Altruistic seagull optimization algorithm enables selection of radiomic features for predicting benign and malignant pulmonary nodules.

Accurately differentiating indeterminate pulmonary nodules remains a significant challenge in clinical practice. This challenge becomes increasingly formidable when dealing with the vast radiomic features obtained from low-dose computed tomography, a lung cancer screening technique being rolling out in many areas of the world. Consequently, this study proposed the Altruistic Seagull Optimization Algorithm (AltSOA) for the selection of radiomic features in predicting the malignancy risk of pulmonary nodules. This innovative approach incorporated altruism into the traditional seagull optimization algorithm to seek a global optimal solution. A multi-objective fitness function was designed for training the pulmonary nodule prediction model, aiming to use fewer radiomic features while ensuring prediction performance. Among global radiomic features, the AltSOA identified 11 interested features, including the gray level co-occurrence matrix. This automatically selected panel of radiomic features enabled precise prediction (area under the curve = 0.8383 (95 % confidence interval 0.7862-0.8863)) of the malignancy risk of pulmonary nodules, surpassing the proficiency of radiologists. Furthermore, the interpretability, clinical utility, and generalizability of the pulmonary nodule prediction model were thoroughly discussed. All results consistently underscore the superiority of the AltSOA in predicting the malignancy risk of pulmonary nodules. And the proposed malignant risk prediction model for pulmonary nodules holds promise for enhancing existing lung cancer screening methods. The supporting source codes of this work can be found at: https://github.com/zzl2022/PBMPN.

PsERF1B-PsMYB10.1-PsbHLH3 module enhances anthocyanin biosynthesis in the flesh-reddening of amber-fleshed plum (cv. Friar) fruit in response to cold storage.

Flesh-reddening usually occurs in the amber-fleshed plum (Prunus salicina Lindl.) fruit during cold storage but not during ambient storage direct after harvest. It is not clear how postharvest cold signal is mediated to regulate the anthocyanin biosynthesis in the forming of flesh-reddening yet. In this study, anthocyanins dramatically accumulated and ethylene produced in the 'Friar' plums during cold storage, in comparison with plums directly stored at ambient temperature. Expression of genes associated with anthocyanin biosynthesis, as well as transcription factors of PsMYB10.1, PsbHLH3, and PsERF1B were strongly stimulated to upregulated in the plums in the period of cold storage. Suppression of ethylene act with 1-methylcyclopropene greatly suppressed flesh-reddening and downregulated the expression of these genes. Transient overexpression and virus-induced gene silencing assays in plum flesh indicated that PsMYB10.1 encodes a positive regulator of anthocyanin accumulation. The transient overexpression of PsERF1B, coupled with PsMYB10.1 and PsbHLH3, could further prompt the anthocyanin biosynthesis in a tobacco leaf system. Results from yeast two-hybrid and luciferase complementation assays verified that PsERF1B directly interacted with PsMYB10.1. PsERF1B and PsMYB10.1 enhanced the activity of the promoter of PsUFGT individually, and the enhancement was prompted by the co-action of PsERF1B and PsMYB10.1. Overall, the stimulation of the PsERF1B-PsMYB10.1-PsbHLH3 module mediated cold signal in the transcriptomic supervision of the anthocyanin biosynthesis in the 'Friar' plums. The results thereby revealed the underlying mechanism of the postharvest alteration of the flesh phenotype of 'Friar' plums subjected to low temperature.

Recent advances in simultaneous detection strategies for multi-mycotoxins in foods.

Mycotoxin contamination has become a challenge in the field of food safety testing, given the increasing emphasis on food safety in recent years. Mycotoxins are widely distributed, in heavily polluted areas. Food contamination with these toxins is difficult to prevent and control. Mycotoxins, as are small-molecule toxic metabolites produced by several species belonging to the genera Aspergillus, Fusarium, and Penicillium growing in food. They are considered teratogenic, carcinogenic, and mutagenic to humans and animals. Food systems are often simultaneously contaminated with multiple mycotoxins. Due to the additive or synergistic toxicological effects caused by the co-existence of multiple mycotoxins, their individual detection requires reliable, accurate, and high-throughput techniques. Currently available, methods for the detection of multiple mycotoxins are mainly based on chromatography, spectroscopy (colorimetry, fluorescence, and surface-enhanced Raman scattering), and electrochemistry. This review provides a comprehensive overview of advances in the multiple detection methods of mycotoxins during the recent 5 years. The principles and features of these techniques are described. The practical applications and challenges associated with assays for multiple detection methods of mycotoxins are summarized. The potential for future development and application is discussed in an effort, to provide standards of references for further research.

