Mechanistic Study of Xanthotoxin-Mediated Inactivation of CYP1A2 and Related Drug-Drug Interaction with Tacrine.

Xanthotoxin (XTT) is a biologically active furanocoumarin widely present in foods and plants. The present study is designed to systematically investigate the enzymatic interaction of XTT with CYP1A2, along with pharmacokinetic alteration of tacrine resulting from the co-administration of XTT. The results showed that XTT induced a time-, concentration-, and NADPH-dependent inhibition of CYP1A2, and the inhibition was irreversible. Co-incubation of glutathione (GSH) and catalase/superoxide dismutase was unable to prevent enzyme inactivation. Nevertheless, competitive inhibitor fluvoxamine exhibited a concentration-dependent protective effect against the XTT-induced CYP1A2 inactivation. A GSH trapping experiment provided strong evidence for the production of epoxide or/and γ-ketoenal intermediates resulting from the metabolic activation of XTT. Furthermore, pretreatment of rats with XTT was found to significantly increase the Cmax and area under the curve of plasma tacrine relative to those of tacrine administration alone.

Immunochemical and LC-MS/MS Detection of Protein Adduction Resulting from Metabolic Activation of Columbin In Vitro and In Vivo.

Columbin (CLB) is a diterpenoid furanolactone compound occurring in some herbal medicines. Administration of CLB has been reported to induce liver injury. The reported CLB hepatotoxicity is suggested to require metabolism to a cis-enedial intermediate. We successfully detected hepatic protein adduction resulting from the metabolic activation of CLB and found that the intermediate reacted with lysine residues or lysine/cysteine residues to produce the corresponding pyrroline derivative or pyrrole derivative. The detection was achieved by proteolysis- and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based methods. Furthermore, we prepared a polyclonal antibody approach which allowed us to detect the protein adduction in the forms of protein immunoblot as well as tissue- and cell-based immunostaining. The antibody technique verified the protein adduction detected by LC-MS/MS.

DNA damage by reactive oxygen species resulting from metabolic activation of 8-epidiosbulbin E acetate in vitro and in vivo.

8-Epidiosbulbin E acetate (EEA), a furan-containing diterpenoid lactone, is one of main component of Dioscorea bulbifera L. (DBL). It has been reported that EEA induces severe hepatotoxicity in mice and that its hepatotoxicity is associated with metabolic activation. The present study demonstrated that exposure to EEA (50, 100 or 200 µM) induced DNA damage, including significant DNA fragmentation, increases of tail DNA and olive tail moment, H2AX phosphorylation and PARP-1 activation, in cultured mouse primary hepatocytes. Similar observation was obtained in mice administered EEA at 50, 100 or 200 mg/kg. Pre-treatment with 10 µM ketoconazole (KTC), 200 µM vitamin C (VC), or 200 µM glutathione ethyl ester (GSH-OEt) reversed the over-production of reactive oxygen species (ROS) induced by EEA and attenuated susceptibility of hepatocytes to EEA-induced cytotoxicity and DNA damage in mouse primary hepatocytes. In contrast, pre-treatment with 1.0 mM L-buthionine sulfoximine (BSO) potentiated over-production of ROS, cytotoxicity and DNA damage induced by EEA. In summary, EEA induced DNA damage in cultured primary hepatocytes and the liver of mice. ROS, possibly along with DNA alkylation, participated in the observed DNA damage.

Estimation precision for a normalized response matrix in linear polarization calibration.

The purpose of polarization calibration is to obtain the response matrix of an instrument such that the subsequent observation data can be corrected. The calibration precision, however, is partially restricted by the noise of the detector. We investigate the precision of the normalized response matrix in the presence of signal-independent additive noise or signal-dependent Poisson shot noise. The influences of the source intensity, type of noise, and calibration configuration on the precision are analyzed. We compare the theoretical model and the experimental measurements of the polarization calibration to show that the relative difference between the two is less than 16%. From this result, we can use the model to determine the minimum source intensity and choose the optimal configurations that provide the required precision.

