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Article ; Online: Computed tomography-guided coil localization for scapula-blocked pulmonary nodules: A trans-scapular approach.

Liu, Xia / Cao, Wei / Xu, Qing-Song

2021 Volume 100, Issue 5, Page(s) e24333

Abstract: Abstract: To evaluate the clinical efficiency, feasibility, and safety of computed tomography (CT)-guided trans-scapular coil localization (TSCL) approach to treating scapula-blocked pulmonary nodules (SBPNs).In total, 105 patients with pulmonary ... ...

Abstract	Abstract: To evaluate the clinical efficiency, feasibility, and safety of computed tomography (CT)-guided trans-scapular coil localization (TSCL) approach to treating scapula-blocked pulmonary nodules (SBPNs).In total, 105 patients with pulmonary nodules underwent CT-guided CL and subsequent video-assisted thoracoscopic surgery (VATS)-guided wedge resection (WR) between January 2016 and July 2020. Six of these patients (5.7%) had SBPNs that led them to undergo CT-guided TSCL. Rates of technical success and localization-related complications were then recorded and analyzed.CT-guided TSCL was associated with a 100% technical success rate, with one coil being placed per patient. The median CT-guided TSCL duration was 15 min. No patients experienced any complications associated with this procedure, and subsequent VATS-guided WR of SBPNs was 100% technically successful. In two patients with invasive adenocarcinoma, additional lobectomy was performed. Median VATS duration and intraoperative blood loss were 120 min and 150 mL, respectively.In summary, these results indicate that CT-guided TSCL could be easily and safely implemented to achieve high success rate when performing the VATS-guided WR of SBPNs.
MeSH term(s)	Aged ; Feasibility Studies ; Female ; Humans ; Male ; Middle Aged ; Multiple Pulmonary Nodules/surgery ; Radiography, Interventional/methods ; Retrospective Studies ; Scapula/surgery ; Thoracic Surgery, Video-Assisted/methods ; Tomography, X-Ray Computed/methods ; Treatment Outcome
Language	English
Publishing date	2021-02-16
Publishing country	United States
Document type	Evaluation Study ; Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000024333
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Article ; Online: Clinical-radiological predictive model in differential diagnosis of small (≤ 20 mm) solitary pulmonary nodules.

Zhao, Hai-Cheng / Xu, Qing-Song / Shi, Yi-Bing / Ma, Xi-Juan

BMC pulmonary medicine

2021 Volume 21, Issue 1, Page(s) 281

Abstract: Background: There is a lack of clinical-radiological predictive models for the small (≤ 20 mm) solitary pulmonary nodules (SPNs). We aim to establish a clinical-radiological predictive model for differentiating malignant and benign small SPNs.: ... ...

Abstract	Background: There is a lack of clinical-radiological predictive models for the small (≤ 20 mm) solitary pulmonary nodules (SPNs). We aim to establish a clinical-radiological predictive model for differentiating malignant and benign small SPNs. Materials and methods: Between January 2013 and December 2018, a retrospective cohort of 250 patients with small SPNs was used to construct the predictive model. A second retrospective cohort of 101 patients treated between January 2019 and December 2020 was used to independently test the model. The model was also compared to two other models that had previously been identified. Results: In the training group, 250 patients with small SPNs including 156 (62.4%) malignant SPNs and 94 (37.6%) benign SPNs patients were included. Multivariate logistic regression analysis indicated that older age, pleural retraction sign, CT bronchus sign, and higher CEA level were the risk factors of malignant small SPNs. The predictive model was established as: X = - 10.111 + [0.129 × age (y)] + [1.214 × pleural retraction sign (present = 1; no present = 0)] + [0.985 × CT bronchus sign (present = 1; no present = 0)] + [0.21 × CEA level (ug/L)]. Our model had a significantly higher region under the receiver operating characteristic (ROC) curve (0.870; 50% CI: 0.828-0.913) than the other two models. Conclusions: We established and validated a predictive model for estimating the pre-test probability of malignant small SPNs, that can help physicians to choose and interpret the outcomes of subsequent diagnostic tests.
MeSH term(s)	Aged ; Diagnosis, Differential ; Female ; Humans ; Logistic Models ; Lung Neoplasms/diagnosis ; Lung Neoplasms/pathology ; Male ; Middle Aged ; ROC Curve ; Retrospective Studies ; Risk Factors ; Solitary Pulmonary Nodule/diagnosis ; Solitary Pulmonary Nodule/pathology ; Tomography, X-Ray Computed
Language	English
Publishing date	2021-09-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2059871-3
ISSN	1471-2466 ; 1471-2466
ISSN (online)	1471-2466
ISSN	1471-2466
DOI	10.1186/s12890-021-01651-y
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Article ; Online: Coil localization assisted wedge resection for pulmonary nodules in patients with malignant history.

