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Datta S, Lee K, Paek H, Manion FJ, Ofoegbu N, Du J, Li Y, Huang LC, Wang J, Lin B, Xu H, Wang X. AutoCriteria: a generalizable clinical trial eligibility criteria extraction system powered by large language models. J Am Med Inform Assoc 2024; 31:375-385. [PMID: 37952206 PMCID: PMC10797270 DOI: 10.1093/jamia/ocad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/19/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Abstract
OBJECTIVES We aim to build a generalizable information extraction system leveraging large language models to extract granular eligibility criteria information for diverse diseases from free text clinical trial protocol documents. We investigate the model's capability to extract criteria entities along with contextual attributes including values, temporality, and modifiers and present the strengths and limitations of this system. MATERIALS AND METHODS The clinical trial data were acquired from https://ClinicalTrials.gov/. We developed a system, AutoCriteria, which comprises the following modules: preprocessing, knowledge ingestion, prompt modeling based on GPT, postprocessing, and interim evaluation. The final system evaluation was performed, both quantitatively and qualitatively, on 180 manually annotated trials encompassing 9 diseases. RESULTS AutoCriteria achieves an overall F1 score of 89.42 across all 9 diseases in extracting the criteria entities, with the highest being 95.44 for nonalcoholic steatohepatitis and the lowest of 84.10 for breast cancer. Its overall accuracy is 78.95% in identifying all contextual information across all diseases. Our thematic analysis indicated accurate logic interpretation of criteria as one of the strengths and overlooking/neglecting the main criteria as one of the weaknesses of AutoCriteria. DISCUSSION AutoCriteria demonstrates strong potential to extract granular eligibility criteria information from trial documents without requiring manual annotations. The prompts developed for AutoCriteria generalize well across different disease areas. Our evaluation suggests that the system handles complex scenarios including multiple arm conditions and logics. CONCLUSION AutoCriteria currently encompasses a diverse range of diseases and holds potential to extend to more in the future. This signifies a generalizable and scalable solution, poised to address the complexities of clinical trial application in real-world settings.
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Bo X, Zhao Y, Qin F, Wu F, Tan M, Ju S, Song Z, Li W, He F, Wei Y, Xu H, Huang X. Cytotoxic metabolites from the mangrove endophytic fungus Aspergillus sp. GXNU QG1a. Nat Prod Res 2024:1-8. [PMID: 38226421 DOI: 10.1080/14786419.2024.2303601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]
Abstract
A new benzoquinone, guxiumasperone A (1), and a new diisoprenyl-cyclohexene-type meroterpenoids, biscognienyne M (2), along with four known diisoprenyl-cyclohexene analogues was isolated from the mangrove endophytic fungus Aspergillus QG1a. Their structures were determined by extensive spectral analysis of 1D and 2D NMR, HR-ESI- MS, and X-ray crystallography. Compound 1 was deduced by a single-crystal X-ray diffraction analysis, and the absolute configuration of 2 was further unequivocally elucidated by comparing the experimental electronic circular dichroism (ECD) data with calculated ECD spectra. Compounds 1 and 2 showed significant cytotoxic activity against selected tumour cells. Particularly, compound 2 exhibited strong activity against A2780 cancer cells with an IC50 value of 6.8 μM.
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Wang HC, Xu H. Immediate Hypersensitivity Caused by the Mesotherapy. Facial Plast Surg 2024. [PMID: 38016659 DOI: 10.1055/a-2218-8248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
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A, De Vivie De Regie JB, Dedovich DV, Degens J, Deiana AM, Del Corso F, Del Peso J, Del Rio F, Deliot F, Delitzsch CM, Della Pietra M, Della Volpe D, Dell'Acqua A, Dell'Asta L, Delmastro M, Delsart PA, Demers S, Demichev M, Denisov SP, D'Eramo L, Derendarz D, Derue F, Dervan P, Desch K, Deutsch C, Di Bello FA, Di Ciaccio A, Di Ciaccio L, Di Domenico A, Di Donato C, Di Girolamo A, Di Gregorio G, Di Luca A, Di Micco B, Di Nardo R, Diaconu C, Diamantopoulou M, Dias FA, Vale TDD, Diaz MA, Diaz Capriles FG, Didenko M, Diehl EB, Diehl L, Díez Cornell S, Diez Pardos C, Dimitriadi C, Dimitrievska A, Dingfelder J, Dinu IM, Dittmeier SJ, Dittus F, Djama F, Djobava T, Djuvsland JI, Doglioni C, Dolejsi J, Dolezal Z, Donadelli M, Dong B, Donini J, D'Onofrio A, D'Onofrio M, Dopke J, Doria A, Dos Santos Fernandes N, Dova MT, Doyle AT, Draguet MA, Dreyer E, Drivas-Koulouris I, Drobac AS, Drozdova M, Du D, du Pree TA, Dubinin F, Dubovsky M, Duchovni E, Duckeck G, Ducu OA, Duda D, Dudarev A, Duden ER, 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Zakharchuk N, Zambito S, Zamora Saa JA, Zang J, Zanzi D, Zaplatilek O, Zeitnitz C, Zeng H, Zeng JC, Zenger DT, Zenin O, Ženiš T, Zenz S, Zerradi S, Zerwas D, Zhai M, Zhang B, Zhang DF, Zhang J, Zhang J, Zhang K, Zhang L, Zhang P, Zhang R, Zhang S, Zhang T, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Z, Zhang Z, Zhao H, Zhao P, Zhao T, Zhao Y, Zhao Z, Zhemchugov A, Zheng K, Zheng X, Zheng Z, Zhong D, Zhou B, Zhou H, Zhou N, Zhou Y, Zhu CG, Zhu J, Zhu Y, Zhu Y, Zhuang X, Zhukov K, Zhulanov V, Zimine NI, Zinsser J, Ziolkowski M, Živković L, Zoccoli A, Zoch K, Zorbas TG, Zormpa O, Zou W, Zwalinski L. Observation of WZγ Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector. PHYSICAL REVIEW LETTERS 2024; 132:021802. [PMID: 38277610 DOI: 10.1103/physrevlett.132.021802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/30/2023] [Accepted: 11/08/2023] [Indexed: 01/28/2024]
Abstract
This Letter reports the observation of WZγ production and a measurement of its cross section using 140.1±1.2 fb^{-1} of proton-proton collision data recorded at a center-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. The WZγ production cross section, with both the W and Z bosons decaying leptonically, pp→WZγ→ℓ^{'}^{±}νℓ^{+}ℓ^{-}γ (ℓ^{(^{'})}=e, μ), is measured in a fiducial phase-space region defined such that the leptons and the photon have high transverse momentum and the photon is isolated. The cross section is found to be 2.01±0.30(stat)±0.16(syst) fb. The corresponding standard model predicted cross section calculated at next-to-leading order in perturbative quantum chromodynamics and at leading order in the electroweak coupling constant is 1.50±0.06 fb. The observed significance of the WZγ signal is 6.3σ, compared with an expected significance of 5.0σ.
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Zuo X, Zhou Y, Duke J, Hripcsak G, Shah N, Banda JM, Reeves R, Miller T, Waitman LR, Natarajan K, Xu H. Standardizing Multi-site Clinical Note Titles to LOINC Document Ontology: A Transformer-based Approach. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2024; 2023:834-843. [PMID: 38222429 PMCID: PMC10785935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The types of clinical notes in electronic health records (EHRs) are diverse and it would be great to standardize them to ensure unified data retrieval, exchange, and integration. The LOINC Document Ontology (DO) is a subset of LOINC that is created specifically for naming and describing clinical documents. Despite the efforts of promoting and improving this ontology, how to efficiently deploy it in real-world clinical settings has yet to be explored. In this study we evaluated the utility of LOINC DO by mapping clinical note titles collected from five institutions to the LOINC DO and classifying the mapping into three classes based on semantic similarity between note titles and LOINC DO codes. Additionally, we developed a standardization pipeline that automatically maps clinical note titles from multiple sites to suitable LOINC DO codes, without accessing the content of clinical notes. The pipeline can be initialized with different large language models, and we compared the performances between them. The results showed that our automated pipeline achieved an accuracy of 0.90. By comparing the manual and automated mapping results, we analyzed the coverage of LOINC DO in describing multi-site clinical note titles and summarized the potential scope for extension.
