Additional file 2: of Structural identifiability of cyclic graphical models of biological networks with latent variables

Proof of Theorem 1. This file includes the details of theoretical derivation of Theorem 1. (PDF 62 kb

Additional file 1: of Structural identifiability of cyclic graphical models of biological networks with latent variables

Identifiability Preservation by Matrix Reduction. This file contains the theoretical justification for the proposed identifiability matrix reduction operations. (PDF 92 kb

DataSheet_1_MRI VS. FDG-PET for diagnosis of response to neoadjuvant therapy in patients with locally advanced rectal cancer.docx

AimIn this study, we aimed to compare the diagnostic values of MRI and FDG-PET for the prediction of the response to neoadjuvant chemoradiotherapy (NACT) of patients with locally advanced Rectal cancer (RC).MethodsElectronic databases, including PubMed, Embase, and the Cochrane library, were systematically searched through December 2021 for studies that investigated the diagnostic value of MRI and FDG-PET in the prediction of the response of patients with locally advanced RC to NACT. The quality of the included studies was assessed using QUADAS. The pooled sensitivity, specificity, positive and negative likelihood ratio (PLR and NLR), and the area under the ROC (AUC) of MRI and FDG-PET were calculated using a bivariate generalized linear mixed model, random-effects model, and hierarchical regression.ResultsA total number of 74 studies with recruited 4,105 locally advanced RC patients were included in this analysis. The pooled sensitivity, specificity, PLR, NLR, and AUC for MRI were 0.83 (95% CI: 0.77–0.88), 0.85 (95% CI: 0.79–0.89), 5.50 (95% CI: 4.11-7.35), 0.20 (95% CI: 0.14–0.27), and 0.91 (95% CI: 0.88–0.93), respectively. The summary sensitivity, specificity, PLR, NLR and AUC for FDG-PET were 0.81 (95% CI: 0.77-0.85), 0.75 (95% CI: 0.70–0.80), 3.29 (95% CI: 2.64–4.10), 0.25 (95% CI: 0.20–0.31), and 0.85 (95% CI: 0.82–0.88), respectively. Moreover, there were no significant differences between MRI and FDG-PET in sensitivity (P = 0.565), and NLR (P = 0.268), while the specificity (P = 0.006), PLR (P = 0.006), and AUC (P = 0.003) of MRI was higher than FDG-PET.ConclusionsMRI might superior than FGD-PET for the prediction of the response of patients with locally advanced RC to NACT.</p

In Situ Generation of Copper Species Nanocrystals in TiO₂ Electrospun Nanofibers: A Multi-hetero-junction Photocatalyst for Highly Efficient Water Reduction

Engineering the multi-hetero-junctions in semiconductor photocatalysts has been recognized as a promising way to achieve highly efficient photocatalytic solar-fuel generation, because the photoinduced heterointerfacial charge transfer can greatly hinder the recombination process of charge-carrier in photocatalysts. In this work, we fabricated copper species nanocrystals/TiO₂ multi-hetero-junction photocatalysts through in situ reduction of CuO nanocrystals in CuO/TiO₂ electrospun nanofibers by a hydrothermal method assisted by glucose. By changing the concentration of glucose, the composition ratio of copper species nanocrystals, including CuO, Cu₂O, and Cu, can be adjusted in multi-hetero-junction nanofibers. Upon simulated sunlight irradiation, the optimal copper species nanocrystals/TiO₂ multi-hetero-junction nanofibers exhibited an H₂ evolution rate of ∼10.04 μmol h^–1, a 17.3 times increase over that of bare TiO₂ nanofibers (∼0.57 μmol h^–1)

Enhanced “Electronic Tongue” for Dental Bacterial Discrimination and Elimination Based on a DNA-Encoded Nanozyme Sensor Array