Characterizing Topics in Social Media Using Dynamics of Conversation.

Online social media provides massive open-ended platforms for users of a wide variety of backgrounds, interests, and beliefs to interact and debate, facilitating countless discussions across a myriad of subjects. With numerous unique voices being lent to the ever-growing information stream, it is essential to consider how the types of conversations that result from a social media post represent the post itself. We hypothesize that the biases and predispositions of users cause them to react to different topics in different ways not necessarily entirely intended by the sender. In this paper, we introduce a set of unique features that capture patterns of discourse, allowing us to empirically explore the relationship between a topic and the conversations it induces. Utilizing "microscopic" trends to describe "macroscopic" phenomena, we set a paradigm for analyzing information dissemination through the user reactions that arise from a topic, eliminating the need to analyze the involved text of the discussions. Using a Reddit dataset, we find that our features not only enable classifiers to accurately distinguish between content genre, but also can identify more subtle semantic differences in content under a single topic as well as isolating outliers whose subject matter is substantially different from the norm.

Background Point Filtering of Low-Channel Infrastructure-Based LiDAR Data Using a Slice-Based Projection Filtering Algorithm.

A light detection and ranging (LiDAR) sensor can obtain richer and more detailed traffic flow information than traditional traffic detectors, which could be valuable data input for various novel intelligent transportation applications. However, the point cloud generated by LiDAR scanning not only includes road user points but also other surrounding object points. It is necessary to remove the worthless points from the point cloud by using a suitable background filtering algorithm to accelerate the micro-level traffic data extraction. This paper presents a background point filtering algorithm using a slice-based projection filtering (SPF) method. First, a 3-D point cloud is projected to 2-D polar coordinates to reduce the point data dimensions and improve the processing efficiency. Then, the point cloud is classified into four categories in a slice unit: Valuable object points (VOPs), worthless object points (WOPs), abnormal ground points (AGPs), and normal ground points (NGPs). Based on the point cloud classification results, the traffic objects (pedestrians and vehicles) and their surrounding information can be easily identified from an individual frame of the point cloud. We proposed an artificial neuron network (ANN)-based model to improve the adaptability of the algorithm in dealing with the road gradient and LiDAR-employing inclination. The experimental results showed that the algorithm of this paper successfully extracted the valuable points, such as road users and curbstones. Compared to the random sample consensus (RANSAC) algorithm and 3-D density-statistic-filtering (3-D-DSF) algorithm, the proposed algorithm in this paper demonstrated better performance in terms of the run-time and background filtering accuracy.

Glutathione Conjugation and Protein Adduction Derived from Oxidative Debromination of Benzbromarone in Mice.

Benzbromarone (BBR), a uricosuric agent, has been known to induce hepatotoxicity, and its toxicity has a close relation to cytochrome P450-mediated metabolic activation. An oxidative debromination metabolite of BBR has been reported in microsomal incubations. The present study attempted to define the oxidative debromination pathway of BBR in vivo. One urinary mercapturic acid (M1) and one glutathione (GSH) conjugate (M2) derived from the oxidative debromination metabolite were detected in BBR-treated mice after solid phase extraction. M1 and M2 shared the same chromatographic behavior and mass spectral identities as those detected in N-acetylcysteine/GSH- and BBR-fortified microsomal incubations. The structure of M1 was characterized by chemical synthesis, along with mass spectrometry analysis. In addition, hepatic protein modification that occurs at cysteine residues (M'3) was observed in mice given BBR. The observed protein adduction reached its peak 4 hours after administration and occurred in a dose-dependent manner. A GSH conjugate derived from oxidative debromination of BBR was detected in livers of mice treated with BBR, and the formation of the GSH conjugate apparently took place earlier than the protein adduction. In summary, our in vivo work provided strong evidence for the proposed oxidative debromination pathway of BBR, which facilitates the understanding of the mechanisms of BBR-induced hepatotoxicity. SIGNIFICANCE STATEMENT: This study investigated the oxidative debromination pathway of benzbromarone (BBR) in vivo. One urinary mercapturic acid (M1) and one glutathione (GSH) conjugate (M2) derived from the oxidative debromination metabolite were detected in BBR-treated mice. M1 and M2 were also observed in microsomal incubations. The structure of M1 was characterized by chemical synthesis followed by mass spectrometry analyses. More importantly, protein adduction derived from oxidative debromination of BBR (M'3) was observed in mice given BBR, and occurred in dose- and time-dependent manners. The success in detection of GSH conjugate, urinary N-acetylcysteine conjugate, and hepatic protein adduction in mice given BBR provided solid evidence for in vivo oxidative debromination of BBR. The studies allowed a better understanding of the metabolic activation of BBR.