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Ma X, Xu H, Chen X, Zou Q, Wang J, Da Y, Yin H. Modern methods and materials used to treat root perforation: effectiveness comparison. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2024; 35:1. [PMID: 38206373 PMCID: PMC10784354 DOI: 10.1007/s10856-023-06770-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
This study aims to experimentally compare the efficacy of different endodontic materials (iRoot BP Plus, Biodentine, MTA, Rootdent, and Trioxide) in the treatment of pulpitis and perforations on extracted tooth specimens. Additionally, the study aims to investigate the influence of iRoot BP Plus endodontic material on the regenerative processes following pulp amputation in laboratory animals. The secondary goal is to evaluate the effect of iRoot BP Plus on the restoration process in laboratory animals after pulp removal. The study presents a micropermeability analysis of the selected biomaterials performed on a sample of 50 single-rooted apical teeth in 2022. All teeth underwent endodontic treatment. Changes in molar morphology were investigated with eight laboratory animals (rabbits, 3 months old, all males) after simulated pulp removal and subsequent treatment with the iRoot BP Plus biomaterials. iRoot BP Plus appeared to be more effective in retrograde apical root filling than other biomaterials, as evidenced by its higher sealing effect. An experiment involving animal participants revealed the presence of protective adaptive mechanisms, which manifested in the form of an inflammatory process within 6 weeks after the dental pulp was removed. The connective tissue replaced the necrosis, and new capillaries began to form intensively. These dental outcomes suggest that iRoot BP Plus enables hermetical sealing in tooth restoration with good adhesion. Thus, it may have the ability to promote more active tissue regeneration after pulp removal.
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Khan H, Mosa ASM, Paka V, Rana MKZ, Mandhadi V, Islam S, Xu H, McClay JC, Sarker S, Rao P, Waitman LR. Mapping Clinical Documents to the Logical Observation Identifiers, Names and Codes (LOINC) Document Ontology using Electronic Health Record Systems Structured Metadata. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2024; 2023:1017-1026. [PMID: 38222329 PMCID: PMC10785913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
As Electronic Health Record (EHR) systems increase in usage, organizations struggle to maintain and categorize clinical documentation so it can be used for clinical care and research. While prior research has often employed natural language processing techniques to categorize free text documents, there are shortcomings relative to computational scalability and the lack of key metadata within notes' text. This study presents a framework that can allow institutions to map their notes to the LOINC document ontology using a Bag of Words approach. After preliminary manual value- set mapping, an automated pipeline that leverages key dimensions of metadata from structured EHR fields aligns the notes with the dimensions of the document ontology. This framework resulted in 73.4% coverage of EHR documents, while also mapping 132 million notes in less than 2 hours; an order of magnitude more efficient than NLP based methods.
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Chen JX, Yang XQ, Wang XY, Han HL, Cai ZJ, Xu H, Yang YB, Ding ZT. Antifeedant, Antifungal Cryptic Polyketides with Six Structural Frameworks from Tea Endophyte Daldinia eschscholtzii Propelled by the Antagonistic Coculture with Phytopathogen Colletotrichum pseudomajus and Different Culture Methods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:378-389. [PMID: 38156646 DOI: 10.1021/acs.jafc.3c06750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The antagonistic coculture with tea phytopathogen Colletotrichum pseudomajus induces antifungal cryptic metabolites from isogenesis endophyte Daldinia eschscholtzii against tea phytopathogens. Sixteen new polyketides with six structural frameworks including ten cryptic ones, named coldaldols A-C (1-3), collediol (5), and daldinrins A-L (10-20 and 23), were found from the coculture of C. pseudomajus and D. eschscholtzii by different culture methods. The unique framework of compounds 11 and 12 featured a benzopyran-C7 polyketone hybrid, and compounds 13-16 were characterized by the novel benzopyran dimer. The structures were determined mainly by spectroscopic methods, including extensive one-dimensional (1D), two-dimensional (2D) NMR, high resolution electrospray ionisation mass spectroscopy (HRESIMS), ECD calculation, and single-crystal X-ray diffraction. The configuration of acyclic compounds 5 and 18 were determined by application of the universal NMR database. Most compounds showed significant antifungal activities against the tea pathogens C. pseudomajus and Alternaria sp. with MICs of 1-8 μg/mL. Compound 12 had stronger antifungal activity than that of positive drug nystatin. The ether bond at C-4 of the benzopyran derivative increased the antifungal activity. Compounds 4-9 and 11-23 showed antifeedant activities against silkworms with feeding deterrence indices of 15-100% at the concentration of 50 μg/cm2.
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Hu F, Zhu Y, Tian J, Xu H, Xue Q. Single-Cell Sequencing Combined with Transcriptome Sequencing Constructs a Predictive Model of Key Genes in Multiple Sclerosis and Explores Molecular Mechanisms Related to Cellular Communication. J Inflamm Res 2024; 17:191-210. [PMID: 38226354 PMCID: PMC10788626 DOI: 10.2147/jir.s442684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
Background Multiple sclerosis (MS) causes chronic inflammation and demyelination of the central nervous system and comprises a class of neurodegenerative diseases in which interactions between multiple immune cell types mediate the involvement of MS development. However, the early diagnosis and treatment of MS remain challenging. Methods Gene expression profiles of MS patients were obtained from the Gene Expression Omnibus (GEO) database. Single-cell and intercellular communication analyses were performed to identify candidate gene sets. Predictive models were constructed using LASSO regression. Relationships between genes and immune cells were analyzed by single sample gene set enrichment analysis (ssGSEA). The molecular mechanisms of key genes were explored using gene enrichment analysis. An miRNA network was constructed to search for target miRNAs related to key genes, and related transcription factors were searched by transcriptional regulation analysis. We utilized the GeneCard database to detect the correlations between disease-regulated genes and key genes. We verified the mRNA expression of 4 key genes by reverse transcription-quantitative PCR (RT‒qPCR). Results Monocyte marker genes were selected as candidate gene sets. CD3D, IL2RG, MS4A6A, and NCF2 were found to be the key genes by LASSO regression. We constructed a prediction model with AUC values of 0.7569 and 0.719. The key genes were closely related to immune factors and immune cells. We explored the signaling pathways and molecular mechanisms involving the key genes by gene enrichment analysis. We obtained and visualized the miRNAs associated with the key genes using the miRcode database. We also predicted the transcription factors involved. We used validated key genes in MS patients, several of which were confirmed by RT‒qPCR. Conclusion The prediction model constructed with the CD3D, IL2RG, MS4A6A, and NCF2 genes has good diagnostic efficacy and provides new ideas for the diagnosis and treatment of MS.
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Wang W, Ling B, Zhao H, He J, Xu H, Lv J, Wang Q. Effect of esketamine on postpartum depression after labor analgesia and potential mechanisms: a randomized, double-blinded controlled trial. BMC Anesthesiol 2024; 24:4. [PMID: 38166663 PMCID: PMC10759400 DOI: 10.1186/s12871-023-02377-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND To evaluate the effect of esketamine combined with ropivacaine hydrochloride on the occurrence of postpartum depression (PPD) after labor analgesia under epidural analgesia pump and explore the possible mechanisms. METHODS A total of 120 women aged 24 to 36 years old who underwent labor analgesia by epidural analgesia pump, with American Society of Anesthesiologists (ASA) physical status II were enrolled. According to the formula of epidural analgesia pump, all participants were randomly divided into two groups: esketamine group (Group E) and control group (Group C). Epidural anaesthesia were operated in all women between L2 and L3 after cervical dilation up to 2 ~ 3 cm. After successful puncture, the epidural catheter was placed 3.5 cm toward the head and 1% lidocaine was injected for 3 ml. The epidural analgesia pump was connected. Esketamine (0.2 mg/kg) combined with 0.75% ropivacaine hydrochloride (20 ml) were diluted by normal saline up to 100 ml in Group E, when only the equal dose of ropivacaine hydrochloride was used in Group C. The visual analogue scale (VAS) before analgesia (T1), 5 (T2), 10 (T3) and 20 (T4) minutes after analgesia were measured. The duration of the first and second stage of labor, the Apgar score of fetus at delivery, postpartum hemorrhage, consumption of esketamine and ropivacaine were recorded. The incidence of PPD was recorded at 1 week and 6 weeks after delivering. The occurrence of side effects such as nausea and vomiting, dizziness, and nightmares were also recorded for 48 h after delivering. The levels of leptin, norepinephrine(NE), and epinephrine(E) in the peripheral venous blood were measured before labor analgesia and at 24 h, 1 week, and 6 weeks after delivering. RESULTS Compared with Group C, the VAS score at T2, T3 and T4 were significantly lower in Group E (P < 0.01). Compared with Group C, the incidence of PPD was significantly lower at 1 week and 6 weeks after delivering in Group E (P < 0.01). Compared with Group C, the levels of leptin were significantly higher at 24 h and 1 week after delivering in Group E (P < 0.01), while NE and E (P < 0.01) were lower at the same time (P < 0.01). There were no significant difference of the duration of the first and second stage of labor, the Apgar score of fetus at delivery, postpartum hemorrhage, consumption of ropivacaine and the side effects for 48 h after delivering between the two groups. CONCLUSION Esketamine combined with ropivacaine hydrochloride used in labor analgesia can significantly reduce the incidence of postpartum depression after delivering without increasing related side effects, which may be related to the regulation of leptin, norepinephrine, and epinephrine in the serum. TRIAL REGISTRATION The trial was registered at the Chinese Clinical Trial Registry on 30/05/2022 (CTRI registration number-ChiCTR2200060387). URL of registry: https://www.chictr.org.cn/bin/home .
