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1.
Langmuir ; 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38845086

ABSTRACT

In this study, we prepared a multicolor structural-fluorescent CdS-PEGDA photonic crystal hydrogel (SFC-CPH) with a dual display mode, which has two different optical states: structural color mode and fluorescent color mode. SFC-CPH displays structural color mode under visible light and fluorescent color mode under ultraviolet light. Initially, monodisperse CdS colloidal particles were synthesized via a hydrothermal method, leading to the self-assembly of a photonic crystal template. The high refractive index of CdS contributes to the photonic crystals' low-angle dependence and vivid structural colors. Then, a variety of fluorescent molecules were doped into poly(ethylene glycol) diacrylate (PEGDA) hydrogel and combined with photonic crystals with distinct structural colors to prepare three distinct colors of SFC-CPH. We also investigated the optical characteristics and surface properties of these photonic crystal hydrogels. Based on these dual-mode display characteristics, we designed several dual-mode display patterns and a method for information encoding. The unique property of this photonic crystal hydrogel material suggests its substantial potential for applications in information storage, security, and encoding, offering innovative avenues in the realm of information display.

2.
J Thorac Dis ; 16(4): 2472-2481, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38738243

ABSTRACT

Background: Esophageal malignancies have a high morbidity rate worldwide, and minimally invasive surgery has emerged as the primary approach for treating esophageal cancer. In recent years, there has been increasing discussion about the potential of employing inflatable mediastinoscopic and laparoscopic approaches as an option for esophagectomy. Building on the primary modification of the inflatable mediastinoscopic technique, we introduced a secondary modification to further minimize surgical trauma. Methods: We conducted a retrospective analysis of patients who underwent inflatable mediastinoscopy combined with laparoscopic esophagectomy at the Second Affiliated Hospital of Naval Medical University from March 2020 to March 2023. The patients were allocated to the following two groups: the traditional (primary modification) group, and the secondary modification group. Operation times, intraoperative bleeding, and postoperative complications were compared between the groups. Results: The procedure was successfully performed in all patients, and conversion to open surgery was not required in any case. There were no statistically significant differences in the surgical operation time, intraoperative bleeding, number of dissected lymph nodes, and rate of postoperative anastomotic leakage between the two groups. However, a statistically significant difference was observed in the length of the mobilized esophagus between the two groups. The mobilization of esophagus to the level of diaphragmatic hiatus via the cervical incision was successfully achieved in more patients in the secondary modification group than the primary modification group. Conclusions: Inflatable mediastinoscopy combined with single-incision plus one-port laparoscopic esophagectomy is a safe and effective surgical procedure. The use of a 5-mm flexible endoscope, ultra-long five-leaf forceps, and LigaSure Maryland forceps facilitates esophageal mobilization and lymph node dissection through a single cervical incision.

3.
Microb Genom ; 10(5)2024 May.
Article in English | MEDLINE | ID: mdl-38785221

ABSTRACT

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.


Subject(s)
COVID-19 , Genome, Viral , SARS-CoV-2 , Wastewater , Wastewater/virology , SARS-CoV-2/genetics , SARS-CoV-2/classification , COVID-19/virology , COVID-19/epidemiology , Humans , Computational Biology/methods , Genomics/methods , Wastewater-Based Epidemiological Monitoring , Phylogeny
4.
J Pharm Biomed Anal ; 247: 116257, 2024 May 24.
Article in English | MEDLINE | ID: mdl-38815520