Intensive Distribution of G2-Quaduplexes in the Pseudorabies Virus Genome and Their Sensitivity to Cations and G-Quadruplex Ligands.

Guanine-rich sequences in the genomes of herpesviruses can fold into G-quadruplexes. Compared with the widely-studied G3-quadruplexes, the dynamic G2-quadruplexes are more sensitive to the cell microenvironment, but they attract less attention. Pseudorabies virus (PRV) is the model species for the study of the latency and reactivation of herpesvirus in the nervous system. A total of 1722 G2-PQSs and 205 G3-PQSs without overlap were identified in the PRV genome. Twelve G2-PQSs from the CDS region exhibited high conservation in the genomes of the Varicellovirus genus. Eleven G2-PQSs were 100% conserved in the repeated region of the annotated PRV genomes. There were 212 non-redundant G2-PQSs in the 3' UTR and 19 non-redundant G2-PQSs in the 5' UTR, which would mediate gene expression in the post-transcription and translation processes. The majority of examined G2-PQSs formed parallel structures and exhibited different sensitivities to cations and small molecules in vitro. Two G2-PQSs, respectively, from 3' UTR of UL5 (encoding helicase motif) and UL9 (encoding sequence-specific ori-binding protein) exhibited diverse regulatory activities with/without specific ligands in vivo. The G-quadruplex ligand, NMM, exhibited a potential for reducing the virulence of the PRV Ea strain. The systematic analysis of the distribution of G2-PQSs in the PRV genomes could guide further studies of the G-quadruplexes' functions in the life cycle of herpesviruses.

Near-crash risk identification and evaluation for takeout delivery motorcycles using roadside LiDAR.

The proliferation of motorcycles in urban areas has raised concerns regarding traffic safety. However, traditional sensors struggle to obtain precise high-resolution trajectory data, which hinder the accurate identification and quantification of near-crash risks for takeout delivery motorcycles. To fill this gap, this study presents a novel approach utilizing roadside light detection and ranging (LiDAR) to identify and evaluate the risk of near crashes of takeout delivery motorcycles. First, a trajectory amendment method incorporating speed and steering angle was introduced to enhance the accuracy and continuity of the trajectory prediction. Second, a trajectory prediction method combining the steering intention and a repulsive force model was proposed for near-crash risk prediction. Subsequently, a near-crash identification method was developed that relied on the closest distance and risk radius. Finally, near-crash risk fields were constructed to quantify risk levels by leveraging velocity, position, and weight. The experimental results demonstrated 92.10 % accuracy in intention prediction, with mean absolute error (MAE) and root mean square error (RMSE) values of 0.53 m and 0.45 m, respectively. In addition to its higher accuracy, the proposed method makes it easier to quantify near-crash risk and supports a proactive approach for visualizing and analyzing traffic safety.

Mineral oil emulsion species and concentration prediction using multi-output neural network based on fluorescence spectra in the solar-blind UV band.