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Xu H, Zhu M, Chen X. Fungal epiphytes differentially regulate salt tolerance of invasive Ipomoea cairica according to salt stress levels. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:4797-4807. [PMID: 38105332 DOI: 10.1007/s11356-023-31540-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Fungal symbionts can improve plant tolerance to salt stress. However, the interaction of epiphytic Fusarium oxysporum and Fusarium fujikuroi with the tolerance of the invasive plant Ipomoea cairica against saline coastal habitats is largely unknown. This study aimed to investigate the interaction of the mixture of the two epiphytic fungi with salt tolerance of I. cairica. Surface-sterilized I. cairica cuttings inoculated (E+) and non-inoculated (E-) with the fungal mixture were cultivated with 2, 3, and 5 parts per thousand (PPT) of NaCl solutions to simulate mild, moderate, and severe salt stress, respectively. The hydroponic experiment showed that the growth inhibition and peroxidation damages of E+ and E- cuttings were aggravated with salinity. Noteworthily, E+ cuttings had higher peroxidase (POD) and catalase (CAT) activities, chlorophyll content, total biomass, aboveground biomass, total shoot length and secondary shoot number, but lower root-to-shoot ratio than E- cuttings under 2 and 3 PPT NaCl conditions. Moreover, E+ had higher superoxide dismutase (SOD) activity and proline content but lower belowground biomass and malondialdehyde (MDA) content than E- cuttings under 3 PPT NaCl condition. However, lower SOD, POD, and CAT activities, and chlorophyll content, but higher MDA content occurred in E+ cuttings than in E- cuttings under 5 PPT NaCl condition. These findings suggested that the mixture of the two epiphytic fungi increased salt tolerance of I. cairica mainly through increasing its antioxidation ability and chlorophyll stability under mildly and moderately saline conditions, but decreased salt tolerance of this plant in an opposite way under severely saline conditions.
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You CZ, Xu H, Zhao FS, Dou J. A Validation Study of CD133 as a Reliable Marker for Identification of Colorectal Cancer Stem-Like Cells. Bull Exp Biol Med 2024; 176:369-375. [PMID: 38340198 DOI: 10.1007/s10517-024-06026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 02/12/2024]
Abstract
Colorectal carcinoma (CRC) is maintained by putative colorectal cancer stem-like cells (CRC-CSCs) that are responsible for CRC metastasis and relapse. Targeting these CSCs can be an effective treatment of CRC. However, reliable identification of CRC-CSCs remains controversial due to the absence of specific markers. It is assumed that glycoprotein CD133 can serve as a useful marker for identification of CRC-CSCs. In this study, we employed CD133 as a marker to identify CRC-CSCs in human (LoVo, HCT116, and SW620) and mouse (CT26) CRC cell lines. In these lines, CD133+ cells were isolated and identified by magnetic-activated cell sorting and flow cytometry. Proliferation, colony formation, and drug resistance of CD133+ cells were analyzed in vitro, and their tumorigenicity was determined in vivo on mice. Proliferation, colony-forming ability, drug resistance, and tumorigenicity of CD133+ cells were higher than those of CD133- cells. Thus, cultured CD133+ cells had the characteristics of CSCs. Hence, glycoprotein CD133 is a reliable marker to identify CRC-CSCs. These results can be used for designing a novel therapeutic target in CRC treatment.
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Savage SR, Zhang Y, Jaehnig EJ, Liao Y, Shi Z, Pham HA, Xu H, Zhang B. IDPpub: Illuminating the Dark Phosphoproteome Through PubMed Mining. Mol Cell Proteomics 2024; 23:100682. [PMID: 37993103 PMCID: PMC10716774 DOI: 10.1016/j.mcpro.2023.100682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Global phosphoproteomics experiments quantify tens of thousands of phosphorylation sites. However, data interpretation is hampered by our limited knowledge on functions, biological contexts, or precipitating enzymes of the phosphosites. This study establishes a repository of phosphosites with associated evidence in biomedical abstracts, using deep learning-based natural language processing techniques. Our model for illuminating the dark phosphoproteome through PubMed mining (IDPpub) was generated by fine-tuning BioBERT, a deep learning tool for biomedical text mining. Trained using sentences containing protein substrates and phosphorylation site positions from 3000 abstracts, the IDPpub model was then used to extract phosphorylation sites from all MEDLINE abstracts. The extracted proteins were normalized to gene symbols using the National Center for Biotechnology Information gene query, and sites were mapped to human UniProt sequences using ProtMapper and mouse UniProt sequences by direct match. Precision and recall were calculated using 150 curated abstracts, and utility was assessed by analyzing the CPTAC (Clinical Proteomics Tumor Analysis Consortium) pan-cancer phosphoproteomics datasets and the PhosphoSitePlus database. Using 10-fold cross validation, pairs of correct substrates and phosphosite positions were extracted with an average precision of 0.93 and recall of 0.94. After entity normalization and site mapping to human reference sequences, an independent validation achieved a precision of 0.91 and recall of 0.77. The IDPpub repository contains 18,458 unique human phosphorylation sites with evidence sentences from 58,227 abstracts and 5918 mouse sites in 14,610 abstracts. This included evidence sentences for 1803 sites identified in CPTAC studies that are not covered by manually curated functional information in PhosphoSitePlus. Evaluation results demonstrate the potential of IDPpub as an effective biomedical text mining tool for collecting phosphosites. Moreover, the repository (http://idppub.ptmax.org), which can be automatically updated, can serve as a powerful complement to existing resources.
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Xu H, Fan Q, Huang M, Cui L, Gao Z, Liu L, Chen Y, Jin J, Jin Q, Wang X. Combination of carrageenan with sodium alginate, gum arabic, and locust bean gum: Effects on rheological properties and quiescent stabilities of partially crystalline emulsions. Int J Biol Macromol 2023; 253:127561. [PMID: 37865364 DOI: 10.1016/j.ijbiomac.2023.127561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
In the present study, carrageenan (CG) was combined with sodium alginate (SA), gum arabic (GA), and locust bean gum (LBG) to obtain four gum combinations (CG, CG + SA, CG + GA, and CG + LBG). The effects of different combinations on rheological properties and quiescent stabilities of PCEs were systematically investigated through characterization of fresh emulsion related parameters (rheological properties, forces between proteins, zeta potentials, surface tensions, interfacial adsorption properties, and multiple light scattering) and storage related parameters (visual appearance, creaming index, viscosities, particle sizes, and microscopic morphology). Rheological results indicated that CG PCEs had the highest apparent viscosities of 7.77-41.91 Pa·s at 0.01 s-1, followed by CG + SA PCEs (2.35-30.62 Pa·s), CG + GA PCEs (2.37-21.16 Pa·s), and CG + LBG PCEs (2.06-19.93 Pa·s). At low thickener concentration (0.02 %), CG PCE exhibited weak gel structure due to higher G' than G″ at all frequencies, while CG + SA, CG + GA, and CG + LBG PCEs had entangled network due to intersection between G' and G″. After three months of storage, CG + SA PCEs showed the lowest creaming index values (11.47-17.75 %), which were significantly lower than CG PCEs (15.35-20.85 %), CG + GA PCEs (15.97-24.42 %), and CG + LBG PCEs (17.13-21.71 %). Meanwhile, all the samples except for 0.02 % CG + SA PCE completely lost fluidity, and their viscosities were above 14,000 mPa·s. It was further found that CG stabilized emulsions showed severe droplet flocculation induced by hydrophobic interactions among adsorbed proteins. Combination of CG with SA, GA, and LBG, especially CG + SA, formed strong network structure and reduced contribution of hydrophobic interactions, which effectively inhibited flocculation of fat droplets, thereby improving rheological properties and storage stabilities of PCEs.