ABSTRACT

Zhi-Ke-Bao pills (ZKB), a traditional Chinese medicine preparation composed of 13 herbs, is generally used to treat cough caused by external wind cold, phlegm, etc in clinical applications, and it plays a core role in relieving cough caused by COVID-19 and influenza in China. Till now, the understanding of its chemical constituents was dramatically limited due to its chemical complexity, restricting its clinical application or development. In this work, a developed ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF MS) method, a targeted and non-targeted strategy and network pharmacology were used to comprehensively characterize the chemical compositions in ZKB and predict its mechanism against cough. A total of 164 compounds (148 targeted compounds and 16 non-targeted ones) were identified or tentatively characterized in ZKB, including 65 flavonoids, 25 alkaloids, 19 organic acids, 41 saponins, 9 coumarins, 2 phenylpropanoids, 2 anthraquinones, and 1 other types. Among them, 37 compounds were unambiguously identified by comparison to reference standards. Meanwhile, the fragmentation behaviors of five main chemical structure types were also summarized. 309 targets and two core signaling pathways of ZKB against cough were predicted by network pharmacology, including MAPK and PI3K-Akt signaling pathways. It was the first time to characterize the chemical compounds of ZKB and reveal its potential mechanism against cough, providing the material basis for further quality control or pharmacodynamic evaluation of ZKB.

5.
Ultrason Sonochem ; 107: 106918, 2024 May 18.
Article in English | MEDLINE | ID: mdl-38772313

ABSTRACT

In this research, the extraction process of polysaccharides from Pithecellobium clypearia Benth (PCBPs) was optimized using dual-frequency ultrasound-assisted extraction (DUAE). The biological activities of PCBPs were investigated by in vitro antioxidant, hypoglycemic, and anti-hyperlipidemic assay. High-performance anion-exchange chromatography, high-performance gel permeation chromatography, SEM, UV-Vis spectroscopy, and FT-IR spectra were used to analyze the monosaccharide composition, molecular weight, microscopic morphology, and characteristic structure of PCBPs. The results showed that the maximum extraction rate of PCBPs was 9.90 ± 0.16% when the ultrasonic time was 8 min, the liquid-to-material ratio was 32 mL/g, and the ultrasonic power was 510 W. The PCBPs also possessed excellent in vitro antioxidant, hypoglycemic, and anti-hyperlipidemic activities. In addition, the average molecular weight of PCBPs was 15.07 kDa. PCBPs consisted of rhamnose, arabinose, galactose, glucose, xylose, mannose, and glucuronic acid, with the molar ratios of 11.07%, 18.54%, 48.17%, 10.44%, 4.62%, 4.96%, and 2.20%, respectively. Moreover, the results of SEM showed that PCBPs mainly showed a fine spherical mesh structure. The above studies provided a valuable theoretical basis for the subsequent in-depth study of PCBPs.

6.
Magn Reson Med ; 2024 May 10.
Article in English | MEDLINE | ID: mdl-38726884

ABSTRACT

PURPOSE: To develop a novel low-rank tensor reconstruction approach leveraging the complete acquired data set to improve precision and repeatability of multiparametric mapping within the cardiovascular MR Multitasking framework. METHODS: A novel approach that alternated between estimation of temporal components and spatial components using the entire data set acquired (i.e., including navigator data and imaging data) was developed to improve reconstruction. The precision and repeatability of the proposed approach were evaluated on numerical simulations, 10 healthy subjects, and 10 cardiomyopathy patients at multiple scan times for 2D myocardial T1/T2 mapping with MR Multitasking and were compared with those of the previous navigator-derived fixed-basis approach. RESULTS: In numerical simulations, the proposed approach outperformed the previous fixed-basis approach with lower T1 and T2 error against the ground truth at all scan times studied and showed better motion fidelity. In human subjects, the proposed approach showed no significantly different sharpness or T1/T2 measurement and significantly improved T1 precision by 20%-25%, T2 precision by 10%-15%, T1 repeatability by about 30%, and T2 repeatability by 25%-35% at 90-s and 50-s scan times The proposed approach at the 50-s scan time also showed comparable results with that of the previous fixed-basis approach at the 90-s scan time. CONCLUSION: The proposed approach improved precision and repeatability for quantitative imaging with MR Multitasking while maintaining comparable motion fidelity, T1/T2 measurement, and septum sharpness and had the potential for further reducing scan time from 90 s to 50 s.