Quantitative analysis of blended corn-olive oil based on Raman spectroscopy and one-dimensional convolutional neural network.

Blended vegetable oil is a vital product in the vegetable oil market, and quantifying high-value vegetable oil is of great significance to protect the rights and interests of consumers. In this study, we established a one-dimensional convolutional neural network (1D CNN) quantitative identification model based on Raman spectra to identify the amount of olive oil in a corn-olive oil blend. The results show that the 1D CNN model based on 315 extended average Raman spectra can quantitatively identify the content of olive oil, with R2p and RMSEP values of 0.9908 and 0.7183 respectively. Compared with partial least squares regression (PLSR) and support vector regression (SVR), although the index is not optimal, it provides a new analytical method for the quantitative identification of vegetable oil.

Dosimetric feasibility of stereotactic ablative radiotherapy in pulmonary vein isolation for atrial fibrillation using intensity-modulated proton therapy.

PURPOSE: To evaluate dosimetric properties of intensity-modulated proton therapy (IMPT) for simulated treatment planning in patients with atrial fibrillation (AF) targeting left atrial-pulmonary vein junction (LA-PVJ), in comparison with volumetric-modulated arc therapy (VMAT) and helical tomotherapy (TOMO). METHODS: Ten thoracic 4D-CT scans with respiratory motion and one with cardiac motion were used for the study. Ten respiratory 4D-CTs were planned with VMAT, TOMO, and IMPT for simulated AF. Targets at the LA-PVJ were defined as wide-area circumferential ablation line. A single fraction of 25 Gy was prescribed to all plans. The interplay effects from cardiac motion were evaluated based on the cardiac 4D-CT scan. Dose-volume histograms (DVHs) of the ITV and normal tissues were compared. Statistical analysis was evaluated via one-way Repeated-Measures ANOVA and Friedman's test with Bonferroni's multiple comparisons test. RESULTS: The median volume of ITV was 8.72cc. All plans had adequate target coverage (V23.75Gy  ≥ 99%). Compared with VMAT and TOMO, IMPT resulted in significantly lower dose of most normal tissues. For VMAT, TOMO, and IMPT plans, Dmean of the whole heart was 5.52 ± 0.90 Gy, 5.89 ± 0.78 Gy, and 3.01 ± 0.57 Gy (P < 0.001), mean dose of pericardium was 4.74 ± 0.76 Gy, 4.98 ± 0.62 Gy, and 2.59 ± 0.44 Gy (P < 0.001), and D0.03cc of left circumflex artery (LCX) was 13.96 ± 5.45 Gy, 14.34 ± 5.91 Gy, and 8.43 ± 7.24 Gy (P < 0.001), respectively. However, no significant advantage for one technique over the others was observed when examining the D0.03cc of esophagus and main bronchi. CONCLUSIONS: IMPT targeting LA-PVJ for patients with AF has high potential to reduce dose to surrounding tissues compared to VMAT or TOMO. Motion mitigation techniques are critical for a particle-therapy approach.

SAMHD1 Inhibits Multiple Enteroviruses by Interfering with the Interaction between VP1 and VP2 Proteins.

Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) possesses multiple biological activities such as virus restriction, innate immunity regulation, and autoimmunity. Our previous study demonstrated that SAMHD1 potently inhibits the replication of enterovirus 71 (EV71). In this study, we observed that SAMHD1 also restricts multiple enteroviruses (EVs), including coxsackievirus A16 (CA16) and enterovirus D68 (EVD68), but not coxsackievirus A6 (CA6). Mechanistically, SAMHD1 competitively interacted with the same domain in VP1 that binds to VP2 of EV71 and EVD68, thereby interfering with the interaction between VP1 and VP2 , and therefore viral assembly. Moreover, we showed that the SAMHD1 T592A mutant maintained the EV71 inhibitory effect by attenuating the interaction between VP1 and VP2, whereas the T592D mutant failed to. We also demonstrated that SAMHD1 could not inhibit CA6 because a different binding site is required for the SAMHD1 and VP1 interaction. Our findings reveal the mechanism of SAMHD1 inhibition of multiple EVs, and this could potentially be important for developing drugs against a broad range of EVs. IMPORTANCE Enterovirus causes a wide variety of diseases, such as hand, foot, and mouth disease (HFMD), which is a severe public problem threatening children under 5 years. Therefore, identifying essential genes which restrict EV infection and exploring the underlying mechanisms are necessary to develop an effective strategy to inhibit EV infection. In this study, we report that host restrictive factor SAMHD1 has broad-spectrum antiviral activity against EV71, CA16, and EVD68 independent of its well-known deoxynucleoside triphosphate triphosphohydrolase (dNTPase) or RNase activity. Mechanistically, SAMHD1 restricts EVs by competitively interacting with the same domain in VP1 that binds to VP2 of EVs, thereby interfering with the interaction between VP1 and VP2, and therefore viral assembly. In contrast, we also demonstrated that SAMHD1 could not inhibit CA6 because a different binding site is required for the SAMHD1 and CA6 VP1 interaction. Our study reveals a novel mechanism for the SAMHD1 anti-EV replication activity.

Total synchronous fluorescence spectroscopy coupled with deep learning to rapidly identify the authenticity of sesame oil.

The quality of sesame oil (SO) has been paid more and more attention. In this study, total synchronous fluorescence (TSyF) spectroscopy and deep neural networks were utilized to identify counterfeit and adulterated sesame oils. Firstly, typical samples including pure SO, counterfeit sesame oil (CSO) and adulterated sesame oil (ASO) were characterized by TSyF spectra. Secondly, three data augmentation methods were selected to increase the number of spectral data and enhance the robustness of the identification model. Then, five deep network architectures, including Simple Recurrent Neural Network (Simple RNN), Long Short-Term Memory (LSTM) network, Gated Recurrent Unit (GRU) network, Bidirectional LSTM (BLSTM) network and LSTM fortified with Convolutional Neural Network (LSTMC), were designed to identify the CSO and trace the source with 100% accuracy. Finally, ASO samples were also 100% correctly identified by training these network architectures. These results supported the feasibility of the novel method.

Exploration of total synchronous fluorescence spectroscopy combined with pre-trained convolutional neural network in the identification and quantification of vegetable oil.

In order to distinguish different vegetable oils, adulterated vegetable oils, and to identify and quantify counterfeit vegetable oils, a method based on a small sample size of total synchronous fluorescence (TSyF) spectra combined with convolutional neural network (CNN) was proposed. Four typical vegetable oils were classified by three ways of fine-tuning the pre-trained CNN, the pre-trained CNN as a feature extractor, and traditional chemometrics. The pre-trained CNN was combined with support vector machines to distinguish adulterated sesame oil and counterfeit sesame oil separately with 100% correct classification rates. The pre-trained CNN combined with partial least square regression was used to predict the level of counterfeit sesame oil. The coefficient of determination for calibration (Rc2) values were all greater than 0.99, and the root mean square errors of validation were 0.81% and 1.72%, respectively. These results show that it is feasible to combine TSyF spectra with CNN for vegetable oil identification.

GBP5 Is an Interferon-Induced Inhibitor of Respiratory Syncytial Virus.