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Aad G, Abbott B, Abeling K, Abicht NJ, Abidi SH, Aboulhorma A, Abramowicz H, Abreu H, Abulaiti Y, Acharya BS, Adam Bourdarios C, Adamczyk L, Addepalli SV, Addison MJ, Adelman J, Adiguzel A, Adye T, Affolder AA, Afik Y, Agaras MN, Agarwala J, Aggarwal A, Agheorghiesei C, Ahmad A, Ahmadov F, Ahmed WS, Ahuja S, Ai X, Aielli G, Aikot A, Ait Tamlihat M, Aitbenchikh B, Aizenberg I, Akbiyik M, Åkesson TPA, Akimov AV, Akiyama D, Akolkar NN, Al Khoury K, Alberghi GL, Albert J, Albicocco P, Albouy GL, Alderweireldt S, Aleksa M, Aleksandrov IN, Alexa C, Alexopoulos T, Alfonsi F, Algren M, Alhroob M, Ali B, Ali HMJ, Ali S, Alibocus SW, Aliev M, Alimonti G, Alkakhi W, Allaire C, Allbrooke BMM, Allen JF, Allendes Flores CA, Allport PP, Aloisio A, Alonso F, Alpigiani C, Alvarez Estevez M, Alvarez Fernandez A, Alves Cardoso M, Alviggi MG, Aly M, Amaral Coutinho Y, Ambler A, Amelung C, Amerl M, Ames CG, Amidei D, Amor Dos Santos SP, Amos KR, Ananiev V, Anastopoulos C, Andeen T, Anders JK, Andrean SY, Andreazza A, Angelidakis S, Angerami A, Anisenkov AV, Annovi A, Antel C, Anthony MT, Antipov E, Antonelli M, Anulli F, Aoki M, Aoki T, Aparisi Pozo JA, Aparo MA, Aperio Bella L, Appelt C, Apyan A, Aranzabal N, Arbiol Val SJ, Arcangeletti C, Arce ATH, Arena E, Arguin JF, Argyropoulos S, Arling JH, Arnaez O, Arnold H, Artoni G, Asada H, Asai K, Asai S, Asbah NA, Assahsah J, Assamagan K, Astalos R, Atashi S, Atkin RJ, Atkinson M, Atmani H, Atmasiddha PA, Augsten K, Auricchio S, Auriol AD, Austrup VA, Avolio G, Axiotis K, Azuelos G, Babal D, Bachacou H, Bachas K, Bachiu A, Backman F, Badea A, Baer TM, Bagnaia P, Bahmani M, Bailey AJ, Bailey VR, Baines JT, Baines L, Baker OK, Bakos E, Bakshi Gupta D, Balakrishnan V, Balasubramanian R, Baldin EM, Balek P, Ballabene E, Balli F, Baltes LM, Balunas WK, Balz J, Banas E, Bandieramonte M, Bandyopadhyay A, Bansal S, Barak L, Barakat M, Barberio EL, Barberis D, Barbero M, Barel MZ, Barends KN, Barillari T, Barisits MS, Barklow T, Baron P, Baron Moreno DA, Baroncelli A, Barone G, Barr AJ, Barr JD, Barranco Navarro L, Barreiro F, Barreiro Guimarães da Costa J, Barron U, Barros Teixeira MG, Barsov S, Bartels F, Bartoldus R, Barton AE, Bartos P, Basan A, Baselga M, Bassalat A, Basso MJ, Basson CR, Bates RL, Batlamous S, Batley JR, Batool B, Battaglia M, Battulga D, Bauce M, Bauer M, Bauer P, Bazzano Hurrell LT, Beacham JB, Beau T, Beaucamp JY, Beauchemin PH, Becherer F, Bechtle P, Beck HP, Becker K, Beddall AJ, Bednyakov VA, Bee CP, Beemster LJ, Beermann TA, Begalli M, Begel M, Behera A, Behr JK, Beirer JF, Beisiegel F, Belfkir M, Bella G, Bellagamba L, Bellerive A, Bellos P, Beloborodov K, Benchekroun D, Bendebba F, Benhammou Y, Benoit M, Bensinger JR, Bentvelsen S, Beresford L, Beretta M, Bergeaas Kuutmann E, Berger N, Bergmann B, Beringer J, Bernardi G, Bernius C, Bernlochner FU, Bernon F, Berrocal Guardia A, Berry T, Berta P, Berthold A, Bertram IA, Bethke S, Betti A, Bevan AJ, Bhalla NK, Bhamjee M, Bhatta S, Bhattacharya DS, Bhattarai P, Bhopatkar VS, Bi R, Bianchi RM, Bianco G, Biebel O, Bielski R, Biglietti M, Bindi M, Bingul A, Bini C, Biondini A, Birch-Sykes CJ, Bird GA, Birman M, Biros M, Biryukov S, Bisanz T, Bisceglie E, Biswal JP, Biswas D, Bitadze A, Bjørke K, Bloch I, Blocker C, Blue A, Blumenschein U, Blumenthal J, Bobbink GJ, Bobrovnikov VS, Boehler M, Boehm B, Bogavac D, Bogdanchikov AG, Bohm C, Boisvert V, Bokan P, Bold T, Bomben M, Bona M, Boonekamp M, Booth CD, Borbély AG, Bordulev IS, Borecka-Bielska HM, Borissov G, Bortoletto D, Boscherini D, Bosman M, Bossio Sola JD, Bouaouda K, Bouchhar N, Boudreau J, Bouhova-Thacker EV, Boumediene D, Bouquet R, Boveia A, Boyd J, Boye D, Boyko IR, Bracinik J, Brahimi N, Brandt G, Brandt O, Braren F, Brau B, Brau JE, Brener R, Brenner L, Brenner R, Bressler S, Britton D, Britzger D, Brock I, Brooijmans G, Brooks WK, Brost E, Brown LM, Bruce LE, Bruckler TL, Bruckman de Renstrom PA, Brüers B, Bruni A, Bruni G, Bruschi M, Bruscino N, Buanes T, Buat Q, Buchin D, Buckley AG, Bulekov O, Bullard BA, Burdin S, Burgard CD, Burger AM, Burghgrave B, Burlayenko O, Burr JTP, Burton CD, Burzynski JC, Busch EL, Büscher V, Bussey PJ, Butler JM, Buttar CM, Butterworth JM, Buttinger W, Buxo Vazquez CJ, Buzykaev AR, Cabrera Urbán S, Cadamuro L, Caforio D, Cai H, Cai Y, Cai Y, Cairo VMM, Cakir O, Calace N, Calafiura P, Calderini G, Calfayan P, Callea G, Caloba LP, Calvet D, Calvet S, Calvet TP, Calvetti M, Camacho Toro R, Camarda S, Camarero Munoz D, Camarri P, Camerlingo MT, Cameron D, Camincher C, Campanelli M, Camplani A, Canale V, Canesse A, Cantero J, Cao Y, Capocasa F, Capua M, Carbone A, Cardarelli R, Cardenas JCJ, Cardillo F, Carducci G, Carli T, Carlino G, Carlotto JI, Carlson BT, Carlson EM, Carminati L, Carnelli A, Carnesale M, Caron S, Carquin E, Carrá S, Carratta G, Carrio Argos F, Carter JWS, Carter TM, Casado MP, Caspar M, Castillo FL, Castillo Garcia L, Castillo Gimenez V, Castro NF, Catinaccio A, Catmore JR, Cavaliere V, Cavalli N, Cavasinni V, Cekmecelioglu YC, Celebi E, Celli F, Centonze MS, Cepaitis V, Cerny K, Cerqueira AS, Cerri A, Cerrito L, Cerutti F, Cervato B, Cervelli A, Cesarini G, Cetin SA, Chadi Z, Chakraborty D, Chan J, Chan WY, Chapman JD, Chapon E, Chargeishvili B, Charlton DG, Charman TP, Chatterjee M, Chauhan C, Chekanov S, Chekulaev SV, Chelkov GA, Chen A, Chen B, Chen B, Chen H, Chen H, Chen J, Chen J, Chen M, Chen S, Chen SJ, Chen X, Chen X, Chen Y, Cheng CL, Cheng HC, Cheong S, Cheplakov A, Cheremushkina E, Cherepanova E, Cherkaoui El Moursli R, Cheu E, Cheung K, Chevalier L, Chiarella V, Chiarelli G, Chiedde N, Chiodini G, Chisholm AS, Chitan A, Chitishvili M, Chizhov MV, Choi K, Chomont AR, Chou Y, Chow EYS, Chowdhury T, Chu KL, Chu MC, Chu X, Chudoba J, Chwastowski JJ, Cieri D, Ciesla KM, Cindro V, Ciocio A, Cirotto F, Citron ZH, Citterio M, Ciubotaru DA, Ciungu BM, Clark A, Clark PJ, Clarry C, Clavijo Columbie JM, Clawson SE, Clement C, Clercx J, Clissa L, Coadou Y, Cobal M, Coccaro A, 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HJ, Yang HT, Yang S, Yang T, Yang X, Yang X, Yang Y, Yang Y, Yang Z, Yao WM, Yap YC, Ye H, Ye H, Ye J, Ye S, Ye X, Yeh Y, Yeletskikh I, Yeo BK, Yexley MR, Yin P, Yorita K, Younas S, Young CJS, Young C, Yu C, Yu Y, Yuan M, Yuan R, Yue L, Zaazoua M, Zabinski B, Zaid E, Zakareishvili T, Zakharchuk N, Zambito S, Zamora Saa JA, Zang J, Zanzi D, Zaplatilek O, Zeitnitz C, Zeng H, Zeng JC, Zenger DT, Zenin O, Ženiš T, Zenz S, Zerradi S, Zerwas D, Zhai M, Zhang B, Zhang DF, Zhang J, Zhang J, Zhang K, Zhang L, Zhang P, Zhang R, Zhang S, Zhang S, Zhang T, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang Z, Zhang Z, Zhao H, Zhao P, Zhao T, Zhao Y, Zhao Z, Zhemchugov A, Zheng J, Zheng K, Zheng X, Zheng Z, Zhong D, Zhou B, Zhou H, Zhou N, Zhou Y, Zhu CG, Zhu J, Zhu Y, Zhu Y, Zhuang X, Zhukov K, Zhulanov V, Zimine NI, Zinsser J, Ziolkowski M, Živković L, Zoccoli A, Zoch K, Zorbas TG, Zormpa O, Zou W, Zwalinski L. Combined Measurement of the Higgs Boson Mass from the H→γγ and H→ZZ^{*}→4ℓ Decay Channels with the ATLAS Detector Using sqrt[s]=7, 8, and 13 TeV pp Collision Data. PHYSICAL REVIEW LETTERS 2023; 131:251802. [PMID: 38181336 DOI: 10.1103/physrevlett.131.251802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 01/07/2024]
Abstract
A measurement of the mass of the Higgs boson combining the H→ZZ^{*}→4ℓ and H→γγ decay channels is presented. The result is based on 140 fb^{-1} of proton-proton collision data collected by the ATLAS detector during LHC run 2 at a center-of-mass energy of 13 TeV combined with the run 1 ATLAS mass measurement, performed at center-of-mass energies of 7 and 8 TeV, yielding a Higgs boson mass of 125.11±0.09(stat)±0.06(syst)=125.11±0.11 GeV. This corresponds to a 0.09% precision achieved on this fundamental parameter of the Standard Model of particle physics.