The accurate monitoring of oil spills is crucial for effective oil spill recovery, volume determination, and cleanup. Oil slicks become emulsified under the effects of wind and waves, which increases the consistency of the oil spills. This phenomenon makes oil spills more challenging to handle and exacerbates environmental pollution. In this study, the variation of the solar-blind ultraviolet (UV) fluorescence spectra obtained from simulated oil spills with different oil types and oil-water ratios was investigated. By designing and constructing a multi-angle excitation and detection system, an apparent fluorescence peak of the oil emulsions was observed at around 290 nm under 220 nm excitation. By utilizing competitive adaptive reweighted sampling (CARS) and multi-output neural network algorithms, both the types and concentrations of the emulsified oils were obtained simultaneously. The classification accuracy for identifying the oil type exceeds 98%, and the mean absolute percentage error (MAPE) for concentration regression is around 2%. The results indicate that active solar-blind UV fluorescence could become a supplementary method for on-site oil spill detection to achieve comprehensive monitoring of oil spills. This study provides potential applications for UV-induced fluorescence spectrometry in oil spill on-site monitoring during the daytime.

Ultraviolet-induced fluorescence of oil spill recognition using a semi-supervised algorithm based on thickness and mixing proportion-emission matrices.

In recent years, marine oil spill accidents have been occurring frequently during extraction and transportation, and seriously damage the ecological balance. Accurate monitoring of oil spills plays a vital role in estimating oil spill volume, determination of liability, and clean-up. The oil that leaks into natural environments is not a single type of oil, but a mixture of various oil products, and the oil film thickness on the sea surface is uneven under the influence of wind and waves. Increasing the mixed oil film thickness dimension and the mix proportion dimension has been proposed to weaken the effect of the detection environment on the fluorescence measurement results. To preserve the relationships between the data of oil films with different thicknesses and the relationships between the data of oil films with different mixing proportions, the three-dimensional fluorescence spectral data of mixed oil films on a seawater surface were measured in the laboratory, producing a thickness-fluorescence matrix and a proportion-fluorescence matrix. The nonlinear variation of the fluorescence spectra was investigated according to the fluorescence lidar equation. This work pre-processes the data by sum normalization and two-dimensional principal component analysis (2DPCA) and uses the dimensionality reduction results as two feature-point views. Then, semi-supervised classification of collaborative training (co-training) with K-nearest neighbors (KNN) and a decision tree (DT) is used to identify the samples. The results show that the average overall accuracy of this coupling model can reach 100%, which is 20.49% higher than that of the thickness-only view. Using unlabeled data can reduce the cost of data acquisition, improve the classification accuracy and generalization ability, and provide theoretical significance and application prospects for discrimination of spectrally similar oil species in natural marine environments.

Combining a Density Gradient of Biomacromolecular Nanoparticles with Biological Effectors in an Electrospun Fiber-Based Nerve Guidance Conduit to Promote Peripheral Nerve Repair.

Peripheral nerve injury is a serious medical problem with limited surgical and clinical treatment options. It is of great significance to integrate multiple guidance cues in one platform of nerve guidance conduits (NGCs) to promote axonal elongation and functional recovery. Here, a multi-functional NGC is constructed to promote nerve regeneration by combining ordered topological structure, density gradient of biomacromolecular nanoparticles, and controlled delivery of biological effectors to provide the topographical, haptotactic, and biological cues, respectively. On the surface of aligned polycaprolactone nanofibers, a density gradient of bioactive nanoparticles capable of delivering recombinant human acidic fibroblast growth factor is deposited. On the graded scaffold, the proliferation of Schwann cells is promoted, and the directional extension of neurites from both PC12 cells and dorsal root ganglions is improved in the direction of increasing particle density. After being implanted in vivo for 6 and 12 weeks to repair a 10-mm rat sciatic nerve defect, the NGC promotes axonal elongation and remyelination, achieving the regeneration of the nerve not only in anatomical structure but also in functional recovery. Taken together, the NGC provides a favorable microenvironment for peripheral nerve regeneration and holds great promise for realizing nerve repair with an efficacy close to autograft.

Formation of RNA adducts resulting from metabolic activation of spice ingredient safrole mediated by P450 enzymes and sulfotransferases.