Xu, Qing-Song / Wang, Tao / Cao, Wei / Rong, Pan-Hao

Medicine

2021 Volume 100, Issue 47, Page(s) e28025

Abstract: Abstract: We describe the clinical efficacy of coil localization (CL) assisted video-assisted thoracoscopic surgery (VATS) wedge resection (WR) for pulmonary nodules (PNs) in patients having a history of malignancy.In a total of 16 patients having PNs ... ...

Abstract	Abstract: We describe the clinical efficacy of coil localization (CL) assisted video-assisted thoracoscopic surgery (VATS) wedge resection (WR) for pulmonary nodules (PNs) in patients having a history of malignancy.In a total of 16 patients having PNs and malignant history, treatment was carried out using computed tomography (CT)-guided CL and subsequent VATS-guided WR procedures from November 2015 to December 2019. Technical success of CL, WR, and long-term outcomes was analyzed.A total of 21 PNs were localized (1.3 PNs per patient). A 100% technical success rate was achieved in this study for CT-guided CL. Each PN was localized with 1 coil. Two and 2 patients experienced pneumothorax and hemoptysis, respectively. VATS-guided WR also achieved a 100% technical success rate. Additional lobectomy was performed in 2 patients due to the invasive adenocarcinoma. The final diagnoses of these 21 PNs were adenocarcinoma (T1N0M0, n = 8), adenocarcinoma in situ (n = 2), pre-cancerosis (n = 1), metastasis (n = 2), and benign (n = 8). All patients underwent CT follow-up for 6 to 48 months. All patients were alive during the follow-up. The cumulative 6-, 12, and 24-month disease-free survival rates were 100%, 92.9%, and 47.3%, respectively. The median disease-free survival was 27.9 months.Pre-operative CT-guided CL can be safely and conveniently used to facilitate a high success rate of VATS-guided WR for PNs in patients with a malignant history. Among the PNs in patients with malignant history, primary lung cancer also occupied approximately half of the PNs.
MeSH term(s)	Adenocarcinoma/diagnostic imaging ; Adenocarcinoma/surgery ; Aged ; Female ; Humans ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/surgery ; Male ; Middle Aged ; Minimally Invasive Surgical Procedures/methods ; Multiple Pulmonary Nodules/diagnostic imaging ; Multiple Pulmonary Nodules/surgery ; Pneumonectomy ; Retrospective Studies ; Solitary Pulmonary Nodule/diagnostic imaging ; Solitary Pulmonary Nodule/surgery ; Thoracic Surgery, Video-Assisted/methods ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2021-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000028025
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Article ; Online: Kernel density-based likelihood ratio tests for linear regression models.

Yan, Feifei / Xu, Qing-Song / Tang, Man-Lai / Chen, Ziqi

Statistics in medicine

2020 Volume 40, Issue 1, Page(s) 119–132

Abstract: In this article, we develop a so-called profile likelihood ratio test (PLRT) based on the estimated error density for the multiple linear regression model. Unlike the existing likelihood ratio test (LRT), our proposed PLRT does not require any ... ...

Abstract	In this article, we develop a so-called profile likelihood ratio test (PLRT) based on the estimated error density for the multiple linear regression model. Unlike the existing likelihood ratio test (LRT), our proposed PLRT does not require any specification on the error distribution. The asymptotic properties are developed and the Wilks phenomenon is studied. Simulation studies are conducted to examine the performance of the PLRT. It is observed that our proposed PLRT generally outperforms the existing LRT, empirical likelihood ratio test and the weighted profile likelihood ratio test in sense that (i) its type I error rates are closer to the prespecified nominal level; (ii) it generally has higher powers; (iii) it performs satisfactorily when moments of the error do not exist (eg, Cauchy distribution); and (iv) it has higher probability of correctly selecting the correct model in the multiple testing problem. A mammalian eye gene expression dataset and a concrete compressive strength dataset are analyzed to illustrate our methodologies.
MeSH term(s)	Computer Simulation ; Humans ; Likelihood Functions ; Linear Models
Language	English
Publishing date	2020-10-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	843037-8
ISSN	1097-0258 ; 0277-6715
ISSN (online)	1097-0258
ISSN	0277-6715
DOI	10.1002/sim.8765
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Zs.A 1756: Show issues

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Article ; Online: REBET: a method to determine the number of cell clusters based on batch effect removal.