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Nisati A, Nishu N, Nisius R, Nitschke JE, Nkadimeng EK, Noacco Rosende SJ, Nobe T, Noel DL, Nommensen T, Norfolk MB, Norisam RRB, Norman BJ, Novak J, Novak T, Novotny L, Novotny R, Nozka L, Ntekas K, Nunes De Moura Junior NMJ, Nurse E, Ocariz J, Ochi A, Ochoa I, Oerdek S, Offermann JT, Ogrodnik A, Oh A, Ohm CC, Oide H, Oishi R, Ojeda ML, Okazaki Y, O'Keefe MW, Okumura Y, Seabra LFO, Olivares Pino SA, Oliveira Damazio D, Oliveira Goncalves D, Oliver JL, Olszewski A, Öncel ÖO, O'Neil DC, O'Neill AP, Onofre A, Onyisi PUE, Oreglia MJ, Orellana GE, Orestano D, Orlando N, Orr RS, O'Shea V, Osojnak LM, Ospanov R, Otero Y Garzon G, Otono H, Ott PS, Ottino GJ, Ouchrif M, Ouellette J, Ould-Saada F, Owen M, Owen RE, Oyulmaz KY, Ozcan VE, Ozturk N, Ozturk S, Pacey HA, Pacheco Pages A, Padilla Aranda C, Padovano G, Pagan Griso S, Palacino G, Palazzo A, Palestini S, Pan J, Pan T, Panchal DK, Pandini CE, Panduro Vazquez JG, Pang H, Pani P, Panizzo G, Paolozzi L, Papadatos C, Parajuli S, Paramonov A, Paraskevopoulos C, Paredes Hernandez D, Park TH, Parker MA, Parodi F, Parrish EW, Parrish VA, Parsons JA, Parzefall U, Pascual Dias B, Pascual Dominguez L, Pasquali F, Pasqualucci E, Passaggio S, Pastore F, Pasuwan P, Patel P, Patel UM, Pater JR, Pauly T, Pearkes J, Pedersen M, Pedro R, Peleganchuk SV, Penc O, Pender EA, Peng H, Penski KE, Penzin M, Peralva BS, Peixoto APP, Pereira Sanchez L, Perepelitsa DV, Perez Codina E, Perganti M, Perini L, Pernegger H, Perrin O, Peters K, Peters RFY, Petersen BA, Petersen TC, Petit E, Petousis V, Petridou C, Petrukhin A, Pettee M, Pettersson NE, Petukhov A, Petukhova K, Peyaud A, Pezoa R, Pezzotti L, Pezzullo G, Pham TM, Pham T, Phillips PW, Piacquadio G, Pianori E, Piazza F, Piegaia R, Pietreanu D, Pilkington AD, Pinamonti M, Pinfold JL, Pereira BCP, Pinto Pinoargote AE, Piper KM, Pirttikoski A, Pitman Donaldson C, Pizzi DA, Pizzimento L, Pizzini A, Pleier MA, Plesanovs V, Pleskot V, Plotnikova E, Poddar G, Poettgen R, Poggioli L, Pokharel I, Polacek S, Polesello G, Poley A, Polifka R, Polini A, Pollard CS, Pollock ZB, Polychronakos V, Pompa Pacchi E, Ponomarenko D, Pontecorvo L, Popa S, Popeneciu GA, Poreba A, Portillo Quintero DM, Pospisil S, Postill MA, Postolache P, Potamianos K, Potepa PA, Potrap IN, Potter CJ, Potti H, Poulsen T, Poveda J, Pozo Astigarraga ME, Prades Ibanez A, Pretel J, Price D, Primavera M, Principe Martin MA, Privara R, Procter T, Proffitt ML, Proklova N, Prokofiev K, Proto G, Protopopescu S, Proudfoot J, Przybycien M, Przygoda WW, Puddefoot JE, Pudzha D, Pyatiizbyantseva D, Qian J, Qichen D, Qin Y, Qiu T, Quadt A, Queitsch-Maitland M, Quetant G, Rabanal Bolanos G, Rafanoharana D, Ragusa F, Rainbolt JL, Raine JA, Rajagopalan S, Ramakoti E, Ran K, Rapheeha NP, Rasheed H, Raskina V, Rassloff DF, Rave S, Ravina B, Ravinovich I, Raymond M, Read AL, Readioff NP, Rebuzzi DM, Redlinger G, Reed AS, Reeves K, Reidelsturz JA, Reikher D, Rej A, Rembser C, Renardi A, Renda M, Rendel MB, Renner F, Rennie AG, Resconi S, Ressegotti M, Rettie S, Reyes Rivera JG, Reynolds B, Reynolds E, Rezanova OL, Reznicek P, Ribaric N, Ricci E, Richter R, Richter S, Richter-Was E, Ridel M, Ridouani S, Rieck P, Riedler P, Rijssenbeek M, Rimoldi A, Rimoldi M, Rinaldi L, Rinn TT, Rinnagel MP, Ripellino G, Riu I, Rivadeneira P, Rivera Vergara JC, Rizatdinova F, Rizvi E, Roberts BA, Roberts BR, Robertson SH, Robin M, Robinson D, Robles Gajardo CM, Robles Manzano M, Robson A, Rocchi A, Roda C, Rodriguez Bosca S, Rodriguez Garcia Y, Rodriguez Rodriguez A, Rodríguez Vera AM, Roe S, Roemer JT, Roepe-Gier AR, Roggel J, Røhne O, Rojas RA, Roland CPA, Roloff J, Romaniouk A, Romano E, Romano M, Romero Hernandez AC, Rompotis N, Roos L, Rosati S, Rosser BJ, Rossi E, Rossi E, Rossi LP, Rossini L, Rosten R, Rotaru M, Rottler B, Rougier C, Rousseau D, Rousso D, Roy A, Roy-Garand S, Rozanov A, Rozen Y, Ruan X, Rubio Jimenez A, Ruby AJ, Ruelas Rivera VH, Ruggeri TA, Ruggiero A, Ruiz-Martinez A, Rummler A, Rurikova Z, Rusakovich NA, Russell HL, Russo G, Rutherfoord JP, Rutherford Colmenares S, Rybacki K, Rybar M, Rye EB, Ryzhov A, Sabater Iglesias JA, Sabatini P, Sabetta L, Sadrozinski HFW, Safai Tehrani F, Safarzadeh Samani B, Safdari M, Saha S, Sahinsoy M, Saimpert M, Saito M, Saito T, Salamani D, Salnikov A, Salt J, Salvador Salas A, Salvatore D, Salvatore F, Salzburger A, Sammel D, Sampsonidis D, Sampsonidou D, Sánchez J, Sanchez Pineda A, Sanchez Sebastian V, Sandaker H, Sander CO, Sandesara JA, Sandhoff M, Sandoval C, Sankey DPC, Sano T, Sansoni A, Santi L, Santoni C, Santos H, Santpur SN, Santra A, Saoucha KA, Saraiva JG, Sardain J, Sasaki O, Sato K, Sauer C, Sauerburger F, Sauvan E, Savard P, Sawada R, Sawyer C, Sawyer L, Sayago Galvan I, Sbarra C, Sbrizzi A, Scanlon T, Schaarschmidt J, Schacht P, Schaefer D, Schäfer U, Schaffer AC, Schaile D, Schamberger RD, Scharf C, Schefer MM, Schegelsky VA, Scheirich D, Schenck F, Schernau M, Scheulen C, Schiavi C, Schioppa EJ, Schioppa M, Schlag B, Schleicher KE, Schlenker S, Schmeing J, Schmidt MA, Schmieden K, Schmitt C, Schmitt S, Schoeffel L, Schoening A, Scholer PG, Schopf E, Schott M, Schovancova J, Schramm S, Schroeder F, Schroer T, Schultz-Coulon HC, Schumacher M, Schumm BA, Schune P, Schuy AJ, Schwartz HR, Schwartzman A, Schwarz TA, Schwemling P, Schwienhorst R, Sciandra A, Sciolla G, Scuri F, Sebastiani CD, Sedlaczek K, Seema P, Seidel SC, Seiden A, Seidlitz BD, Seitz C, Seixas JM, Sekhniaidze G, Sekula SJ, Selem L, Semprini-Cesari N, Sengupta D, Senthilkumar V, Serin L, Serkin L, Sessa M, Severini H, Sforza F, Sfyrla A, Shabalina E, Shaheen R, Shahinian JD, Shaked Renous D, Shan LY, Shapiro M, Sharma A, Sharma AS, Sharma P, Sharma S, Shatalov PB, Shaw K, Shaw SM, Shcherbakova A, Shen Q, Sherwood P, Shi L, Shi X, Shimmin CO, Shimogama Y, Shinner JD, Shipsey IPJ, Shirabe S, Shiyakova M, Shlomi J, Shochet MJ, Shojaii J, Shope DR, Shrestha B, Shrestha S, Shrif EM, Shroff MJ, Sicho P, Sickles AM, Sideras Haddad E, Sidoti A, Siegert F, Sijacki D, Sikora R, Sili F, Silva JM, Silva Oliveira MV, Silverstein SB, Simion S, Simoniello R, Simpson EL, Simpson H, Simpson LR, Simpson ND, Simsek S, Sindhu S, Sinervo P, Singh S, Sinha S, Sinha S, Sioli M, Siral I, Sitnikova E, Sivoklokov SY, Sjölin J, Skaf A, Skorda E, Skubic P, Slawinska M, Smakhtin V, Smart BH, Smiesko J, Smirnov SY, Smirnov Y, Smirnova LN, Smirnova O, Smith AC, Smith EA, Smith HA, Smith JL, Smith R, Smizanska M, Smolek K, Snesarev