7.
Anal Chem ; 96(21): 8528-8533, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38728651

ABSTRACT

In the realm of nanopore sensor technology, an enduring challenge lies in achieving the discerning detection of small biomolecules with a sufficiently high signal-to-noise ratio. This study introduces a method for reliably quantifying the concentration of target small molecules, utilizing tetrahedral DNA nanostructures as surrogates for the captured molecules through a magnetic-bead-based competition substitution mechanism. Magnetic Fe3O4-DNA tetrahedron nanoparticles (MNPs) are incorporated into a nanopore electrochemical system for small-molecule sensing. In the presence of the target, the DNA tetrahedron, featuring an aptamer tail acting as a molecular carrier, detaches from the MNPs due to aptamer deformation. Following removal of the MNPs, the DNA tetrahedron bound to the target traversed the nanopore by applying a positive potential. This approach exhibits various advantages, including heightened sensitivity, selectivity, an improved signal-to-noise ratio (SNR), and robust anti-interference capabilities. Our findings demonstrate that this innovative methodology has the potential to significantly enhance the sensing of various small-molecule targets by nanopores, thereby advancing the sensitivity and dynamic range. This progress holds promise for the development of precise clinical diagnostic tools.


Subject(s)
Aptamers, Nucleotide , DNA , Nanopores , Nanostructures , DNA/chemistry , DNA/analysis , Aptamers, Nucleotide/chemistry , Nanostructures/chemistry , Electrochemical Techniques/methods , Biosensing Techniques/methods
8.
J Am Chem Soc ; 146(21): 14445-14452, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38739877

ABSTRACT

Transition-metal-catalyzed C-Si/Ge cross-coupling offers promising avenues for the synthesis of organosilanes/organogermanes, yet it is fraught with long-standing challenges. A Ni/Ti-catalyzed strategy is reported here, allowing the use of disubstituted malononitriles as tertiary C(sp3) coupling partners to couple with chlorosilanes and chlorogermanes, respectively. This method enables the catalytic cleavage of the C(sp3)-CN bond of the quaternary carbon followed by the formation of C(sp3)-Si/C(sp3)-Ge bonds from ubiquitously available starting materials. The efficiency and generality are showcased by a broad scope for both of the coupling partners, therefore holding the potential to synthesize structurally diverse quaternary organosilanes and organogermanes that were difficult to access previously.

9.
Glob Chang Biol ; 30(5): e17350, 2024 May.
Article in English | MEDLINE | ID: mdl-38804101

ABSTRACT

With over one-third of terrestrial net primary productivity transferring to the litter layer annually, the carbon release from litter serves as a crucial valve in atmospheric carbon dioxide concentrations. However, few quantitative global projections of litter carbon release rate in response to climate change exist. Here, we combined a global foliar litter carbon release dataset (8973 samples) to generate spatially explicitly estimates of the response of their residence time (τ) to climate change. Results show a global mean litter carbon release rate ( k $$ k $$ ) of 0.69 year-1 (ranging from 0.09-5.6 year-1). Under future climate scenarios, global mean τ is projected to decrease by a mean of 2.7% (SSP 1-2.6) and 5.9% (SSP 5-8.5) during 2071-2100 period. Locally, the alleviation of temperature and moisture restrictions corresponded to obvious decreases in τ in cold and arid regions, respectively. In contract, τ in tropical humid broadleaf forests increased by 4.6% under SSP 5-8.5. Our findings highlight the vegetation type as a powerful proxy for explaining global patterns in foliar litter carbon release rates and the role of climate conditions in predicting responses of carbon release to climate change. Our observation-based estimates could refine carbon cycle parameterization, improving projections of carbon cycle-climate feedbacks.