Guanylate binding protein 5 (GBP5) belongs to the GTPase subfamily, which is mainly induced by interferon gamma (IFN-γ) and is involved in many important cellular processes, including inflammasome activation and innate immunity against a wide variety of microbial pathogens. However, it is unknown whether GBP5 inhibits respiratory syncytial virus (RSV) infection. In this study, we identified GBP5 as an effector of the anti-RSV activity of IFN-γ and found that in children, the weaker immune response, especially the weaker IFN-γ response and the decreased GBP5 expression, leads to RSV susceptibility. Furthermore, we revealed that GBP5 reduced the cell-associated levels of the RSV small hydrophobic (SH) protein, which was identified as a viroporin. In contrast, overexpression of the SH protein rescued RSV replication in the presence of GBP5. The GBP5-induced decrease in intracellular SH protein levels is because GBP5 promotes the release of the SH protein into the cell culture. Moreover, the GBP5 C583A mutants with changes at the C terminus or the GBP5 ΔC mutant lacking the C-terminal region, which impairs GBP5 localization in the Golgi, could not inhibit RSV infection, whereas the GTPase-defective GBP5 maintained RSV inhibition, suggesting that Golgi localization but not the GTPase activity of GBP5 is required for RSV inhibition. Interestingly, we found that RSV infection or RSV G protein downregulates GBP5 expression by upregulating DZIP3, an E3 ligase, which induces GBP5 degradation through the K48 ubiquitination and proteasomal pathways. Thus, this study reveals a complicated interplay between host restrictive factor GBP5 and RSV infection and provides important information for understanding the pathogenesis of RSV.IMPORTANCE RSV is a highly contagious virus that causes multiple infections in infants within their first year of life. It can also easily cause infection in elderly or immunocompromised individuals, suggesting that individual differences in immunity play an important role in RSV infection. Therefore, exploring the pathogenic mechanisms of RSV and identifying essential genes which inhibit RSV infection are necessary to develop an effective strategy to control RSV infection. Here, we report that the IFN-inducible gene GBP5 potently inhibits RSV replication by reducing the cell-associated levels of the RSV small hydrophobic (SH) protein, which is a viroporin. In contrast, the RSV G protein was shown to upregulate the expression of the DZIP3 protein, an E3 ligase that degrades GBP5 through the proteasomal pathway. Our study provides important information for the understanding of the pathogenic mechanisms of RSV and host immunity as well as the complicated interplay between the virus and host.

Identification and quantification of counterfeit sesame oil by 3D fluorescence spectroscopy and convolutional neural network.

The method of 3D fluorescence spectroscopy combined with convolutional neural network (CNN) was developed to identify the counterfeit sesame oil. AlexNet, a pre-trained CNN architecture, was transferred to extract spectral characteristics. Then these features extracted by AlexNet were used as the input of the support vector machine (SVM) to determine whether the sample was counterfeit and its ingredients simultaneously, and both the accuracy were 100%. According to different counterfeit ingredients, these features extracted by AlexNet were used as the input of partial least squares (PLS) to predict the volume percentage concentration of sesame oil essence. There was a good linear relationship between the predicted and actual values of the three sets of counterfeit samples (R2 > 0.99), and the root mean square error of prediction (RMSEP) values were 0.99%, 2.20% and 1.64%, respectively. The results confirmed the validity of this novel method in sesame oil identification.

Performance of Homologous and Heterologous Prime-Boost Immunization Regimens of Recombinant Adenovirus and Modified Vaccinia Virus Ankara Expressing an Ag85B-TB10.4 Fusion Protein against Mycobacterium tuberculosis.

Tuberculosis (TB) remains a serious health issue around the word. Adenovirus (Ad)-based vaccine and modified vaccinia virus Ankara (MVA)-based vaccine have emerged as two of the most promising immunization candidates over the past few years. However, the performance of the homologous and heterologous prime-boost immunization regimens of these two viral vector-based vaccines remains unclear. In the present study, we constructed recombinant Ad and MVA expressing an Ag85B-TB10.4 fusion protein (AdH4 and MVAH4) and evaluated the impact of their different immunization regimens on the humoral and cellular immune responses. We found that the viral vector-based vaccines could generate significantly higher levels of antigen-specific antibodies, IFN-γ-producing splenocytes, CD69⁺CD8⁺ T cells, and IFN-γ secretion when compared with bacillus Calmette-Guérin (BCG) in a mouse model. AdH4-containing immunization regimens (AdH4-AdH4, AdH4-MVAH4, and MVAH4-AdH4) induced significantly stronger antibody responses, much more IFN-γ-producing splenocytes and CD69⁺CD8⁺ T cells, and higher levels of IFN-γ secretion when compared with the MVAH4-MVAH4 immunization regimen. The number of IFN-γ-producing splenocytes sensitive to CD8⁺ T-cell restricted peptides of Ag85B (9-1p and 9-2p) and Th1-related cytokines (IFN-γ and TNF-α) in the AdH4-MVAH4 heterologous prime-boost regimen immunization group was significantly higher than that in the other viral vector-based vaccine- and BCG-immunized groups, respectively. These results indicate that an immunization regimen involving AdH4 may have a higher capacity to induce humoral and cellular immune responses against TB in mice than that by regimens containing BCG or MVAH4 alone, and the AdH4-MVAH4 prime-boost regimen may generate an ideal protective effect.

