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1.
PLoS One ; 19(6): e0305166, 2024.
Article in English | MEDLINE | ID: mdl-38861543

ABSTRACT

CNN has demonstrated remarkable performance in EEG signal detection, yet it still faces limitations in terms of global perception. Additionally, due to individual differences in EEG signals, the generalization ability of epilepsy detection models is week. To address this issue, this paper presents a cross-patient epilepsy detection method utilizing a multi-head self-attention mechanism. This method first utilizes Short-Time Fourier Transform (STFT) to transform the original EEG signals into time-frequency features, then models local information using Convolutional Neural Network (CNN), subsequently captures global dependency relationships between features using the multi-head self-attention mechanism of Transformer, and finally performs epilepsy detection using these features. Meanwhile, this model employs a light multi-head attention mechanism module with an alternating structure, which can comprehensively extract multi-scale features while significantly reducing computational costs. Experimental results on the CHB-MIT dataset show that the proposed model achieves accuracy, sensitivity, specificity, F1 score, and AUC of 92.89%, 96.17%, 92.99%, 94.41%, and 96.77%, respectively. Compared to the existing methods, the method proposed in this paper obtains better performance along with better generalization.


Subject(s)
Electroencephalography , Epilepsy , Neural Networks, Computer , Humans , Epilepsy/diagnosis , Epilepsy/physiopathology , Electroencephalography/methods , Fourier Analysis , Signal Processing, Computer-Assisted , Algorithms
2.
J Am Chem Soc ; 146(21): 14715-14723, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38741481

ABSTRACT

In this work, the chemical reduction of a hybrid pyracylene-hexa-peri-hexabenzocoronene (HPH) nanographene was investigated with different alkali metals (Na, K, Rb) to reveal its remarkable multielectron acceptor abilities. The UV-vis and 1H NMR spectroscopy monitoring of the stepwise reduction reactions supports the existence of all intermediate reduction states up to the hexaanion for HPH. Tuning the experimental conditions enabled the synthesis of the HPH anions with gradually increasing reduction states (up to -5) isolated with different alkali metal ions as crystalline materials. The single-crystal X-ray diffraction structure analysis demonstrates that the highly negatively charged HPH anions (-4 and -5) exhibit a drastic geometry change from boat-shaped (observed in the neutral parent, mono- and dianions) to a chair conformation, which was proved to be fully reversible by NMR spectroscopy. DFT calculations show that this geometry change is induced by an enhanced interaction between the coordinated metal ions and negatively charged HPH core in the chair conformation.

3.
World J Gastrointest Surg ; 16(5): 1280-1290, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38817290

ABSTRACT

BACKGROUND: Robotic surgery (RS) is gaining popularity; however, evidence for abdominoperineal resection (APR) of rectal cancer (RC) is scarce. AIM: To compare the efficacy of RS and laparoscopic surgery (LS) in APR for RC. METHODS: We retrospectively identified patients with RC who underwent APR by RS or LS from April 2016 to June 2022. Data regarding short-term surgical outcomes were compared between the two groups. To reduce the effect of potential confounding factors, propensity score matching was used, with a 1:1 ratio between the RS and LS groups. A meta-analysis of seven trials was performed to compare the efficacy of robotic and laparoscopic APR for RC surgery. RESULTS: Of 133 patients, after propensity score matching, there were 42 patients in each group. The postoperative complication rate was significantly lower in the RS group (17/42, 40.5%) than in the LS group (27/42, 64.3%) (P = 0.029). There was no significant difference in operative time (P = 0.564), intraoperative transfusion (P = 0.314), reoperation rate (P = 0.314), lymph nodes harvested (P = 0.309), or circumferential resection margin (CRM) positive rate (P = 0.314) between the two groups. The meta-analysis showed patients in the RS group had fewer positive CRMs (P = 0.04), lesser estimated blood loss (P < 0.00001), shorter postoperative hospital stays (P = 0.02), and fewer postoperative complications (P = 0.002) than patients in the LS group. CONCLUSION: Our study shows that RS is a safe and effective approach for APR in RC and offers better short-term outcomes than LS.

