bacteria wrapped in extracellular matrix and polymers. The study of biofilm morphological transformation has been around for a long time and has attracted widespread attention. In this paper, we present a model for biofilm growth based on the interaction force, in which bacteria are treated as tiny particles and locations of particles are updated by calculating the repulsive forces among particles. We adapt a continuity equation to indicate nutrient concentration variation in the substrate. Based on the above, we study the morphological transformation of biofilms. We find that nutrient concentration and nutrient diffusion rate dominate different biofilm morphological transition processes, in which biofilms would grow into fractal morphology under the conditions of low nutrient concentration and nutrient diffusivity. At the same time, we expand our model by introducing a second particle to mimic extracellular polymeric substances (EPS) in biofilms. We find that the interaction between different particles can lead to phase separation patterns between cells and EPSs, and the adhesion effect of EPS can attenuate this phenomenon. In contrast to single particle system models, branches are inhibited due to EPS filling in dual particle system models, and this invalidation is boosted by the enhancement of the depletion effect.

The formation mechanism of Bacillus subtilis biofilm surface morphology under competitive environment.

Material properties and growth environments affect the surface morphology of biofilms. Taken the biofilm growing in competitive environments as the object, which is compared with the single biofilm, we find that the competitive environment has an impact on the biofilm thickness and wrinkle patterns. Through diffusion-limited growth theoretical model analysis, it shows that the competitive environment is caused by cells competing for nutrition, and the competitive environment reacts on biofilms, which affect the phenotypic differentiation, causing changes in the stiffness of the biofilm. Using the theoretical and finite element simulation, we compare these results of bi-layer and tri-layer film-substrate models with experimental observations, and find that tri-layer film-substrate model is in line with the reality, which means that the layer between the biofilm and substrate plays an import role for wrinkle formation. Based on the above analysis, we further study effects of biofilm stiffness and interlayer thickness on wrinkles under competitive environment.