Safrole (SFL) is an IARC class 2B carcinogen. To better understand the mechanism involved in SFL toxicity, we explored the potential interactions between SFL metabolites and RNA. Three guanosine adducts (G1-G3), two adenosine adducts (A1-A2), and two cytosine adducts (C1-C2) were detected by LC-MS/MS in mouse liver S9 incubations, cultured mouse primary hepatocytes, and liver tissues of mice after exposure to SFL. These adducts were chemically synthesized, and one of the guanosine adducts was structurally characterized by 1H-NMR. Studies in vitro and in vivo showed that SFL was oxidized by cytochrome P450 enzymes to the corresponding 1'-hydroxyl metabolite which was further metabolized by sulfotransferases to form allylic sulfate esters. The formed reactive intermediate(s) subsequently reacted with bases of RNA, leading to RNA adduction, which could play a partial role in the toxicities of SFL through the alteration of RNA biochemical properties and interruption of RNA functions.

Inflammation Intensifies Monocrotaline-Induced Liver Injury.

Pyrrolizidine alkaloids (PAs) are the most common toxins of plant origin, and it is evident that PAs pollute soil, water, nearby plants, and derived foods. Cases of human poisoning due to ingestion of PA-contaminated foods have been reported in several countries. Monocrotaline (MCT) is a pyrrolizidine alkaloid from the plants of Crotalaria genus that causes hepatic and cardiopulmonary toxicities, and the exhibition of the toxicities requires the metabolic activation by CYP3A4 to form electrophilic dehydro-monocrotaline (DHM). The present study demonstrated that myeloperoxidase (MPO) also participated in the bioactivation of MCT. N-Chloromonocrotaline was detected in both HClO/MCT incubations and MPO/H2O2/MgCl2/MCT incubations. DHM-derived N-acetylcysteine (NAC) conjugates were detected in the above incubations fortified with NAC. Lipopolysaccharide-induced inflammation in mice resulted in an elevated level of hepatic MPO activity, increased metabolic activation of MCT, and intensified elevation of serum ALT and AST activity induced by MCT. MPO inhibitor 4-aminobenzoic acid hydrazide was found to reverse these alterations. Mpo-KO mice were resistant to the observed potentiating effect of inflammation on MCT-induced liver injury. In conclusion, inflammation intensified MCT-induced liver injury. MPO participated in the observed potentiating effect of inflammation on the hepatotoxicity induced by MCT.

Modelling epidemic spread in cities using public transportation as a proxy for generalized mobility trends.

We study how public transportation data can inform the modeling of the spread of infectious diseases based on SIR dynamics. We present a model where public transportation data is used as an indicator of broader mobility patterns within a city, including the use of private transportation, walking etc. The mobility parameter derived from this data is used to model the infection rate. As a test case, we study the impact of the usage of the New York City subway on the spread of COVID-19 within the city during 2020. We show that utilizing subway transport data as an indicator of the general mobility trends within the city, and therefore as an indicator of the effective infection rate, improves the quality of forecasting COVID-19 spread in New York City. Our model predicts the two peaks in the spread of COVID-19 cases in NYC in 2020, unlike a standard SIR model that misses the second peak entirely.

Electrospun nanofibers for manipulating soft tissue regeneration.

Soft tissue damage is a common clinical problem that affects the lives of a large number of patients all over the world. It is of great importance to develop functional scaffolds to manipulate and promote the repair and regeneration of soft tissues. Owing to their unique composition and structural properties, electrospun nanofibers have attracted much attention for soft tissue regeneration. Electrospun nanofibers can be easily constructed and functionally modified to regulate their composition, morphology, structure, three-dimensional architecture, and biological functions, as well as specific light/electric/magnetic properties. By integrating multiple types of guidance cues, such as topographical and biochemical cues and external stimuli, electrospun nanofiber scaffolds can be used to manipulate cell behaviors and thus facilitate tissue regeneration. In this review article, we have first described the construction of electrospun nanofibers with specific morphology and topography and their capability of modulating cell migration, cell morphology, and stem cell differentiation. We have then discussed the role of electrospun nanofiber scaffolds in promoting the regeneration of different types of soft tissues, including nerves, skin, heart, blood vessels, and cornea, from the point of view of the anatomical structures and physiological regeneration processes of tissues. By presenting and discussing the recent progress of electrospun nanofibers in manipulating soft tissue regeneration, we hope to provide a possible solution and reference for the repair of tissue damage in clinical practice.