4.
Bioorg Chem ; 148: 107424, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38728908

ABSTRACT

Pyrazolopyrimidine derivatives, including pyrazolopyrimidines, 6-aminopyrazolopyrimidines, 6-[(formyloxy)methyl]pyrazolopyrimidines, 6-(hydroxymethyl)pyrazolopyrimidine, and 6-(aminomethyl)pyrazolopyrimidines have been successfully prepared and tested against NCI-H226, NPC-TW01, and Jurkat cancer cell lines. Among the tested pyrazolopyrimidine compounds, we found 6-aminopyrazolopyrimidines and 6-(aminomethyl)pyrazolopyrimidines with essential o-ClPh or p-ClPh substituted moieties on N-1 pyrazole ring exhibited the best IC50 inhibition activity for Jurkat cells. Furthermore, optimization of the SAR study on the C-6 position of pyrazolopyrimidine ring demonstrated that 6-(N-substituted-methyl)pyrazolopyrimidines 17b, 17d, and 19d possessed the significant IC50 inhibitory activity for the different leukemia cell lines, especially for Jurkat, K-562, and HL-60. On the other hand, further SAR inhibition and docking model studies revealed that compound 19d, which has a 3-(1H-imidazol-1-yl)propan-1-amino side-chain on the C-6 position, was able to form four hydrogen bonds with residues Ala226, Leu152, and Glu194 and specifically extended into the P1 pocket subsite with Aurora A, resulting in improved inhibitory activity almost similar to SNS-314. To explore the anti-cancer mechanism, compound 19d was measured by Western blot analysis in Jurkat T-cells, however, it showed non-responsibility to Aurora B. For the further structural modifications on the lateral chain of compound 19d, compounds 24 with longer lateral chain were designed and synthesized for testing leukemia cell lines. However, compounds 24 was significantly decrease inhibition potency against leukemia cell lines. Based on the in-vitro results, compounds 17b and 19d could be considered to be the best potential lead drug in our study for the development of new and effective therapies for leukemia treatment. On the other hand, the DHFR inhibition results indicated compound 19d possessed good inhibitory activity and better than the reported naphthalene derivative. Through further comparisons of the model superposition of three-dimensional (3D) conformations in DHFR, compound 19d presented a similar structural alignment to Methotrexate and the reported naphthalene derivative and led to similar drug-like functional relationships. As a results, compound 19d would be a potential DHFR inhibitor for anti-leukemia drug candidate.


Subject(s)
Antineoplastic Agents , Cell Proliferation , Drug Design , Drug Screening Assays, Antitumor , Pyrazoles , Pyrimidines , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Pyrimidines/pharmacology , Pyrimidines/chemistry , Pyrimidines/chemical synthesis , Structure-Activity Relationship , Cell Proliferation/drug effects , Molecular Structure , Pyrazoles/pharmacology , Pyrazoles/chemistry , Pyrazoles/chemical synthesis , Molecular Docking Simulation , Dose-Response Relationship, Drug , Cell Line, Tumor , Leukemia/drug therapy , Leukemia/pathology , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/chemistry
5.
ACS Biomater Sci Eng ; 10(5): 2880-2893, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38630940

ABSTRACT

Cobalt-chromium-molybdenum (CoCrMo) alloys are common wear-exposed biomedical alloys and are manufactured in multiple ways, increasingly using additive manufacturing processes such as laser powder bed fusion (LPBF). Here, we investigate the effect of proteins and the manufacturing process (wrought vs LPBF) and building orientation (LPBF-XY and XZ) on the corrosion, metal release, tribocorrosion, and surface oxide composition by means of electrochemical, mechanical, microscopic, diffractive, and spectroscopic methods. The study was conducted at pH 7.3 in 5 g/L NaCl and 5 mM 2-(N-morpholino) ethanesulfonic acid (MES) buffer, which was found to be necessary to avoid metal phosphate and metal-protein aggregate precipitation. The effect of 10 g/L bovine serum albumin (BSA) and 2.5 g/L fibrinogen (Fbn) was studied. BSA and Fbn strongly enhanced the release of Co, Cr, and Mo and slightly enhanced the corrosion (still in the passive domain) for all CoCrMo alloys and most for LPBF-XZ, followed by LPBF-XY and the wrought CoCrMo. BSA and Fbn, most pronounced when combined, significantly decreased the coefficient of friction due to lubrication, the wear track width and severity of the wear mechanism, and the tribocorrosion for all alloys, with no clear effect of the manufacturing type. The wear track area was significantly more oxidized than the area outside of the wear track. In the reference solution without proteins, a strong Mo oxidation in the wear track surface oxide was indicative of a pH decrease and cell separation of the anodic and cathodic areas. This effect was absent in the presence of the proteins.


