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Article ; Online: Pyogenic liver abscess caused by extended-spectrum β-lactamase-producing hypervirulent diagnosed by third-generation sequencing

Ting Zhang / Xiangyun Huang / Tianmin Xu / Shuo Li / Manman Cui

Journal of International Medical Research, Vol

a case report and literature review

2023 Volume 51

Abstract: We report a case of a woman with diabetes mellitus and choledocholithiasis who had a low fever with chills and severe weakness for 7 days. The patient’s abdominal tenderness was positive. Computed tomography and magnetic resonance imaging showed a giant ... ...

Abstract	We report a case of a woman with diabetes mellitus and choledocholithiasis who had a low fever with chills and severe weakness for 7 days. The patient’s abdominal tenderness was positive. Computed tomography and magnetic resonance imaging showed a giant abscess in the liver. The production of extended-spectrum β-lactamases by hypervirulent Klebsiella pneumoniae was found in the purulent fluid of the liver by nanopore-based metagenomic third-generation sequencing combined with an antibiotic susceptibility test. The patient recovered after intravenous antibiotic therapy and percutaneous drainage. Patients with a history of diabetes mellitus and choledocholithiasis should be aware of the possibility of pyogenic liver abscesses caused by hypervirulent Klebsiella pneumoniae . To rapidly control the development of this disease, nanopore-based metagenomic third-generation sequencing plays an important role not only in rapidly identifying pathogens, but also in guiding the use of antibiotics.
Keywords	Medicine (General) ; R5-920
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Vertical changes in the hard tissues after space closure by miniscrew sliding mechanics

Hong Su / Zimeng Zhuang / Bing Han / Tianmin Xu / Gui Chen

Head & Face Medicine, Vol 19, Iss 1, Pp 1-

a three-dimensional modality analysis

2023 Volume 8

Abstract: Abstract Objectives This study aimed to investigate vertical changes in the maxillary central incisor and the maxillary first molar, along with alterations in the mandibular plane angle during space closure using miniscrew sliding mechanics. Methods ... ...

Abstract	Abstract Objectives This study aimed to investigate vertical changes in the maxillary central incisor and the maxillary first molar, along with alterations in the mandibular plane angle during space closure using miniscrew sliding mechanics. Methods Twenty adult patients treated at Peking University Hospital of Stomatology between 2008 and 2013 were included. Digital dental models and craniofacial cone-beam computed tomography (CBCT) scans were obtained at the start of treatment (T0) and immediately after space closure (T1). Stable miniscrews were used for superimposing maxillary digital dental models (T0 and T1), and vertical changes in the maxillary first molar and the maxillary central incisor were measured. Three-dimensional changes in the mandibular plane were assessed through CBCT superimposition. Results The maxillary central incisor exhibited an average extrusion of 2.56 ± 0.18 mm, while the maxillary first molar showed an average intrusion of 1.25 ± 1.11 mm with a distal movement of 0.97 ± 0.99 mm. Additionally, the mandibular plane angle decreased by an average of 0.83 ± 1.65°. All three indices exhibited statistically significant differences. Conclusion During space closure using the miniscrew sliding technique, significant changes occurred in both the sagittal and vertical dimensions of the upper dentition. This included extrusion of the maxillary central incisors, intrusion of the maxillary first molars, and a slight counterclockwise rotation of the mandibular plane.
Keywords	Miniscrew ; Sliding mechanics ; Space closure ; Vertical change ; Specialties of internal medicine ; RC581-951
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hydroxymethylation and tumors

Tianmin Xu / Haoyue Gao

Human Genomics, Vol 14, Iss 1, Pp 1-

can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?

2020 Volume 10

Abstract: Abstract 5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine ... ...

Abstract	Abstract 5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine bases of recent years. Unlike 5mC, global 5hmC levels vary from tissues that have differential distribution both in mammalian tissues and in the genome. DNA hydroxymethylation is the process that 5mC oxidates into 5hmC with the catalysis of TET (ten-eleven translocation) enzymes. It is an essential option of DNA demethylation, which modulates gene expression by adjusting the DNA methylation level. Various factors can regulate the demethylation of DNA, such as environmental toxins and mental stress. In this review, we summarize the progress in the formation of 5hmC, and obtaining 5hmC in a cell-free DNA sample presents multiple advantages and challenges for the subject. Furthermore, the clinical potential for 5hmC modification in dealing with cancer early diagnosis, prognostic evaluation, and prediction of therapeutic effect is also mentioned.
Keywords	5-Hydroxymethylcytosine ; 5-Methylcytosine ; DNA demethylation ; Cancer epigenetics ; Cell-free DNA ; Medicine ; R ; Genetics ; QH426-470
Subject code	612
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigating the Underlying Mechanisms of Circular RNAs and Their Application in Clinical Research of Cervical Cancer

Jian Liu / He Zhu / Li Fu / Tianmin Xu

Frontiers in Genetics, Vol

2021 Volume 12

Abstract: Circular RNAs (circRNAs) are non-coding RNA molecules, and these are differentially expressed in various diseases, including cancer, suggesting that circRNAs can regulate certain diseases. CircRNAs can act as miRNAs sponges, RNA-binding protein (RBP) ... ...