Neural tissue engineering: From bioactive scaffolds and in situ monitoring to regeneration.

Peripheral nerve injury is a large-scale problem that annually affects more than several millions of people all over the world. It remains a great challenge to effectively repair nerve defects. Tissue engineered nerve guidance conduits (NGCs) provide a promising platform for peripheral nerve repair through the integration of bioactive scaffolds, biological effectors, and cellular components. Herein, we firstly describe the pathogenesis of peripheral nerve injuries at different orders of severity to clarify their microenvironments and discuss the clinical treatment methods and challenges. Then, we discuss the recent progress on the design and construction of NGCs in combination with biological effectors and cellular components for nerve repair. Afterward, we give perspectives on imaging the nerve and/or the conduit to allow for the in situ monitoring of the nerve regeneration process. We also cover the applications of different postoperative intervention treatments, such as electric field, magnetic field, light, and ultrasound, to the well-designed conduit and/or the nerve for improving the repair efficacy. Finally, we explore the prospects of multifunctional platforms to promote the repair of peripheral nerve injury.

Hepatic RNA adduction derived from metabolic activation of retrorsine in vitro and in vivo.

Pyrrolizidine alkaloids (PAs) are among the most significant hepatotoxins widely distributed in plant species. Incidence of liver injuries caused by PAs has been reported worldwide, and the reactive metabolites of PAs are known to play a critical role in causing the hepatotoxicity. To better understand the toxicity-induction mechanisms, we explored the interactions of PA metabolites with cellular RNA molecules, and examined their effects on the biochemical and metabolic properties of hepatic RNAs. After exposure to retrorsine, adduction on adenosine and guanosine were detected in mouse liver microsomal incubations, cultured mouse primary hepatocytes, and mouse liver tissues. NMR analysis showed that the exocyclic amino group participated in the adduction. We found drastically altered properties and metabolism of the adducted RNA such as reverse-transcriptability, translatability, and RNase-susceptibility. In addition, endogenous modification of N6-methyladenosine (m6A) was remarkably reduced.

Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer.

Endometrial cancer (EC) is one of the three fatal tumors of the female reproductive system. Epigenetic alterations have been reported to be important in tumorigenesis, especially the chromatin accessibility changes and transcription factor binding differences. However, the regulatory mechanism underlying epigenetic alterations in EC development remains unclear. Here, we identified and characterized transcription factor binding site clustered regions (TFCRs) by integrating chromatin accessibility and transcription factor binding information. We totally identified 78,820 TFCRs and explored the relationship between TFCRs and regulatory elements, gene expression and mutation. Finally, we constructed a bioinformatic framework to identify candidate oncogenes and screened 13 candidate key genes, which may serve as potential diagnostic markers or therapeutic targets of EC.

Mechanistic study of bergamottin-induced inactivation of CYP2C9.

Bergamottin (BGM) is a major furanocoumarin constituent of grapefruit and is reported to have inhibitory effects on cytochrome P450 enzymes. This study investigated the chemical interactions between BGM and the enzyme CYP2C9. BGM exhibited time-, concentration-, and NADPH-dependent inhibition of CYP2C9. Co-incubation with diclofenac, a reversible inhibitor of CYP2C9, attenuated the time-dependent enzyme inhibition. Exhaustive dialysis did not restore enzyme activity post-inhibition. Glutathione (GSH) and catalase/superoxide dismutase failed to reverse BGM-induced CYP2C9 inactivation. A GSH trapping study suggested that BGM was metabolized to an epoxide and/or γ-ketoenal that may have been responsible for the enzyme inactivation. In conclusion, BGM can be characterized as a mechanism-based inactivator of CYP2C9 acting via the formation of an epoxide and/or γ-ketoenal.