Subject(s)
Carbon , Climate Change , Plant Leaves , Plant Leaves/metabolism , Carbon/metabolism , Carbon Cycle , Forests , Carbon Dioxide/metabolism , Carbon Dioxide/analysis , Global Warming , Trees/metabolism
10.
Chem Commun (Camb) ; 2024 May 28.
Article in English | MEDLINE | ID: mdl-38804199

ABSTRACT

A commercial anti-cancer drug, axitinib, exhibits very stable dual emissions for discrimination of human serum albumin.

11.
Adv Sci (Weinh) ; : e2402645, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38738739

ABSTRACT

The photocatalytic reduction of CO2 represents an environmentally friendly and sustainable approach for generating valuable chemicals. In this study, a thiophene-modified highly conjugated asymmetric covalent triazine framework (As-CTF-S) is developed for this purpose. Significantly, single-component intramolecular energy transfer can enhance the photogenerated charge separation, leading to the efficient conversion of CO2 to CO during photocatalysis. As a result, without the need for additional photosensitizers or organic sacrificial agents, As-CTF-S demonstrates the highest photocatalytic ability of 353.2 µmol g-1 and achieves a selectivity of ≈99.95% within a 4 h period under visible light irradiation. This study provides molecular insights into the rational control of charge transfer pathways for high-efficiency CO2 photoreduction using single-component organic semiconductor catalysts.

12.
J Ethnopharmacol ; 330: 118224, 2024 Aug 10.
Article in English | MEDLINE | ID: mdl-38642623

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Sophorae tonkinensis Radix et Rhizoma (STR) is an extensively applied traditional Chinese medicine (TCM) in southwest China. However, its clinical application is relatively limited due to its hepatotoxicity effects. AIM OF THE STUDY: To understand the material foundation and liver injury mechanism of STR. MATERIALS AND METHODS: Chemical compositions in STR and its prototypes in mice were profiled by ultra-performance liquid chromatography coupled quadrupole-time of flight mass spectrometry (UPLC-Q/TOF MS). STR-induced liver injury (SILI) was comprehensively evaluated by STR-treated mice mode. The histopathologic and biochemical analyses were performed to evaluate liver injury levels. Subsequently, network pharmacology and multi-omics were used to analyze the potential mechanism of SILI in vivo. And the target genes were further verified by Western blot. RESULTS: A total of 152 compounds were identified or tentatively characterized in STR, including 29 alkaloids, 21 organic acids, 75 flavonoids, 1 quinone, and 26 other types. Among them, 19 components were presented in STR-medicated serum. The histopathologic and biochemical analysis revealed that hepatic injury occurred after 4 weeks of intragastric administration of STR. Network pharmacology analysis revealed that IL6, TNF, STAT3, etc. were the main core targets, and the bile secretion might play a key role in SILI. The metabolic pathways such as taurine and hypotaurine metabolism, purine metabolism, and vitamin B6 metabolism were identified in the STR exposed groups. Among them, taurine, hypotaurine, hypoxanthine, pyridoxal, and 4-pyridoxate were selected based on their high impact value and potential biological function in the process of liver injury post STR treatment. CONCLUSIONS: The mechanism and material foundation of SILI were revealed and profiled by a multi-omics strategy combined with network pharmacology and chemical profiling. Meanwhile, new insights were taken into understand the pathological mechanism of SILI.


Subject(s)
Chemical and Drug Induced Liver Injury , Drugs, Chinese Herbal , Rhizome , Animals , Chemical and Drug Induced Liver Injury/pathology , Chemical and Drug Induced Liver Injury/metabolism , Mice , Male , Drugs, Chinese Herbal/pharmacology , Sophora/chemistry , Liver/drug effects , Liver/pathology , Liver/metabolism , Metabolomics , Chromatography, High Pressure Liquid , Network Pharmacology , Multiomics , Animals, Outbred Strains
13.
Phytochemistry ; 222: 114096, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38641141