Abstract	Circular RNAs (circRNAs) are non-coding RNA molecules, and these are differentially expressed in various diseases, including cancer, suggesting that circRNAs can regulate certain diseases. CircRNAs can act as miRNAs sponges, RNA-binding protein (RBP) sponges, and translation regulators, and they can become an important part of the regulation of gene expression. Furthermore, because of their biomedical features in body fluids, such as high abundance, conservation, and stability, circRNAs are seen as potential biomarkers for various cancers. Cervical cancer (CC) is one of the main causes of cancer-related death in women, and there have been a large number of studies that analyze circRNAs as a new object to be evaluated in CC. Therefore, this review, by understanding the role of circRNAs in CC, may create innovative strategies in the future clinical diagnosis, treatment, and prognosis of CC and promote the development of personalized and highly accurate cancer therapy.
Keywords	cervical cancer ; circRNAs ; precision medicine ; molecular marker ; miRNAs sponges ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Progress and Clinical Application of Single-Cell Transcriptional Sequencing Technology in Cancer Research

Jian Liu / Tianmin Xu / Yuemei Jin / Bingyu Huang / Yan Zhang

Frontiers in Oncology, Vol

2021 Volume 10

Abstract: Cancer has been a daunting challenge for human beings because of its clonal heterogeneity and compositional complexity. Tumors are composed of cancer cells and a variety of non-cancer cells, which together with the extracellular matrix form the tumor ... ...

Abstract	Cancer has been a daunting challenge for human beings because of its clonal heterogeneity and compositional complexity. Tumors are composed of cancer cells and a variety of non-cancer cells, which together with the extracellular matrix form the tumor microenvironment. These cancer-related cells and components and immune mechanisms can affect the development and progression of cancer and are associated with patient diagnosis, treatment and prognosis. As the first choice for the study of complex biological systems, single-cell transcriptional sequencing (scRNA-seq) has been widely used in cancer research. ScRNA-seq has made breakthrough discoveries in tumor heterogeneity, tumor evolution, metastasis and spread, development of chemoresistance, and the relationship between the tumor microenvironment and the immune system. These results will guide clinical cancer treatment and promote personalized and highly accurate cancer treatment. In this paper, we summarize the latest research progress of scRNA-seq and its guiding significance for clinical treatment.
Keywords	scRNA-seq ; precision medicine ; tumor heterogeneity ; tumor microenvironment ; cancer cells ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Subject code	610
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Accuracy and reliability of maxillary digital model (MDM) superimposition in evaluating teeth movement in adults compared with CBCT maxillary superimposition

Yichen Pan / Xin Wang / Fanfan Dai / Gui Chen / Tianmin Xu

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 8

Abstract: Abstract Superimposition of 3D maxillary digital dental models of different time points based on palatal vault region has been used to evaluate tooth movement during orthodontic treatment. This study evaluated the accuracy and reliability of 3D maxillary ...

Abstract	Abstract Superimposition of 3D maxillary digital dental models of different time points based on palatal vault region has been used to evaluate tooth movement during orthodontic treatment. This study evaluated the accuracy and reliability of 3D maxillary digital model (MDM) superimposition in adults by comparing it with CBCT maxillary superimposition. In CBCT maxillary superimposition, voxel-based superimposition was firstly conducted, and MDMs were matched with corresponding CBCT models (CBCT-MDM superimposition). MDM superimposition (palatal vault regional superimposition) were performed on another pair of pre- and posttreatment MDMs. The position and orientation of upper first molars (U6s) and upper central incisors (U1s) on the posttreatment MDMs were compared to assess the accuracy of the MDM superimposition methods. The reliability was validated in both MDM superimposition and CBCT maxillary superimposition. In terms of accuracy, the average linear deviations in U6 and U1 positions were less than ± 0.3 mm, the average angular deviations of U6s and U1s were less than ± 0.2°, both have no significant difference from zero. The ICCs for MDM superimposition ranged from 0.85 to 0.99. The ICCs for CBCT-MDM superimposition were larger than 0.99 in all items. MDM superimposition was an efficient, accurate and reliable method for evaluating teeth movement in adults, although its reliability is slightly lower than CBCT maxillary superimposition.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Unsupervised random forest for affinity estimation

Yunai Yi / Diya Sun / Peixin Li / Tae-Kyun Kim / Tianmin Xu / Yuru Pei

Computational Visual Media, Vol 8, Iss 2, Pp 257-

2021 Volume 272

Abstract: Abstract This paper presents an unsupervised clustering random-forest-based metric for affinity estimation in large and high-dimensional data. The criterion used for node splitting during forest construction can handle rank-deficiency when measuring ... ...