Bacterial infections are the second leading cause of death around the world, especially those caused by delayed treatment and misdiagnosis. Therefore, rapid discrimination and effective elimination of multiple bacteria are of great importance for improving the survival rate in clinic. Herein, a novel colorimetric sensor array for bacterial discrimination and elimination is constructed using programmable DNA-encoded iron oxide nanoparticles (IONPs) as sensing elements. Utilizing differential interactions of bacteria on DNA-encoded IONPs, 11 kinds of dental bacteria and 6 kinds of proteins have been successfully identified by linear discriminant analysis (LDA). Moreover, the developed sensing system also performs well in the quantitative determination of individual bacteria and identification of bacterial mixtures. More importantly, the practicability of this sensing strategy is further verified by precise differentiation of blind and artificial saliva samples. Furthermore, the sensor array is used for efficiently killing multiple bacteria, demonstrating great potential in clinical prophylaxis and therapy

DataSheet_1_Construction of an m6A- and neutrophil extracellular traps-related lncRNA model to predict hepatocellular carcinoma prognosis and immune landscape.pdf

PurposeTo investigate the impact of N6-methyladenosine- (m6A) and neutrophil extracellular traps- (NETs) related lncRNAs (MNlncRNAs) on the prognosis of hepatocellular carcinoma (HCC).MethodsWe collected m6A and NETs-related genes from published studies. We identified the MNlncRNAs by correlation analysis. Cox regression and the least absolute selection operator (LASSO) method were used to select predictive MNlncRNAs. The expressions of predictive MNlncRNAs were detected by cell and tissue experiments. Survival, medication sensitivity, and immunological microenvironment evaluations were used to assess the model’s prognostic utility. Finally, we performed cellular experiments to further validate the model’s prognostic reliability.ResultsWe obtained a total of 209 MNlncRNAs. 7 MNlncRNAs comprised the prognostic model, which successfully stratifies HCC patients, with the area under the curve (AUC) ranging from 0.7 to 0.8. In vitro tests confirmed that higher risk patients had worse prognosis. Risk score, immunological microenvironment, and immune checkpoint gene expression were all significantly correlated with each other in HCC. In the group at high risk, immunotherapy could be more successful. Cellular assays confirmed that HCC cells with high risk scores have a higher proliferation and invasive capacity.ConclusionThe MNlncRNAs-related prognostic model aided in determining HCC prognosis, revealing novel therapeutic options, notably immunotherapy.</p

DataSheet_1_L−shaped association of triglyceride glucose index and sensorineural hearing loss: results from a cross-sectional study and Mendelian randomization analysis.docx

BackgroundThe association between the sensorineural hearing loss (SNHL) and triglyceride-glucose (TyG) index remains inadequately understood. This investigation seeks to elucidate the connection between the TyG index and SNHL.MethodsIn this cross-sectional study, we utilized datasets sourced from the National Health and Nutrition Examination Survey (NHANES). A comprehensive analysis was conducted on 1,851 participants aged 20 to 69, utilizing complete audiometry data from the NHANES database spanning from 2007 to 2018. All enrolled participants had accessible hearing data, and the average thresholds were measured and calculated as both low-frequency pure-tone average and high-frequency pure-tone average. Sensorineural hearing loss (SNHL) was defined as an average pure tone of 20 dB or higher in at least one better ear. Our analysis involved the application of multivariate linear regression models to examine the linear relationship between the TyG index and SNHL. To delineate any non-linear associations, we utilized fitted smoothing curves and conducted threshold effect analysis. Furthermore, we conducted a two-sample Mendelian randomization (MR) study, leveraging genetic data from genome-wide association studies (GWAS) on circulating lipids, blood glucose, and SNHL. The primary analytical method for the MR study was the application of the inverse-variance-weighted (IVW) approach.ResultsIn our multivariate linear regression analysis, a substantial positive correlation emerged between the TyG index and SNHL [2.10 (1.80-2.44), p −4). In addition, blood glucose was found to have a protective effect on SNHL (OR = 0.886, p = 1.012 × 10−2).ConclusionsAn L-shaped association was identified among the TyG index, fasting blood glucose, and SNHL in the American population. TyG index of more than 9.07 and blood glucose of more than 94 mg/dL were significantly and positively associated with SNHL risk, respectively.</p