ABSTRACT

Forsythiae Fructus (FF), the dried fruit of F. suspensa, is commonly used to treat fever, inflammation, etc in China or other Asian countries. FF is usually used as the core herb in traditional Chinese medicine preparations for the treatment of influenza, such as Shuang-huang-lian oral liquid and Yin-qiao powder, etc. Since the wide application and core role of FF, its research progress was summarized in terms of traditional uses, phytochemistry, pharmacology, pharmacokinetics, quality control, and toxicity. Meanwhile, the anti-influenza substances and mechanism of FF were emphasized. Till now, a total of 290 chemical components are identified in F. suspensa, and among them, 248 components were isolated and identified from FF, including 42 phenylethanoid glycosides, 48 lignans, 59 terpenoids, 14 flavonoids, 3 steroids, 24 cyclohexyl ethanol derivatives, 14 alkaloids, 26 organic acids, and 18 other types. FF and their pure compounds have the pharmacological activities of anti-virus, anti-inflammation, anti-oxidant, anti-bacteria, anti-tumor, neuroprotection, hepatoprotection, etc. Inhibition of TLR7, RIG-I, MAVS, NF-κB, MyD88 signaling pathway were the reported anti-influenza mechanisms of FF and phenylethanoid glycosides and lignans are the main active groups. However, the bioavailability of phenylethanoid glycosides and lignans of FF in vivo was low, which needed to be improved. Simultaneously, the un-elucidated compounds and anti-influenza substances of FF strongly needed to be explored. The current quality control of FF was only about forsythoside A and phillyrin, more active components should be taken into consideration. Moreover, there are no reports of toxicity of FF yet, but the toxicity of FF should be not neglected in clinical applications.


Subject(s)
Forsythia , Quality Control , Forsythia/chemistry , Humans , Fruit/chemistry , Phytochemicals/pharmacology , Phytochemicals/chemistry , Phytochemicals/isolation & purification , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/pharmacology , Drugs, Chinese Herbal/isolation & purification , Animals , Molecular Structure
14.
Sci Total Environ ; 930: 172801, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38679088

ABSTRACT

Numerous pharmaceuticals and personal care products (PPCPs) co-exist with various types of microplastics (MPs) in the environment, making it extremely hard to experimentally measure all their adsorption interactions. Thus, a precise prediction model is on demand. In this study, we combined the commonly used Dubinin-Astakhov (DA) model and the linear solvation energy relationships (LSERs) model to predict the adsorption capacity (Q0) and adsorption affinity (E) of MPs for PPCPs, including the key parameters of MP (specific surface area, oxygen-containing functional groups), and the Kamlet-Taft solvation parameters of organic contaminants. The model was validated with the experimental data of 8 PPCPs and 8 MPs (i.e. pristine and aged PE, PET, PS, PVC) plus some published adsorption data. This new model also indicated that the adsorption of PPCPs on those MPs was primarily governed by hydrophobic interaction and hydrogen bonding. The developed model can predict the adsorption of PPCPs onto MPs with a high accuracy and can also provide insights into the understanding of interaction forces in the adsorption process.

15.
Phys Med Biol ; 69(11)2024 May 14.
Article in English | MEDLINE | ID: mdl-38636505

ABSTRACT

Objective.Pharmacokinetic parametric images obtained through dynamic fluorescence molecular tomography (DFMT) has ability of capturing dynamic changes in fluorescence concentration, thereby providing three-dimensional metabolic information for applications in biological research and drug development. However, data processing of DFMT is time-consuming, involves a vast amount of data, and the problem itself is ill-posed, which significantly limits the application of pharmacokinetic parametric images reconstruction. In this study, group sparse-based Taylor expansion method is proposed to address these problems.Approach.Firstly, Taylor expansion framework is introduced to reduce time and computational cost. Secondly, group sparsity based on structural prior is introduced to improve reconstruction accuracy. Thirdly, alternating iterative solution based on accelerated gradient descent algorithm is introduced to solve the problem.Main results.Numerical simulation andin vivoexperimental results demonstrate that, in comparison to existing methods, the proposed approach significantly enhances reconstruction speed without a degradation of quality, particularly when confronted with background fluorescence interference from other organs.Significance.Our research greatly reduces time and computational cost, providing strong support for real-time monitoring of liver metabolism.