Abstract	Abstract This paper presents an unsupervised clustering random-forest-based metric for affinity estimation in large and high-dimensional data. The criterion used for node splitting during forest construction can handle rank-deficiency when measuring cluster compactness. The binary forest-based metric is extended to continuous metrics by exploiting both the common traversal path and the smallest shared parent node. The proposed forest-based metric efficiently estimates affinity by passing down data pairs in the forest using a limited number of decision trees. A pseudo-leaf-splitting (PLS) algorithm is introduced to account for spatial relationships, which regularizes affinity measures and overcomes inconsistent leaf assign-ments. The random-forest-based metric with PLS facilitates the establishment of consistent and point-wise correspondences. The proposed method has been applied to automatic phrase recognition using color and depth videos and point-wise correspondence. Extensive experiments demonstrate the effectiveness of the proposed method in affinity estimation in a comparison with the state-of-the-art.
Keywords	affinity estimation ; forest-based metric ; unsupervised clustering forest ; pseudo-leaf-splitting (PLS) ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	006
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of digital diagnostic templates by cluster analysis based on 2249 lateral cephalograms of Chinese Han population

Hong Su / Wenhsuan Lu / Jingjing Deng / Gui Chen / Ruoping Jiang / Yan Wei / Xiaoyun Zhang / Tianmin Xu / Bing Han

Head & Face Medicine, Vol 18, Iss 1, Pp 1-

2022 Volume 12

Abstract: Abstract Background To establish the digital diagnostic templates by cluster analysis based on a set of cephalometric films and evaluate the outcome of the different treatment methods in the patients affiliated to the same cephalometric morphology ... ...

Abstract	Abstract Background To establish the digital diagnostic templates by cluster analysis based on a set of cephalometric films and evaluate the outcome of the different treatment methods in the patients affiliated to the same cephalometric morphology template (CMT). These templates could be used for the automatic diagnosis of dentofacial deformities and prediction of treatment outcomes in the future. Methods In this study, we assessed the coordinates of 60 different landmarks on the cephalograms of 2249 patients (14.35 ± 4.99 years, range from 7 to 62) with dentofacial deformities. The cephalometric data were subjected to dentist for clustering without a priori pattern definitions to generate biologically informative CMTs. Three templates were selected to evaluate the treatment outcome of patients affiliated to the same CMT. Results The cluster analysis yielded 21 distinct groups. The total discriminant accuracy was 89.1%, while the cross-validation accuracy was 85.0%, showing that the clusters were robust. All CMTs were automatically created and drawn using a computer, based on the average coordinates of each cluster. Individuals affiliated to the same CMT showed similar dentofacial features. We also evaluated differences in the outcomes of patients affiliated to the same CMT. Conclusions Our results demonstrated the utility of clustering methods for grouping dentofacial deformities with similar dentofacial features. Clustering methods can be used to evaluate the differences in the outcomes of patients affiliated to the same CMT, which has good clinical application value.
Keywords	Dentofacial deformity ; Cluster analysis ; Discriminant analysis ; Cephalometric morphology template ; Diagnosis ; Specialties of internal medicine ; RC581-951
Subject code	610
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Automatic Masseter Muscle Accurate Segmentation from CBCT Using Deep Learning-Based Model

Yiran Jiang / Fangxin Shang / Jiale Peng / Jie Liang / Yi Fan / Zhongpeng Yang / Yuhan Qi / Yehui Yang / Tianmin Xu / Ruoping Jiang

Journal of Clinical Medicine, Vol 12, Iss 1, p

2022 Volume 55

Abstract: Segmentation of the masseter muscle (MM) on cone-beam computed tomography (CBCT) is challenging due to the lack of sufficient soft-tissue contrast. Moreover, manual segmentation is laborious and time-consuming. The purpose of this study was to propose a ... ...