AA, Snider SR, Snoek HL, Snyder S, Sobie R, Soffer A, Solans Sanchez CA, Soldatov EY, Soldevila U, Solodkov AA, Solomon S, Soloshenko A, Solovieva K, Solovyanov OV, Solovyev V, Sommer P, Sonay A, Song WY, Sonneveld JM, Sopczak A, Sopio AL, Sopkova F, Sothilingam V, Sottocornola S, Soualah R, Soumaimi Z, South D, Spagnolo S, Spalla M, Sperlich D, Spigo G, Spina M, Spinali S, Spiteri DP, Spousta M, Staats EJ, Stabile A, Stamen R, Stamenkovic M, Stampekis A, Standke M, Stanecka E, Stange MV, Stanislaus B, Stanitzki MM, Stapf B, Starchenko EA, Stark GH, Stark J, Starko DM, Staroba P, Starovoitov P, Stärz S, Staszewski R, Stavropoulos G, Steentoft J, Steinberg P, Stelzer B, Stelzer HJ, Stelzer-Chilton O, Stenzel H, Stevenson TJ, Stewart GA, Stewart JR, Stockton MC, Stoicea G, Stolarski M, Stonjek S, Straessner A, Strandberg J, Strandberg S, Strauss M, Strebler T, Strizenec P, Ströhmer R, Strom DM, Strom LR, Stroynowski R, Strubig A, Stucci SA, Stugu B, Stupak J, Styles NA, Su D, Su S, Su W, Su X, Sugizaki K, Sulin VV, Sullivan MJ, Sultan DMS, Sultanaliyeva L, Sultansoy S, Sumida T, Sun S, Sun S, Gudnadottir OS, Sur N, Sutton MR, Suzuki H, Svatos M, Swiatlowski M, Swirski T, Sykora I, Sykora M, Sykora T, Ta D, Tackmann K, Taffard A, Tafirout R, Tafoya Vargas JS, Takeva EP, Takubo Y, Talby M, Talyshev AA, Tam KC, Tamir NM, Tanaka A, Tanaka J, Tanaka R, Tanasini M, Tao Z, Tapia Araya S, Tapprogge S, Tarek Abouelfadl Mohamed A, Tarem S, Tariq K, Tarna G, Tartarelli GF, Tas P, Tasevsky M, Tassi E, Tate AC, Tateno G, Tayalati Y, Taylor GN, Taylor W, Teagle H, Tee AS, Teixeira De Lima R, Teixeira-Dias P, Teoh JJ, Terashi K, Terron J, Terzo S, Testa M, Teuscher RJ, Thaler A, Theiner O, Themistokleous N, Theveneaux-Pelzer T, Thielmann O, Thomas DW, Thomas JP, Thompson EA, Thompson PD, Thomson E, Tian Y, Tikhomirov V, Tikhonov YA, Timoshenko S, Timoshyn D, Ting EXL, Tipton P, Tlou SH, Tnourji A, Todome K, Todorova-Nova S, Todt S, Togawa M, Tojo J, Tokár S, Tokushuku K, Toldaiev O, Tombs R, Tomoto M, Tompkins L, Topolnicki KW, Torrence E, Torres H, Torró Pastor E, Toscani M, Tosciri C, Tost M, Tovey DR, Traeet A, Trandafir IS, Trefzger T, Tricoli A, Trigger IM, Trincaz-Duvoid S, Trischuk DA, Trocmé B, Troncon C, Truong L, Trzebinski M, Trzupek A, Tsai F, Tsai M, Tsiamis A, Tsiareshka PV, Tsigaridas S, Tsirigotis A, Tsiskaridze V, Tskhadadze EG, Tsopoulou M, Tsujikawa Y, Tsukerman II, Tsulaia V, Tsuno S, Tsur O, Tsuri K, Tsybychev D, Tu Y, Tudorache A, Tudorache V, Tuna AN, Turchikhin S, Turk Cakir I, Turra R, Turtuvshin T, Tuts PM, Tzamarias S, Tzanis P, Tzovara E, Uchida K, Ukegawa F, Ulloa Poblete PA, Umaka EN, Unal G, Unal M, Undrus A, Unel G, Urban J, Urquijo P, Usai G, Ushioda R, Usman M, Uysal Z, Vacavant L, Vacek V, Vachon B, Vadla KOH, Vafeiadis T, Vaitkus A, Valderanis C, Valdes Santurio E, Valente M, Valentinetti S, Valero A, Valiente Moreno E, Vallier A, Valls Ferrer JA, Van Arneman DR, Van Daalen TR, Van Der Graaf A, Van Gemmeren P, Van Rijnbach M, Van Stroud S, Van Vulpen I, Vanadia M, Vandelli W, Vandenbroucke M, Vandewall ER, Vannicola D, Vannoli L, Vari R, Varnes EW, Varni C, Varol T, Varouchas D, Varriale L, Varvell KE, Vasile ME, Vaslin L, Vasquez GA, Vazeille F, Vazquez Schroeder T, Veatch J, Vecchio V, Veen MJ, Veliscek I, Veloce LM, Veloso F, Veneziano S, Ventura A, Verbytskyi A, Verducci M, Vergis C, Verissimo De Araujo M, Verkerke W, Vermeulen JC, Vernieri C, Vessella M, Vetterli MC, Vgenopoulos A, Viaux Maira N, Vickey T, Vickey Boeriu OE, Viehhauser GHA, Vigani L, Villa M, Villaplana Perez M, Villhauer EM, Vilucchi E, Vincter MG, Virdee GS, Vishwakarma A, Visibile A, Vittori C, Vivarelli I, Vladimirov V, Voevodina E, Vogel F, Vokac P, Von Ahnen J, Von Toerne E, Vormwald B, Vorobel V, Vorobev K, Vos M, Voss K, Vossebeld JH, Vozak M, Vozdecky L, Vranjes N, Vranjes Milosavljevic M, Vreeswijk M, Vuillermet R, Vujinovic O, Vukotic I, Wada S, Wagner C, Wagner JM, Wagner W, Wahdan S, Wahlberg H, Wakasa R, Wakida M, Walder J, Walker R, Walkowiak W, Wall A, Wamorkar T, Wang AZ, Wang C, Wang C, Wang H, Wang J, Wang RJ, Wang R, Wang R, Wang SM, Wang S, Wang T, Wang WT, Wang W, Wang X, Wang X, Wang X, Wang Y, Wang Y, Wang Z, Wang Z, Wang Z, Warburton A, Ward RJ, Warrack N, Watson AT, Watson H, Watson MF, Watton E, Watts G, Waugh BM, Weber C, Weber HA, Weber MS, Weber SM, Wei C, Wei Y, Weidberg AR, Weik EJ, Weingarten J, Weirich M, Weiser C, Wells CJ, Wenaus T, Wendland B, Wengler T, Wenke NS, Wermes N, Wessels M, Whalen K, Wharton AM, White AS, White A, White MJ, Whiteson D, Wickremasinghe L, Wiedenmann W, Wiel C, Wielers M, Wiglesworth C, Wilbern DJ, Wilkens HG, Williams DM, Williams HH, Williams S, Willocq S, Wilson BJ, Windischhofer PJ, Winkel FI, Winklmeier F, Winter BT, Winter JK, Wittgen M, Wobisch M, Wolffs Z, Wölker R, Wollrath J, Wolter MW, Wolters H, Wongel AF, Worm SD, Wosiek BK, Woźniak KW, Wozniewski S, Wraight K, Wu C, Wu J, Wu M, Wu M, Wu SL, Wu X, Wu Y, Wu Z, Wuerzinger J, Wyatt TR, Wynne BM, Xella S, Xia L, Xia M, Xiang J, Xiao X, Xie M, Xie X, Xin S, Xiong J, Xu D, Xu H, Xu L, Xu R, Xu T, Xu Y, Xu Z, Xu Z, Yabsley B, Yacoob S, Yamaguchi N, Yamaguchi Y, Yamashita E, Yamauchi H, Yamazaki T, Yamazaki Y, Yan J, Yan S, Yan Z, Yang HJ, Yang HT, Yang S, Yang T, Yang X, Yang X, Yang Y, Yang Y, Yang Z, Yao WM, Yap YC, Ye H, Ye H, Ye J, Ye S, Ye X, Yeh Y, Yeletskikh I, Yeo BK, Yexley MR, Yin P, Yorita K, Younas S, Young CJS, Young C, Yu Y, Yuan M, Yuan R, Yue L, Zaazoua M, Zabinski B, Zaid E, Zakareishvili T, Zakharchuk N, Zambito S, Zamora Saa JA, Zang J, Zanzi D, Zaplatilek O, Zeitnitz C, Zeng H, Zeng JC, Zenger DT, Zenin O, Ženiš T, Zenz S, Zerradi S, Zerwas D, Zhai M, Zhang B, Zhang DF, Zhang J, Zhang J, Zhang K, Zhang L, Zhang P, Zhang R, Zhang S, Zhang T, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Z, Zhang Z, Zhao H, Zhao P, Zhao T, Zhao Y, Zhao Z, Zhemchugov A, Zheng K, Zheng X, Zheng Z, Zhong D, Zhou B, Zhou H, Zhou N, Zhou Y, Zhu CG, Zhu J, Zhu Y, Zhu Y, Zhuang X, Zhukov K, Zhulanov V, Zimine NI, Zinsser J, Ziolkowski M, Živković L, Zoccoli A, Zoch K, Zorbas TG, Zormpa O, Zou W, Zwalinski L. Search for Dark Photons in Rare Z Boson Decays with the ATLAS Detector. PHYSICAL REVIEW LETTERS 2023; 131:251801. [PMID: 38181367 DOI: 10.1103/physrevlett.131.251801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/11/2023] [Indexed: 01/07/2024]
Abstract