Subject(s)
Lasers , Serum Albumin, Bovine , Corrosion , Serum Albumin, Bovine/chemistry , Cattle , Animals , Powders , Fibrinogen/chemistry , Materials Testing , Cobalt/chemistry , Surface Properties , Chromium/chemistry , Vitallium/chemistry
6.
Viruses ; 16(4)2024 04 16.
Article in English | MEDLINE | ID: mdl-38675960

ABSTRACT

Reactivation and infection with cytomegalovirus (CMV) are frequently observed in recipients of solid organ transplants, bone marrow transplants, and individuals with HIV infection. This presents an increasing risk of allograft rejection, opportunistic infection, graft failure, and patient mortality. Among immunocompromised hosts, interstitial pneumonia is the most critical clinical manifestation of CMV infection. Recent studies have demonstrated the potential therapeutic benefits of exosomes derived from mesenchymal stem cells (MSC-exos) in preclinical models of acute lung injury, including pneumonia, ARDS, and sepsis. However, the role of MSC-exos in the pathogenesis of infectious viral diseases, such as CMV pneumonia, remains unclear. In a mouse model of murine CMV-induced pneumonia, we observed that intravenous administration of mouse MSC (mMSC)-exos reduced lung damage, decreased the hyperinflammatory response, and shifted macrophage polarization from the M1 to the M2 phenotype. Treatment with mMSC-exos also significantly reduced the infiltration of inflammatory cells and pulmonary fibrosis. Furthermore, in vitro studies revealed that mMSC-exos reversed the hyperinflammatory phenotype of bone marrow-derived macrophages infected with murine CMV. Mechanistically, mMSC-exos treatment decreased activation of the NF-κB/NLRP3 signaling pathway both in vivo and in vitro. In summary, our findings indicate that mMSC-exo treatment is effective in severe CMV pneumonia by reducing lung inflammation and fibrosis through the NF-κB/NLRP3 signaling pathway, thus providing promising therapeutic potential for clinical CMV infection.


Subject(s)
Disease Models, Animal , Exosomes , Mesenchymal Stem Cells , Muromegalovirus , NF-kappa B , NLR Family, Pyrin Domain-Containing 3 Protein , Signal Transduction , Animals , Exosomes/metabolism , Mesenchymal Stem Cells/metabolism , Mice , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , NF-kappa B/metabolism , Muromegalovirus/physiology , Mice, Inbred C57BL , Macrophages/immunology , Cytomegalovirus Infections/therapy , Cytomegalovirus Infections/virology , Lung/virology , Lung/pathology , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , Herpesviridae Infections/therapy , Herpesviridae Infections/virology , Herpesviridae Infections/immunology , Pneumonia/therapy , Pneumonia/virology
7.
Bioorg Chem ; 147: 107312, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38599053