Subject(s)
Image Processing, Computer-Assisted , Liver , Liver/diagnostic imaging , Liver/metabolism , Image Processing, Computer-Assisted/methods , Animals , Tomography/methods , Mice , Optical Imaging/methods , Algorithms , Fluorescence
16.
Bioorg Chem ; 147: 107352, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38640719

ABSTRACT

Glypican-3 (GPC3) is markedly overexpressed in hepatocellular carcinoma (HCC) and not expressed in normal liver tissues. In this study, a novel peptide PET imaging agent ([18F]AlF-NOTA-IPB-GPC3P) was developed to target GPC3 expressed in tumors. The overall radiochemical yield of [18F]AlF-NOTA-IPB-GPC3P was 10-15 %, and its lipophilicity, expressed as the logD value at a pH of 7.4, was -1.18 ± 0.06 (n = 3). Compared to the previously reported tracer [18F]AlF-GP2633, [18F]AlF-NOTA-IPB-GPC3P exhibited higher cellular uptake (15.13 vs 5.96) and internalized rate (80.63 % vs 35.93 %) in Huh7 cells at 120 min. Micro-PET/CT and biodistribution studies further demonstrated that [18F]AlF-NOTA-IPB-GPC3P exhibited significantly increased tumor uptake and prolonged tumor residence in Huh7 tumors compared to [18F]AlF-GP2633 (4.66 ± 0.22 % ID/g vs 0.72 ± 0.09 % ID/g at 60 min, p < 0.001; 5.05 ± 0.23 % ID/g vs 0.35 ± 0.08 % ID/g at 120 min, p < 0.001, respectively). Furthermore, the tumor-to-organ ratios of [18F]AlF-NOTA-IPB-GPC3P surpassed those of [18F]AlF-GP2633. Our results support the utilization of [18F]AlF-NOTA-IPB-GPC3P as a PET imaging agent targeting the GPC3 receptor for tumor detection.


Subject(s)
Fluorine Radioisotopes , Glypicans , Positron-Emission Tomography , Animals , Humans , Mice , Carcinoma, Hepatocellular/diagnostic imaging , Carcinoma, Hepatocellular/metabolism , Cell Line, Tumor , Fluorine Radioisotopes/chemistry , Glypicans/metabolism , Heterocyclic Compounds, 1-Ring , Liver Neoplasms/diagnostic imaging , Mice, Nude , Molecular Structure , Radiopharmaceuticals/chemical synthesis , Radiopharmaceuticals/chemistry , Structure-Activity Relationship , Tissue Distribution
18.
Comput Biol Chem ; 110: 108064, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38677014

ABSTRACT

MOTIVATION: Elucidating protein function is a central problem in biochemistry, genetics, and molecular biology. Developing computational methods for protein function prediction is critical due to the significant gap between sequence and functional data. Recent advances in protein structure prediction, which strongly correlates with function, make it feasible to use structure to predict function. However, current structure-based methods overlook the fact that individual residues may contribute differently to the protein's function and do not take into account the correlation between protein residues and their functions. The challenge of effectively utilizing the relationship between protein residues and function-level information to predict protein function remains unsolved. RESULT: We proposed a protein function prediction method based on Soft Mask Graph Networks and Residue-Label Attention (POLAT), which could combine sequence features, predicted structure features, and function-level information to get an accurate prediction. We use soft mask graph networks to adaptively extract the residues relevant to functions. A residue-label attention mechanism is adopted to obtain the protein-level encoded features of a protein, which are then concatenated with a protein-level embedding and fed into a dense classifier to determine the probabilities of each function. POLAT achieves 0.670, 0.515, 0.578 Fmax and 0.677, 0.409, 0.507 AUPR on the PDB cdhit test set for the MFO, BPO, and CCO domains, respectively, outperforming the existing structure-based SOTA method GAT-GO (Fmax 0.633, 0.492, 0.547; AUPR 0.660, 0.381, 0.479). POLAT is also competitive in extensive experiments among sequence-based and multimodal methods and achieves the SOTA performance in three out of six metrics.