Fang, Zhao-Yu / Lin, Cui-Xiang / Xu, Yun-Pei / Li, Hong-Dong / Xu, Qing-Song

Briefings in bioinformatics

2021 Volume 22, Issue 6

Abstract: In single-cell RNA-seq (scRNA-seq) data analysis, a fundamental problem is to determine the number of cell clusters based on the gene expression profiles. However, the performance of current methods is still far from satisfactory, presumably due to their ...

Abstract	In single-cell RNA-seq (scRNA-seq) data analysis, a fundamental problem is to determine the number of cell clusters based on the gene expression profiles. However, the performance of current methods is still far from satisfactory, presumably due to their limitations in capturing the expression variability among cell clusters. Batch effects represent the undesired variability between data measured in different batches. When data are obtained from different labs or protocols batch effects occur. Motivated by the practice of batch effect removal, we considered cell clusters as batches. We hypothesized that the number of cell clusters (i.e. batches) could be correctly determined if the variances among clusters (i.e. batch effects) were removed. We developed a new method, namely, removal of batch effect and testing (REBET), for determining the number of cell clusters. In this method, cells are first partitioned into k clusters. Second, the batch effects among these k clusters are then removed. Third, the quality of batch effect removal is evaluated with the average range of normalized mutual information (ARNMI), which measures how uniformly the cells with batch-effects-removal are mixed. By testing a range of k values, the k value that corresponds to the lowest ARNMI is determined to be the optimal number of clusters. We compared REBET with state-of-the-art methods on 32 simulated datasets and 14 published scRNA-seq datasets. The results show that REBET can accurately and robustly estimate the number of cell clusters and outperform existing methods. Contact: H.D.L. (hongdong@csu.edu.cn) or Q.S.X. (qsxu@csu.edu.cn).
MeSH term(s)	Algorithms ; Cluster Analysis ; Databases, Genetic ; RNA-Seq/methods ; Reproducibility of Results ; Single-Cell Analysis/methods
Language	English
Publishing date	2021-06-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbab204
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Zs.A 6262: Show issues

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Article ; Online: Transarterial embolization with hepatectomy for ruptured hepatocellular carcinoma: a meta-analysis.

Zhang, Feng-Qin / Li, Lin / Huang, Ping-Chao / Fu, Yu-Fei / Xu, Qing-Song

Minimally invasive therapy & allied technologies : MITAT : official journal of the Society for Minimally Invasive Therapy

2021 Volume 31, Issue 5, Page(s) 676–683

Abstract: Purpose: To compare the clinical effectiveness between transarterial embolization (TAE) with staged hepatectomy (SH) and emergency hepatectomy (EH) for ruptured hepatocellular carcinoma (HCC).: Material and methods: Pubmed, Embase, and Cochrane ... ...

Abstract	Purpose: To compare the clinical effectiveness between transarterial embolization (TAE) with staged hepatectomy (SH) and emergency hepatectomy (EH) for ruptured hepatocellular carcinoma (HCC). Material and methods: Pubmed, Embase, and Cochrane Library databases were screened for eligible publications from the inception of the databases till February 2021. Results: This meta-analysis included seven studies comprising 162 patients who underwent TAE with SH and 266 patients who underwent EH. The pooled intraoperative blood loss was less in the TAE with SH cohort, as compared to the EH cohort without significant difference ( Conclusions: Compared with EH for ruptured HCC, TAE with SH could effectively decrease intraoperative blood loss and 30-day mortality. However, the long-term DFS and OS might not be beneficial to preoperative TAE.
MeSH term(s)	Blood Loss, Surgical ; Carcinoma, Hepatocellular/pathology ; Carcinoma, Hepatocellular/surgery ; Embolization, Therapeutic ; Hepatectomy ; Humans ; Liver Neoplasms/pathology ; Liver Neoplasms/surgery ; Retrospective Studies ; Rupture, Spontaneous/complications ; Rupture, Spontaneous/surgery ; Treatment Outcome
Language	English
Publishing date	2021-10-11
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Review
ZDB-ID	1317160-4
ISSN	1365-2931 ; 1364-5706
ISSN (online)	1365-2931
ISSN	1364-5706
DOI	10.1080/13645706.2021.1986724
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Zs.A 3467: Show issues

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Article ; Online: Computed tomography-guided lung biopsy: a randomized controlled trial of low-dose versus standard-dose protocol.