ABSTRACT

A series of water-soluble PEGylated 1,2,4-triazoles 5-8 were successfully synthesized from methyl 5-(chloromethyl)-1-aryl-1H-1,2,4-triazole-3-carboxylates 1. All of the water-soluble PEGylated 1,2,4-triazoles were characterized by FT-IR and 1H NMR spectroscopy. The solubility, in vitro plasma stability, and anti-inflammatory activity were also determined and compared to original methyl 5-(halomethyl)-1-aryl-1H-1,2,4-triazole-3-carboxylates. For SAR study, all PEGylated 1,2,4-triazoles 5-8 performed potential anti-inflammatory activity on LPS-induced RAW 264.7 cells (IC50 = 3.42-7.81 µM). Moreover, the western blot result showed PEGylated 1,2,4-triazole 7d performed 5.43 and 2.37 folds inhibitory activity over iNOS and COX-2 expressions. On the other hand, the cell viability study revealed PEGylated 1,2,4-triazoles 7 and 8 with PEG molecular weight more than 600 presented better cell safety (cell viability > 95 %). Through the solubility and in vitro plasma stability studies, PEGylated 1,2,4-triazoles 7a-d exhibited higher hydrophilicity and prolonged 2.01 folds of half-life in compound 7d. Furthermore, the in vivo anti-inflammatory and gastric safety results indicated PEGylated 1,2,4-triazole 7d more effectively decreased the inflammatory response in edema and COX-2 expression and exhibited higher gastric safety than Indomethacin. Following the in vitro and in vivo study results, PEGylated 1,2,4-triazole 7d possessed favorable solubility, plasma stability features, safety, and significant anti-inflammatory activity to become the potential water-soluble anti-inflammatory candidate.


Subject(s)
Polyethylene Glycols , Solubility , Triazoles , Water , Triazoles/chemistry , Triazoles/pharmacology , Triazoles/chemical synthesis , Animals , Mice , Water/chemistry , Polyethylene Glycols/chemistry , Structure-Activity Relationship , Edema/drug therapy , Edema/chemically induced , Cyclooxygenase 2/metabolism , Cell Survival/drug effects , RAW 264.7 Cells , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/chemical synthesis , Anti-Inflammatory Agents/chemistry , Molecular Structure , Lipopolysaccharides/pharmacology , Lipopolysaccharides/antagonists & inhibitors , Rats , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Anti-Inflammatory Agents, Non-Steroidal/chemical synthesis , Anti-Inflammatory Agents, Non-Steroidal/chemistry , Male , Dose-Response Relationship, Drug , Carrageenan
8.
Sensors (Basel) ; 24(7)2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38610478

ABSTRACT

With the rapid growth of the Internet of Things (IoT), massive terminal devices are connected to the network, generating a large amount of IoT data. The reliable sharing of IoT data is crucial for fields such as smart home and healthcare, as it promotes the intelligence of the IoT and provides faster problem solutions. Traditional data sharing schemes usually rely on a trusted centralized server to achieve each attempted access from users to data, which faces serious challenges of a single point of failure, low reliability, and an opaque access process in current IoT environments. To address these disadvantages, we propose a secure and dynamic access control scheme for the IoT, named SDACS, which enables data owners to achieve decentralized and fine-grained access control in an auditable and reliable way. For access control, attribute-based control (ABAC), Hyperledger Fabric, and interplanetary file system (IPFS) were used, with four kinds of access control contracts deployed on blockchain to coordinate and implement access policies. Additionally, a lightweight, certificateless authentication protocol was proposed to minimize the disclosure of identity information and ensure the double-layer protection of data through secure off-chain identity authentication and message transmission. The experimental and theoretical analysis demonstrated that our scheme can maintain high throughput while achieving high security and stability in IoT data security sharing scenarios.

9.
Front Neurol ; 15: 1378076, 2024.
Article in English | MEDLINE | ID: mdl-38633533

ABSTRACT

Introduction: In recent years, the use of EEG signals for seizure detection has gained widespread academic attention. Aiming at the problem of overfitting deep learning models due to the small number of EEG signal data during epilepsy detection, this paper proposes an epilepsy detection method that combines data augmentation and deep learning. Methods: First, the Adversarial and Mixup Data Augmentation (AMDA) method is used to realize the data augmentation, which effectively enriches the number of training samples. To further improve the classification accuracy and robustness of epilepsy detection, this paper proposes a one-dimensional convolutional neural network and gated recurrent unit (AM-1D CNN-GRU) network model based on attention mechanism for epilepsy detection. Results and discussion: The experimental results show that the performance of epilepsy detection achieved by using augmented data is significantly improved, and the accuracy, sensitivity, and area under the subject's working characteristic curve are up to 96.06, 95.48%, and 0.9637, respectively. Compared with the non-augmented data, all indicators are increased by more than 6.2%. Meanwhile, the detection performance was significantly improved compared with other epilepsy detection methods. The results of this research can provide a reference for the clinical application of epilepsy detection.