Subject(s)
Computational Biology , Proteins , Proteins/chemistry , Proteins/metabolism , Protein Conformation , Algorithms
19.
Fish Shellfish Immunol ; 148: 109504, 2024 May.
Article in English | MEDLINE | ID: mdl-38508539

ABSTRACT

Aeromonas hydrophila is a commonly pathogenic bacterium in cultivated eels, but its pathogenicity to American eel (Anguilla rostrata) and the molecular mechanism of host anti-A. hydrophila infection remains uncertain. In this study, LD50 of A. hydrophila to American eels was determined and bacterial load in the liver and kidney of eels was assessed post 2.56 doses of LD50 of A. hydrophila infection. The results showed that the LD50 of A. hydrophila to American eels was determined to be 3.9 × 105 cfu/g body weight (7.8 × 106 cfu/fish), and the bacterial load peaked at 36 h post the infection (hpi) in the liver. Then, the histopathology was highlighted by congestion in splenic blood vessels, atrophied glomeruli, and necrotic hepatocytes. Additionally, the results of qRT-PCR revealed that 18 host immune-related genes showed significantly up or downregulated post-infection compare to that of pre-infection. Finally, results of the RNA-seq revealed 10 hub DEGs and 7 encoded proteins play essential role to the anti-A. hydrophila infection in American eels. Pathogenicity of A. hydrophila to American eels and RNA-seq of host anti-A. hydrophila infection were firstly reported in this study, shedding new light on our understanding of the A. hydrophila pathogenesis and the host immune response to the A. hydrophila infection strategies in gene transcript.


Subject(s)
Anguilla , Fish Diseases , Animals , Aeromonas hydrophila , Virulence , Bacterial Outer Membrane Proteins , Gene Expression Profiling/veterinary
20.
Bioorg Chem ; 145: 107193, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38442611

ABSTRACT

Immunotherapy has brought great benefits to cancer patients, but only some patients benefit from it. Noninvasive, real-time and dynamic monitoring of the effectiveness of immunotherapy through PET imaging may provide assistance for the treatment plan of immunotherapy. In this study, we designed and synthesized a new targeted PD-L1 peptide NOTA-PEG2-Asp2-PDL1P, which was labeled with nuclide 18F to obtain a new imaging agent [18F]AlF-NOTA-PEG2-Asp2-PDL1P. The total radiochemical yield of [18F]AlF-NOTA-PEG2-Asp2-PDL1P was 13.7 % (Uncorrected radiochemical yield, n > 5). [18F]AlF-NOTA-PEG2-Asp2-PDL1P achieved high radiochemical purity (>95 %) with a molar activity more than 51.2 GBq/µmol. [18F]AlF-NOTA-PEG2-Asp2-PDL1P exhibited good hydrophilicity and had good stability both in vivo and in vitro, it can specifically targets B16F10 tumor with PD-L1 expression, and had a relatively high retention in tumor, a relatively fast clearance in vivo and a higher tumor-to-non-target ratio, all of which could make [18F]AlF-NOTA-PEG2-Asp2-PDL1P a potential tracer for PD-L1 prediction before clinical immunotherapy.


Subject(s)
Heterocyclic Compounds, 1-Ring , Heterocyclic Compounds , Neoplasms , Humans , Heterocyclic Compounds/chemistry , Molecular Probes , B7-H1 Antigen/metabolism , Fluorine Radioisotopes/chemistry , Positron-Emission Tomography/methods , Radiopharmaceuticals/chemistry , Cell Line, Tumor
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