Extracellular elevation of adrenomedullin, a gene associated with schizophrenia, suppresses heat shock protein 1A/1B mRNA.

Several recent gene expression studies on schizophrenia, including one using monozygotic twins discordant for the disease, have reported the upregulation of adrenomedullin (ADM), which was initially identified as a vasodilator hormone. It has been hypothesized that upregulation of ADM may be a susceptibility factor for schizophrenia, although the exact role of ADM in the central nervous system remains unclear. In this study, we used a microarray analysis to investigate the changes in global gene expression induced by the administration of exogenous ADM in SK-N-SH cells, which allowed us to evaluate the effects of elevated ADM on the central nervous system. A quantitative reverse-transcription PCR study showed that the levels of HSPA1A/1B mRNA, another gene that has been associated with schizophrenia, were significantly suppressed after exogenous ADM treatment. These results indicate that elevated ADM may be involved in the etiology of schizophrenia through the regulation of heat shock protein signaling.

Self-assembly formation of lipid bilayer coatings on bare aluminum oxide: overcoming the force of interfacial water.

Widely used in catalysis and biosensing applications, aluminum oxide has become popular for surface functionalization with biological macromolecules, including lipid bilayer coatings. However, it is difficult to form supported lipid bilayers on aluminum oxide, and current methods require covalent surface modification, which masks the interfacial properties of aluminum oxide, and/or complex fabrication techniques with specific conditions. Herein, we addressed this issue by identifying simple and robust strategies to form fluidic lipid bilayers on aluminum oxide. The fabrication of a single lipid bilayer coating was achieved by two methods, vesicle fusion under acidic conditions and solvent-assisted lipid bilayer (SALB) formation under near-physiological pH conditions. Importantly, quartz crystal microbalance with dissipation (QCM-D) monitoring measurements determined that the hydration layer of a supported lipid bilayer on aluminum oxide is appreciably thicker than that of a bilayer on silicon oxide. Fluorescence recovery after photobleaching (FRAP) analysis indicated that the diffusion coefficient of lateral lipid mobility was up to 3-fold greater on silicon oxide than on aluminum oxide. In spite of this hydrodynamic coupling, the diffusion coefficient on aluminum oxide, but not silicon oxide, was sensitive to the ionic strength condition. Extended-DLVO model calculations estimated the thermodynamics of lipid-substrate interactions on aluminum oxide and silicon oxide, and predict that the range of the repulsive hydration force is greater on aluminum oxide, which in turn leads to an increased equilibrium separation distance. Hence, while a strong hydration force likely contributes to the difficulty of bilayer fabrication on aluminum oxide, it also confers advantages by stabilizing lipid bilayers with thicker hydration layers due to confined interfacial water. Such knowledge provides the basis for improved surface functionalization strategies on aluminum oxide, underscoring the practical importance of surface hydration.

Optimized method for determining free L-cysteine in rat plasma by high-performance liquid chromatography with the 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole conversion reagent.

The analytical method was optimized for L-cysteine (Cys) in rat plasma with co-existing L-cystine (Cyss). We observed that more than 100% Cyss in rat plasma was converted to Cys under typical conditions for the conversion with 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate (SBD-F). Another conversion reagent, 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (ABD-F), was then employed, with which the reaction could be carried out at a low temperature without the use of a reducing reagent. Under the optimized conditions of 4 °C and pH 8.3, the conversion ratio of Cyss to Cys in rat plasma was as low as 5-7%. We determined the Cys concentration in plasma of the portal vein of rats that had been orally administered with Cys and Cyss by applying this method. The result indicated that Cys administration and also Cyss administration effectively increased the plasma Cys level. The method developed in this study is well suited for determining the thiol compounds in biological samples.