10.
Curr Mol Pharmacol ; 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38494933

ABSTRACT

BACKGROUND: Irritable Bowel Syndrome (IBS) is a prevalent gastrointestinal disorder that significantly diminishes the quality of life for affected individuals. The pathophysiology of IBS remains poorly understood, and available therapeutic options for IBS are limited. The crucial roles of brain-gut interaction, which is mediated by the Hypothalamic-Pituitary-Adrenocortical (HPA) axis and the autonomic nervous system in IBS, have attracted increasing attention. OBJECTIVE: The objective of this study was to examine the impact of paeoniflorin (PF) on anxiety and visceral hypersensitivity in maternal separation-induced IBS-like rats. METHODS: The IBS-like rat model was established through the implementation of Maternal Separation (MS) and subsequently subjected to various doses of PF administered via oral gavage for 14 days. Anxiety-like behavior was evaluated using the Open Field Test (OFT) and Elevated Plus Maze (EPM) test. The assessment of visceral sensitivity involved the utilization of the Abdominal Withdrawal Reflex (AWR) score and electromyographic (EMG) responses of the external oblique muscle in response to colorectal distention. The levels of adrenocorticotropic hormone (ACTH), corticosterone (CORT), and corticotrophin-releasing hormone (CRH) were examined by ELISA. Quantitative real-time PCR (qRT-PCR) and immunofluorescence were employed to detect the expressions of CRH receptors 1 (CRHR1) and 2 (CRHR2). Glucocorticoid receptors (GR), mineralocorticoid receptor (MR), brain-derived neurotrophic factor (BDNF), tyrosine receptor kinase B (TrkB), and phospholipase C γ1 (PLCγ1) were examined by Western blot. RESULTS AND DISCUSSION: The results showed that MS induced anxiety-like behavior and visceral hypersensitivity, while PF treatment attenuated these changes. Furthermore, the HPA axis hyperactivity in MS rats was attenuated by PF treatment, indicated by reduced serum ACTH, CORT, and CRH levels and recovered hippocampal CRHR1 and GR expressions. In addition, PF inhibited BDNF/TrkB signaling by downregulating the protein levels of BDNF, TrkB, and phospho-PLCγ1 in the colon. CONCLUSION: These findings suggest that PF alleviated anxiety and visceral hypersensitivity in MS-induced IBS-like rats, which may be the modulation of HPA axis activity and BDNF/TrkB/PLCγ1 signaling pathway.

11.
Chemistry ; 30(26): e202304145, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38433113

ABSTRACT

Chemical reduction of a [4]cumulene with cesium metal was explored, and the structural changes stemming from electron acquisition are detailed using X-ray crystallography. It is found that the [4]cumulene undergoes dramatic geometric changes upon stepwise reduction, including bending of the cumulenic core and twisting of the endgroups from orthogonal to planar. The structural deformation is consistent with early theoretical reports that suggest that the twisting should occur upon reduction of both even and odd [n]cumulenes. The current results, on the other hand, are inconsistent with a previous experimental study of a [3]cumulene in which the predicted twisting is not observed upon reduction. DFT calculations reveal that the barrier to deformation is an order of magnitude lower in a [3]cumulene than a [4]cumulene, allowing the barrier to be overcome in the solid-state.

12.
Curr Top Med Chem ; 24(8): 667-685, 2024.
Article in English | MEDLINE | ID: mdl-38549525

ABSTRACT

Peptides acquire target affinity based on the combination of residues in their sequences and the conformation formed by their flexible folding, an ability that makes them very attractive biomaterials in therapeutic, diagnostic, and assay fields. With the development of computer technology, computer-aided design and screening of affinity peptides has become a more efficient and faster method. This review summarizes successful cases of computer-aided design and screening of affinity peptide ligands in recent years and lists the computer programs and online servers used in the process. In particular, the characteristics of different design and screening methods are summarized and categorized to help researchers choose between different methods. In addition, experimentally validated sequences are listed, and their applications are described, providing directions for the future development and application of computational peptide screening and design.