A search for events with a dark photon produced in association with a dark Higgs boson via rare decays of the standard model Z boson is presented, using 139 fb^{-1} of sqrt[s]=13 TeV proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider. The dark boson decays into a pair of dark photons, and at least two of the three dark photons must each decay into a pair of electrons or muons, resulting in at least two same-flavor opposite-charge lepton pairs in the final state. The data are found to be consistent with the background prediction, and upper limits are set on the dark photon's coupling to the dark Higgs boson times the kinetic mixing between the standard model photon and the dark photon, α_{D}ϵ^{2}, in the dark photon mass range of [5, 40] GeV except for the ϒ mass window [8.8, 11.1] GeV. This search explores new parameter space not previously excluded by other experiments.
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Chen XH, Ding LN, Zong XY, Xu H, Wang WB, Ding R, Qu B. The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications. Gene 2023; 888:147760. [PMID: 37661026 DOI: 10.1016/j.gene.2023.147760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023]
Abstract
Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.
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Gu Y, Xu H, Yang J, Li R. An improved memetic algorithm to solve the energy-efficient distributed flexible job shop scheduling problem with transportation and start-stop constraints. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:21467-21498. [PMID: 38124606 DOI: 10.3934/mbe.2023950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In the current global cooperative production environment, modern industries are confronted with intricate production plans, demanding the adoption of contemporary production scheduling strategies. Within this context, distributed manufacturing has emerged as a prominent trend. Manufacturing enterprises, especially those engaged in activities like automotive mold production and welding, are facing a significant challenge in managing a significant amount of small-scale tasks characterized by short processing times. In this situation, it becomes imperative to consider the transportation time of jobs between machines. This paper simultaneously considers the transportation time of jobs between machines and the start-stop operation of the machines, which is the first time to our knowledge. An improved memetic algorithm (IMA) is proposed to solve the multi-objective distributed flexible job shop scheduling problem (MODFJSP) with the goal of minimizing maximum completion time and energy consumption. Then, a new multi-start simulated annealing algorithm is proposed and integrated into the IMA to improve the exploration ability and diversity of the algorithm. Furthermore, a new multiple-initialization rule is designed to enhance the quality of the initial population. Additionally, four improved variable neighborhood search strategies and two energy-saving strategies are designed to enhance the search ability and reduce energy consumption. To verify the effectiveness of the IMA, we conducted extensive testing and comprehensive evaluation on 20 instances. The results indicate that, when faced with the MODFJSP, the IMA can achieve better solutions in almost all instances, which is of great significance for the improvement of production scheduling in intelligent manufacturing.
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Hu Y, Chen Y, Xu H. Towards More Generalizable and Accurate Sentence Classification in Medical Abstracts with Less Data. JOURNAL OF HEALTHCARE INFORMATICS RESEARCH 2023; 7:542-556. [PMID: 37927376 PMCID: PMC10620359 DOI: 10.1007/s41666-023-00141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/12/2023] [Accepted: 07/28/2023] [Indexed: 11/07/2023]
Abstract
With the unprecedented growth of biomedical publications, it is important to have structured abstracts in bibliographic databases (i.e., PubMed), thus, to facilitate the information retrieval and knowledge synthesis in needs of researchers. Here, we propose a few-shot prompt learning-based approach to classify sentences in medical abstracts of randomized clinical trials (RCT) and observational studies (OS) to subsections of Introduction, Background, Methods, Results, and Conclusion, using an existing corpus of RCT (PubMed 200k/20k RCT) and a newly built corpus of OS (PubMed 20k OS). Five manually designed templates in a combination of 4 BERT model variants were tested and compared to a previous hierarchical sequential labeling network architecture and traditional BERT-based sentence classification method. On the PubMed 200k and 20k RCT datasets, we achieved overall F1 scores of 0.9508 and 0.9401, respectively. Under few-shot settings, we demonstrated that only 20% of training data is sufficient to achieve a comparable F1 score by the HSLN model (0.9266 by us and 0.9263 by HSLN). When trained on the RCT dataset, our method achieved a 0.9065 F1 score on the OS dataset. When trained on the OS dataset, our method achieved a 0.9203 F1 score on the RCT dataset. We show that the prompt learning-based method outperformed the existing method, even when fewer training samples were used. Moreover, the proposed method shows better generalizability across two types of medical publications when compared with the existing approach. We make the datasets and codes publicly available at: https://github.com/YanHu-or-SawyerHu/prompt-learning-based-sentence-classifier-in-medical-abstracts.
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Xu H, Wang Y, Gao H. [Advances in pathophysiology, diagnosis and treatment of adult severe-associated thrombotic microangiopathy]. ZHONGHUA WEI ZHONG BING JI JIU YI XUE 2023; 35:1335-1339. [PMID: 38149400 DOI: 10.3760/cma.j.cn121430-20230808-00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Thrombotic microangiopathy (TMA) is a group of highly heterogeneous, acute and severe clinicopathological syndromes, characterized by microangiopathic hemolytic anemia (MAHA), thrombocytopenia and ischemic injury of end organs. TMA has the characteristics of dangerous condition, multiple organ involvement and high mortality. Patients with severe TMA need to be admitted to intensive care unit (ICU) for organ function support therapy. Early and rapid evaluation, differential diagnosis, and timely and effective treatment are the key to improve the prognosis of TMA patients. Here, we review the pathophysiological changes, diagnosis differential diagnosis, and treatment of the severe TMA in adult.