Abstract	Segmentation of the masseter muscle (MM) on cone-beam computed tomography (CBCT) is challenging due to the lack of sufficient soft-tissue contrast. Moreover, manual segmentation is laborious and time-consuming. The purpose of this study was to propose a deep learning-based automatic approach to accurately segment the MM from CBCT under the refinement of high-quality paired computed tomography (CT). Fifty independent CBCT and 42 clinically hard-to-obtain paired CBCT and CT were manually annotated by two observers. A 3D U-shape network was carefully designed to segment the MM effectively. Manual annotations on CT were set as the ground truth. Additionally, an extra five CT and five CBCT auto-segmentation results were revised by one oral and maxillofacial anatomy expert to evaluate their clinical suitability. CBCT auto-segmentation results were comparable to the CT counterparts and significantly improved the similarity with the ground truth compared with manual annotations on CBCT. The automatic approach was more than 332 times shorter than that of a human operation. Only 0.52% of the manual revision fraction was required. This automatic model could simultaneously and accurately segment the MM structures on CBCT and CT, which can improve clinical efficiency and efficacy, and provide critical information for personalized treatment and long-term follow-up.
Keywords	deep learning ; machine learning ; CBCT ; masseter muscle ; orthodontic(s) ; canio-maxillofacial surgery ; Medicine ; R
Subject code	006
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Deviations in palatal region between indirect and direct digital models: an in vivo study.

Zhongpeng, Yang / Tianmin, Xu / Ruoping, Jiang

BMC oral health

2019 Volume 19, Issue 1, Page(s) 66

Abstract: Background: Studies focusing on accuracy of intraoral digital models in the palatal region are scarce. The present study aimed to investigate the influence of different scanning sequences on palatal trueness and to assess deviation and distribution ... ...

Abstract	Background: Studies focusing on accuracy of intraoral digital models in the palatal region are scarce. The present study aimed to investigate the influence of different scanning sequences on palatal trueness and to assess deviation and distribution character of trueness in palate. Methods: Overall, 35 participants accepted three types of procedures to acquire upper digital models. Indirect models digitalised from plaster models were considered as the reference. Two direct digital models were acquired using TRIOS 3 POD intraoral scanners, namely Groups Tr1 and Tr2, wherein intraoral scanning differed in terms of palatal scanning sequences. Based on a modified dental-level superimposition method, 3D measurements of trueness in palate and palatal vault region (PVR) for palatal stable regional superimposition in Groups Tr1 and Tr2, respectively, were performed. Absolute deviations were measured for trueness, while signed deviations were analysed for shape distortion. Colour-coded maps were used for quantitative analysis of deviation distribution pattern. Paired t test was used to analyse differences in palatal trueness between different scanning sequences. One-way repeated-measures analysis of variance and Bonferroni test were used to compare trueness measurements among different superimposition methods. Intraclass correlation coefficient (ICC) was used to verify reproducibility of the proposed method. Results: Palatal trueness in Group Tr1 (118.59 ± 37.67 μm) was slightly less accurate than that (108.25 ± 33.83 μm) in Group Tr2 (p = 0.012 < 0.05). Trueness of PVR in Groups Tr1 (127.35 ± 54.11 μm) and Tr2 (118.17 ± 49.52 μm) did not differ significantly (p = 0.149). Moreover, no significant difference was noted in distortion of the palatal region and PVR in Groups Tr1 and Tr2 (p = 0.582 and 0.615, respectively). A similar pattern of palatal trueness was noted in a majority of participants (22/35). For 3D palatal trueness measurement, there were different applications for different superimposition methods. ICC for the proposed method was > 0.90. Conclusions: Scanning sequences can affect palatal trueness. Palatal scanning should be initiated at the palatal side of the posterior teeth where the initial scan begins. For 3D PVR superimposition, distal boundary of the selected region should be adjusted mesially whilst referring to intraoral digital models. Trial registration: The trial has been registered (registration No: R000039467 , Trial ID: UMIN000034617, date of registration: 2018/10/24'retrospectively registered').
MeSH term(s)	Computer-Aided Design ; Dental Arch/anatomy & histology ; Dental Arch/diagnostic imaging ; Dental Impression Materials ; Dental Impression Technique ; Dental Models ; Dental Prosthesis Design/methods ; Humans ; Image Processing, Computer-Assisted/instrumentation ; Image Processing, Computer-Assisted/methods ; Imaging, Three-Dimensional/methods ; Palate/anatomy & histology ; Reproducibility of Results ; Retrospective Studies
Chemical Substances	Dental Impression Materials
Language	English
Publishing date	2019-04-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2091511-1
ISSN	1472-6831 ; 1472-6831
ISSN (online)	1472-6831
ISSN	1472-6831
DOI	10.1186/s12903-019-0751-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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