Subject(s)
Computer Simulation , Peptides , Ligands , Peptides/chemistry , Drug Design , Computer-Aided Design , Humans
13.
Adv Mater ; 36(23): e2402981, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38513638

ABSTRACT

The photothermal therapeutic effect on tumors located at different subcutaneous depths varies due to the attenuation of light by tissue. Here, based on the wavelength-dependent optical attenuation properties of tissues, the tumor depth is assessed using a multichannel lanthanide nanocomposite. A zeolitic imidazolate framework (ZIF-8)-coated nanocomposite is able to deliver high amounts of the hydrophilic heat shock protein 90 inhibitor epigallocatechin gallate through a hydrogen-bonding network formed by the encapsulated highly polarized polyoxometalate guest. It is superior to both bare and PEGylated ZIF-8 for drug delivery. With the assessment of tumor depth and accumulated amount of nanocomposite by fluorescence, an irradiation prescription can be customized to release sufficient HSP90 inhibitor and generate heat for sensitized photothermal treatment of tumors, which not only ensured therapeutic efficacy but also minimized damage to the surrounding tissues.


Subject(s)
Catechin , Lanthanoid Series Elements , Nanocomposites , Nanocomposites/chemistry , Nanocomposites/therapeutic use , Lanthanoid Series Elements/chemistry , Animals , Catechin/analogs & derivatives , Catechin/chemistry , Mice , Humans , Cell Line, Tumor , Metal-Organic Frameworks/chemistry , Neoplasms/drug therapy , Neoplasms/pathology , Photothermal Therapy , Imidazoles/chemistry , Temperature , Zeolites/chemistry , Drug Carriers/chemistry
14.
Nat Chem ; 16(6): 998-1002, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38448656

ABSTRACT

π-Conjugated macrocycles behave differently from analogous linear chains because their electronic wavefunctions resemble a quantum particle on a ring, leading to aromaticity or anti-aromaticity. [18]Annulene, (CH)18, is the archetypal non-benzenoid aromatic hydrocarbon. Molecules with circuits of 4n + 2 π electrons, such as [18]annulene (n = 4), are aromatic, with enhanced stability and diatropic ring currents (magnetic shielding inside the ring), whereas those with 4n π electrons, such as the dianion of [18]annulene, are expected to be anti-aromatic and exhibit the opposite behaviour. Here we use 1H NMR spectroscopy to re-evaluate the structure of the [18]annulene dianion. We also show that it can be reduced further to an aromatic tetraanion, which has the same shape as the dianion. The crystal structure of the tetraanion lithium salt confirms its geometry and reveals a metallocene-like sandwich, with five Li+ cations intercalated between two [18]annulene tetraanions. We also report a heteroleptic sandwich, with [18]annulene and corannulene tetraanion decks.

15.
Bioinformatics ; 40(3)2024 Mar 04.
Article in English | MEDLINE | ID: mdl-38429953

ABSTRACT

MOTIVATION: Promoters with desirable properties are crucial in biotechnological applications. Generative AI (GenAI) has demonstrated potential in creating novel synthetic promoters with significantly enhanced functionality. However, these methods' reliance on various programming frameworks and specific task-oriented contexts limits their flexibilities. Overcoming these limitations is essential for researchers to fully leverage the power of GenAI to design promoters for their tasks. RESULTS: Here, we introduce GPro (Generative AI-empowered toolkit for promoter design), a user-friendly toolkit that integrates a collection of cutting-edge GenAI-empowered approaches for promoter design. This toolkit provides a standardized pipeline covering essential promoter design processes, including training, optimization, and evaluation. Several detailed demos are provided to reproduce state-of-the-art promoter design pipelines. GPro's user-friendly interface makes it accessible to a wide range of users including non-AI experts. It also offers a variety of optional algorithms for each design process, and gives users the flexibility to compare methods and create customized pipelines. AVAILABILITY AND IMPLEMENTATION: GPro is released as an open-source software under the MIT license. The source code for GPro is available on GitHub for Linux, macOS, and Windows: https://github.com/WangLabTHU/GPro, and is available for download via Zenodo repository at https://zenodo.org/doi/10.5281/zenodo.10681733.