Electrospun Carbon Nanofibers/Carbon Nanotubes/Polyaniline Ternary Composites with Enhanced Electrochemical Performance for Flexible Solid-State Supercapacitors

Design and synthesis of hierarchical carbon hybrid based pseudocapacitive electrodes is the next step forward for achieving high-performance supercapacitors. Here, the freestanding electrospun carbon nanofibers/carbon nanotubes/polyaniline (CNFs/CNTs/PANI) ternary composites have been fabricated successfully. Importantly, the hierarchical carbon hybrids by dense CNT forests decorated CNFs serving as supports are crucial for the ternary composites to achieve high electrochemical properties. The hierarchical CNFs/CNTs hybrids serving as inner current collectors can afford plentiful transport channels for more rapidly transporting and collecting electrons, greatly reduce the ion diffusion length, and increase the utilization of pseudocapacitive materials. As expected, the ternary composites as electrodes present high specific capacitance (i.e., 315 F/g at 1 A/g) and dramatic rate capability (i.e., 235 F/g at 32 A/g) in three-electrode configuration. Moreover, the as-fabricated flexible solid-state supercapacitor based on the ternary composites also achieves desired electrochemical properties with high capacitance, high-rate capability, high energy/power density (i.e., 5.1 Wh/kg at 10.1 kW/kg), and remarkable cycling stability (i.e., 92% capacitance retention after 10 000 cycles at 2 A/g). These extraordinary electrochemical properties can be attributed to the well-designed structural advantages and synergistic effects

Charge Transport within a Three-Dimensional DNA Nanostructure Framework

Three-dimensional (3D) DNA nanostructures have shown great promise for various applications including molecular sensing and therapeutics. Here we report kinetic studies of DNA-mediated charge transport (CT) within a 3D DNA nanostructure framework. A tetrahedral DNA nanostructure was used to investigate the through-duplex and through-space CT of small redox molecules (methylene blue (MB) and ferrocene (Fc)) that were bound to specific positions above the surface of the gold electrode. CT rate measurements provide unambiguous evidence that the intercalative MB probe undergoes efficient mediated CT over longer distances along the duplex, whereas the nonintercalative Fc probe tunnels electrons through the space. This study sheds new light on DNA-based molecular electronics and on designing high-performance biosensor devices

A low-molecular-weight heparin-coated doxorubicin-liposome for the prevention of melanoma metastasis

<div><p></p><p>Tumor metastasis is the biggest challenge in cancer therapy. During the metastasis process, metastatic cells could acquire stealth ability toward immune system through the formation of a protection cloak by hijacking platelets (PTs). Heparins, a heterogeneous mixture of glycosaminoglycans, can inhibit metastatic cascades by blocking P-selectin-mediated intercellular adhesion between tumor cells and PTs. In this study, low-molecular-weight heparin-coated doxorubicin-loaded liposome (LMWH-DOX-Lip) was developed for metastasis preventative therapy. The formation of LMWH-DOX-Lip was based on electrostatic interactions between the negatively charged heparins and cationic lipids. LMWH-DOX-Lip prepared at the optimum prescription possessed high entrapment efficiency, ideal particle size and zeta potential. Morphology of LMWH-DOX-Lip was characterized by atomic force microscopy and transmission electron microscopy. The results of confocal microscopic observations and flow cytometry analysis indicated that LMWH-DOX-Lip mediated an efficient cellular uptake in B16F10 melanoma cell line. Besides, LMWH-DOX-Lip displayed an increased cytotoxic over their unmodified counterparts. Furthermore, the inhibition effect of LMWH-DOX-Lip on adhesion between tumor cells and PTs/P-selectin was observed. <i>In vivo</i> study performed on a pulmonary melanoma mouse model revealed a substantially tumor metastasis prevention by LMWH-DOX-Lip. All these results suggested that LMWH-DOX-Lip could significantly inhibit metastasis through preventing the tumor cell–platelet interactions and in the meantime suppressed tumor growth.</p></div