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Duan C, Liu H, Yang X, Liu J, Deng Y, Wang T, Xing J, Hu Z, Xu H. Sirtuin1 inhibits calcium oxalate crystal-induced kidney injury by regulating TLR4 signaling and macrophage-mediated inflammatory activation. Cell Signal 2023; 112:110887. [PMID: 37717713 DOI: 10.1016/j.cellsig.2023.110887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Sirtuin1 (Sirt1) activation significantly attenuated calcium oxalate (CaOx) crystal deposition and renal inflammatory injury by regulating renal immune microenvironment. Here, to elucidate the molecular mechanism underlying the therapeutic effects of Sirt1 on macrophage related inflammation and tubular epithelial cells (TECs) necrosis, we constructed a macrophage and CaOx monohydrate (COM)-stimulated tubular cell co-culture system to mimic immune microenvironment in kidney and established a mouse model of CaOx nephrocalcinosis in wild-type and myeloid-specific Sirt1 knockout mice. Target prediction analyses of Gene Expression Omnibus Datasets showed that only miR-34b-5p is regulated by lipopolysaccharides and upregulated by SRT1720 and targets the TLR4 3'-untranslated region. In vitro, SRT1720 suppressed TLR4 expression and M1 macrophage polarization and decreased reactive oxygen species (ROS) production and mitochondrial damage in COM-stimulated TECs by targeting miR-34b-5p. Mechanically, Sirt1 promoted miR-34b-5p expression by suppressing the tri-methylation of H3K27, which directly bound to the miR-34b-5p promoter and abolished the miR-34b-5p transcription. Furthermore, loss of Sirt1 aggravated CaOx nephrocalcinosis-induced inflammatory and oxidative kidney injury, while AgomiR-34b reversed these effects. Therefore, our data suggested that Sirt1 inhibited TLR4 signaling and M1 macrophage polarization and decreased inflammatory and oxidative injury of TECs in vitro and in vivo.
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Yang T, Zhao F, Zhao J, Geng J, Shao C, Liu J, Sheng F, Zhou L, Xu H, Jia R. Negatively charged bladder acellular matrix loaded with positively charged adipose-derived mesenchymal stem cell-derived small extracellular vesicles for bladder tissue engineering. J Control Release 2023; 364:718-733. [PMID: 37944669 DOI: 10.1016/j.jconrel.2023.10.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/19/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
Adipose-derived mesenchymal stem cell-derived small extracellular vesicles (Ad-MSC-sEVs/AMEs) combined with scaffold materials are used in tissue-engineered bladders; however, the lack of retention leads to limited distribution of AMEs in the scaffold areas and low bioavailability of AMEs after bladder reconstruction. To improve retention of AMEs, we developed a novel strategy that modifies the surface charge of the bladder acellular matrix (BAM) via oxidative self-polymerization of dopamine-reducing graphene oxide (GO) and AMEs using ε-polylysine-polyethylene-distearyl phosphatidylethanolamine (PPD). We evaluated two BAM surface modification methods and evaluated the biocompatibility of materials and PPD and electrostatic adherence effects between PPD-modified AMEs and rGO-PDA/BAM in vivo and in vitro. Surface modification increased retention of AMEs, enhanced regeneration of bladder structures, and increased electrical conductivity of rGO-PDA/BAM, thereby improving bladder function recovery. RNA-sequencing revealed 543 miRNAs in human AMEs and 514 miRNAs in rat AMEs. A Venn diagram was used to show target genes of miRNA with the highest proportion predicted by the four databases; related biological processes and pathways were predicted by KEGG and GO analyses. We report a strategy for improving bioavailability of AMEs for bladder reconstruction and reveal that enriched miR-21-5p targets PIK3R1 and activates the PI3K/Akt pathway to promote cell proliferation and migration.
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Xu H, Chen X, Qian P, Li F. A two-stage segmentation of sublingual veins based on compact fully convolutional networks for Traditional Chinese Medicine images. Health Inf Sci Syst 2023; 11:19. [PMID: 37035725 PMCID: PMC10079802 DOI: 10.1007/s13755-023-00214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/19/2023] [Indexed: 04/08/2023] Open
Abstract
As one of the key methods of Traditional Chinese Medicine inspection, tongue diagnosis manifests the advantages of simplicity and directness. Sublingual veins can provide essential information about human health. In order to automate tongue diagnosis, sublingual veins segmentation has become one important issue in the field of Chinese medicine medical image processing. At present, the primary methods for sublingual veins segmentation are traditional feature engineering methods and the feature representation methods represented by deep learning. The former, which mainly based on colour space, belongs to unsupervised classification method. The latter, which includes U-Net and other deep neural network models, belongs to supervised classification method. Current feature engineering methods can only capture low dimensional information, which makes it difficult to extract efficient features for sublingual veins. On the other hand, current deep learning methods use down-sampling structures, which manifest weak robustness and low accuracy. So, it is difficult for current segmentation approaches to recognize tiny branches of sublingual veins. To overcome the above limits, this paper proposes a novel two-stage semantic segmentation method for sublingual veins. In the first stage, a fully convolutional network without down-sampling is used to realize the accurate segmentation of the tongue that includes the sublingual veins to be segmented in the next stage. During the tongue segmentation, the proposed networks can effectively reduce the loss of medical images spatial feature information. At the same time, in order to expand the receptive field, the dilated convolution has been introduced to the proposed networks, which can capture multi-scale information of segmentation images. In the second stage, another fully convolutional network has been used to segment the sublingual veins on the base of the results from the first stage. In this model, proper dilated convolutional rates have been selected to avoid gridding issue. In order to keep the quality of the images to be segmented, several particular data pre-processing and post-processing have been used, which includes specular highlight removal, data augmentation, erosion and dilation. Finally, in order to evaluate the performance of the proposed model, segmentation results have been compared with the state-of-the-art methods on the base of the dataset from Shanghai University of Traditional Chinese Medicine. The effectiveness of sublingual veins segmentation has been proved.
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Gao W, Lu Y, Huang O, Chen X, He J, Chen W, Li Y, Xu H, Wu J, Shen K. Safety analysis of immediate breast reconstruction with a deep inferior epigastric perforator (DIEP) flap in the post-COVID-19 era: a comparison between pre- and post-pandemic cohorts. Gland Surg 2023; 12:1475-1484. [PMID: 38107490 PMCID: PMC10721559 DOI: 10.21037/gs-23-143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/17/2023] [Indexed: 12/19/2023]
Abstract
Background The demand for immediate breast reconstruction with a deep inferior epigastric perforator (DIEP) flap is recovering as coronavirus disease 2019 (COVID-19) transitions from a pandemic to an endemic. This study sought to evaluate the safety of resuming DIEP flap reconstruction in the post-COVID-19 era. Methods Consecutive breast cancer patients who underwent immediate breast reconstruction with a DIEP flap at the Comprehensive Breast Health Center, Ruijin Hospital were retrospectively included in the study. The patients were divided into a post-pandemic group (Group A) and a pre-pandemic group (Group B). The clinicopathological factors, surgical procedures, and rates of post-operative complications were compared between the two groups using the Mann-Whitney U test and Chi-squared test. Results A total of 167 patients were included in the study, of whom 119 (71.3%) were in Group A and 48 (28.7%) were in Group B. The two groups had similar clinicopathological features, including age (P=0.988), body mass index (P=0.504), and tumor, node, metastasis (TNM) stage (P=0.932). The Group A patients were more likely to receive single perforator DIEP flap transplantation than the Group B patients (n=28, 22.8% vs. n=3, 5.8%, P=0.007). There was a numerical decrease in the mean operating time of Group A patients compared to Group B patients (9.82 vs. 10.12 hours, P=0.172). The mean length of stay after the surgery was significantly shorter after the pandemic than before the pandemic (11.2 vs. 14.3 days, P<0.001). The complication rates between the two groups were similar. Conclusions This study provides evidence that resuming DIEP reconstruction is safe in the post-COVID-19 era.
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Ling B, Zhu Y, Yan Z, Chen H, Xu H, Wang Q, Yu W, Wang W. Effect of single intravenous injection of esketamine on postpartum depression after labor analgesia and potential mechanisms: a randomized, double-blinded controlled trial. BMC Pharmacol Toxicol 2023; 24:66. [PMID: 37996953 PMCID: PMC10668401 DOI: 10.1186/s40360-023-00705-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The study was designed to investigate effects of single intravenous injection of esketamine on the incidence of postpartum depression (PPD) after labor analgesia and explore the potential mechanisms. METHODS A total of 120 women who underwent labor analgesia by epidural analgesia pump were enrolled and divided into two groups randomly. Esketamine at a dose of 0.2 mg/kg was intravenously injected after fetal disengagement in the test group and placebo was administered in the control group. The occurrence of PPD and side effects after delivery were recorded. Some indicators related to stress and inflammation were measured before labor analgesia and at 24 h, 1 week, and 6 weeks after delivery in this study. Data were analyzed by independent t-test, repeated measures analysis of variance and Chi-square test in SPSS software (version 25.0). It was considered statistically significant since a p value less than 0.05. RESULTS The incidence of PPD was significantly decreased both for one week and six weeks after delivery by using of esketamine (3.4% vs. 15.3%, p = 0.004 and 5.2% vs. 18.6%, p = 0.006, respectively). There were also significant differences between the stress and inflammation-related indicators in different time points in this study, while the side effects for 48 h after delivery were similar between the two groups. CONCLUSIONS Single intravenous injection of esketamine after delivery in participants underwent labor analgesia can decrease the occurrence of postpartum depression for one week and six weeks after delivery, while the side effects were not increased. The antidepressant effects of esketamine may be related to the reduction of stress response and inflammation. TRIAL REGISTRATION The trial was registered at the Chinese Clinical Trial Registry on 5/30/2022 (CTRI registration number-ChiCTR2200060387). URL of registry: https://www.chictr.org.cn/bin/home .
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