Subject(s)
Algorithms , Software , Promoter Regions, Genetic , Artificial Intelligence
16.
J Cell Mol Med ; 28(7): e18198, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38506093

ABSTRACT

Mounting evidence has highlighted the multifunctional characteristics of glutamine metabolism (GM) in cancer initiation, progression and therapeutic regimens. However, the overall role of GM in the tumour microenvironment (TME), clinical stratification and therapeutic efficacy in patients with ovarian cancer (OC) has not been fully elucidated. Here, three distinct GM clusters were identified and exhibited different prognostic values, biological functions and immune infiltration in TME. Subsequently, glutamine metabolism prognostic index (GMPI) was constructed as a new scoring model to quantify the GM subtypes and was verified as an independent predictor of OC. Patients with low-GMPI exhibited favourable survival outcomes, lower enrichment of several oncogenic pathways, less immunosuppressive cell infiltration and better immunotherapy responses. Single-cell sequencing analysis revealed a unique evolutionary trajectory of OC cells from high-GMPI to low-GMPI, and OC cells with different GMPI might communicate with distinct cell populations through ligand-receptor interactions. Critically, the therapeutic efficacy of several drug candidates was validated based on patient-derived organoids (PDOs). The proposed GMPI could serve as a reliable signature for predicting patient prognosis and contribute to optimising therapeutic strategies for OC.


Subject(s)
Glutamine , Ovarian Neoplasms , Humans , Female , Prognosis , Tumor Microenvironment , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/genetics , Cognition
17.
Metabolomics ; 20(2): 30, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38416246

ABSTRACT

INTRODUCTION: Odontogenic keratocysts (OKCs) are locally aggressive and have a high rate of recurrence, but the pathogenesis of OKCs is not fully understood. We aimed to investigate the serum metabolomic profile of OKCs and discover potential biomarkers. METHODS: Metabolomic analysis was performed on 42 serum samples from 22 OKC patients and 20 healthy controls (HCs) using gas chromatography‒mass spectrometry to identify dysregulated metabolites in the OKC samples. LASSO regression and receiver operating characteristic (ROC) curve analyses were used to select and validate metabolic biomarkers and develop diagnostic models. RESULTS: A total of 73 metabolites were identified in the serum samples, and 24 metabolites were dysregulated in the OKC samples, of which 4 were upregulated. Finally, a diagnostic panel of 10 metabolites was constructed that accurately diagnosed OKCs (sensitivity of 100%, specificity of 100%, area under the curve of 1.00). CONCLUSION: This study is the first to investigate the metabolic characteristics and potential metabolic biomarkers in the serum of OKC patients using GC‒MS. Our study provides further evidence to explore the pathogenesis of OKC.


Subject(s)
Metabolomics , Odontogenic Cysts , Humans , Odontogenic Cysts/diagnosis , Biomarkers , Gas Chromatography-Mass Spectrometry , ROC Curve
18.
Biochem Genet ; 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38379039

ABSTRACT

Psoriasis is a kind of severe immune-mediated systemic skin disorder, becoming a worldwide public health concern. Daturataturin A (DTA), a withanolide compound, exerts excellent anti-inflammatory and anti-proliferative properties. The objective of this study is to elucidate the effect of DTA on psoriasis and its potential mechanism. We established psoriasis-like keratinocytes model by stimulating HaCaT cells with M5 cocktail cytokines including Interleukin (IL)-17A, IL-22, oncostatin M, IL-1α, and tumor necrosis factor-α (TNF-α), followed by intervention with DTA. The potential effects and mechanisms of DTA on psoriasis were evaluated in vitro. DTA was found to be able to inhibit hyperproliferation, promote apoptosis, decrease the release of pro-inflammatory cytokines, downregulate keratin expression, and improve lipid metabolism via regulating the peroxisome proliferator-activated receptor (PPAR) signaling pathway by M5 cocktail cytokines stimulation in HaCaT cells. DTA ameliorated lipid metabolism of psoriasis and exerted the potential anti-psoriasis effects by regulating PPAR pathway in vitro, suggesting that DTA may act as a new therapeutic agent for psoriasis.

19.
In Vivo ; 38(2): 699-709, 2024.
Article in English | MEDLINE | ID: mdl-38418134

ABSTRACT

BACKGROUND/AIM: Evidence suggests that gut microbiota can affect various neurological diseases, including stroke. Stroke patients have an increase in harmful gut bacteria and a decrease in beneficial bacteria. This increases intestinal permeability, increases the risk of infection, and even affects many inflammatory factors. While probiotics may affect stroke prognosis by improving the gut environment. This study aimed to investigate the effect of probiotic Bifico on the neural function in mice after focal cerebral ischemia and explore its mechanisms of action. MATERIALS AND METHODS: A focal cerebral ischemia model was established in mice. Four weeks before modeling, animals were divided into three groups: Stroke plus Vehicle group, Stroke plus Pre-Bifico group and Bifico group. The infarct volume and neurobehaviors were evaluated. Whole-gene expression profiling was performed at different days after treatment (D1, D7, D14, D28) by RNA-seq. Differentially expressed genes (DEGs) were the processed for Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG). Some inflammation and immune related genes were screened and their expression was analyzed. RESULTS: Compared to the Stroke plus Vehicle group and Bifico group, the infarct volume and neurological score were significantly reduced in the Pre-Bifico group. There were 2 DEGs at D1, 193 DEGs at D7, 70 DEGs at D28 between Stroke plus Pre-Bifico group and Stroke plus Vehicle group. For GO analysis, there were 139 significant terms at D7 and 195 at D28. For KEGG, there were 2 significant pathways at D7 and 9 at D28. Among 87 genes related to inflammation and immunity, 6 DEGs were identified. The expression of CCL9 was significantly elevated at most time points after stroke compared to the Stroke plus Vehicle group, while that of CCL6, CXCL10, CD48, CD72 and CLEC7A was highly expressed only in the recovery stage of stroke. CONCLUSION: Oral pre-treatment with Bifico for 28 days can reduce cerebral infarction and promote recovery of neurological function in stroke mice, which may be ascribed to the regulation of immunity and inflammation in the brain.


Subject(s)
Brain Ischemia , Ischemic Stroke , Stroke , Humans , Mice , Animals , Gene Expression Profiling , Stroke/complications , Stroke/genetics , Inflammation/genetics , Brain Ischemia/complications , Brain Ischemia/genetics , Infarction , Transcriptome
20.
Inorg Chem ; 63(21): 9579-9587, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38374612

ABSTRACT

A family of rare-earth complexes [RE(III) = Y, La, Gd, Tb, Dy, and Er] with doubly reduced dibenzo[a,e]cyclooctatetraene (DBCOT) has been synthesized and structurally characterized. X-ray diffraction analysis confirms that all products of the [RE(DBCOT)(THF)4][RE(DBCOT)2] composition consist of the anionic sandwich [RE(DBCOT)2]- and the cationic counterpart [RE(DBCOT)(THF)4]+. Within the sandwich, two elongated π decks are slightly bent toward the metal center (avg. 7.3°) with a rotation angle of 35.9-37.6°. The RE(III) ion is entrapped between the central eight-membered rings of DBCOT2- in a η8 fashion. The trends in the RE-COT bond lengths are consistent with the variations of the ionic radii of RE(III) centers. The 1H NMR spectra of the diamagnetic Y(III) and La(III) analogues illustrate the distinct solution behavior for the cationic and anionic parts in this series. Magnetic measurements for the Dy analogue reveal single-molecule magnetism, which was rationalized by considering the effect of crystal-field splitting for both building units analyzed by electronic structure calculations.

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