Fu, Yu-Fei / Li, Guang-Chao / Xu, Qing-Song / Shi, Yi-Bing / Wang, Chen / Wang, Tao

European radiology

2019 Volume 30, Issue 3, Page(s) 1584–1592

Abstract: Objectives: To assess the relative diagnostic utility of low- and standard-dose computed tomography (CT)-guided lung biopsy.: Methods: In this single-center, single-blind, prospective, randomized controlled trial, patients were enrolled between ... ...

Abstract	Objectives: To assess the relative diagnostic utility of low- and standard-dose computed tomography (CT)-guided lung biopsy. Methods: In this single-center, single-blind, prospective, randomized controlled trial, patients were enrolled between November 2016 and June 2017. Enrolled study participants were randomly selected to undergo either low- or standard-dose CT-guided lung biopsy. Diagnostic accuracy was the primary study endpoint, whereas technical success, radiation dose, and associated complications were secondary study endpoints. Results: In total, 280 patients underwent study enrollment and randomization, with 271 (low-dose group, 135; standard-dose group, 136) receiving the assigned interventions. Both groups had a 100% technical success rate for CT-guided lung biopsy, and complication rates were similar between groups (p > 0.05). The mean dose-length product (36.0 ± 14.1 mGy cm vs. 361.8 ± 108.0 mGy cm, p < 0.001) and effective dose (0.5 ± 0.2 mSv vs. 5.1 ± 1.5 mSv, p < 0.001) were significantly reduced in the low-dose group participants. Sensitivity, specificity, and overall diagnostic accuracy rates in the low-dose group were 91.8%, 100%, and 94.6%, respectively, whereas in the standard-dose group, the corresponding values were 89.6%, 100%, and 92.4%, respectively. These results indicated that diagnostic performance did not differ significantly between the 2 groups. Using univariate and multivariate analyses, we found larger lesion size (p = 0.038) and procedure-related pneumothorax (p = 0.033) to both be independent predictors of diagnostic failure. Conclusions: Our results demonstrate that low-dose CT-guided lung biopsy can yield comparable diagnostic accuracy to standard-dose CT guidance, while significantly reducing the radiation dose delivered to patients. Trial registration: ClinicalTrials.gov NCT02971176 KEY POINTS: • Low-dose CT-guided lung biopsy is a safe and simple method for diagnosis of lung lesions. • Low-dose CT-guided lung biopsy can yield comparable diagnostic accuracy to standard-dose CT guidance. • Low-dose CT-guided lung biopsy can achieve a 90% reduction in radiation exposure when compared with standard-dose CT guidance.
MeSH term(s)	Female ; Humans ; Image-Guided Biopsy/methods ; Lung/diagnostic imaging ; Lung Neoplasms/diagnosis ; Male ; Middle Aged ; Prospective Studies ; ROC Curve ; Radiation Dosage ; Radiation Exposure ; Single-Blind Method ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2019-11-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1085366-2
ISSN	1432-1084 ; 0938-7994 ; 1613-3749
ISSN (online)	1432-1084
ISSN	0938-7994 ; 1613-3749
DOI	10.1007/s00330-019-06464-6
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Zs.A 3300: Show issues

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Article ; Online: protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.

Xiao, Nan / Cao, Dong-Sheng / Zhu, Min-Feng / Xu, Qing-Song

Bioinformatics (Oxford, England)

2015 Volume 31, Issue 11, Page(s) 1857–1859

Abstract: Unlabelled: Amino acid sequence-derived structural and physiochemical descriptors are extensively utilized for the research of structural, functional, expression and interaction profiles of proteins and peptides. We developed protr, a comprehensive R ... ...

Abstract	Unlabelled: Amino acid sequence-derived structural and physiochemical descriptors are extensively utilized for the research of structural, functional, expression and interaction profiles of proteins and peptides. We developed protr, a comprehensive R package for generating various numerical representation schemes of proteins and peptides from amino acid sequence. The package calculates eight descriptor groups composed of 22 types of commonly used descriptors that include about 22 700 descriptor values. It allows users to select amino acid properties from the AAindex database, and use self-defined properties to construct customized descriptors. For proteochemometric modeling, it calculates six types of scales-based descriptors derived by various dimensionality reduction methods. The protr package also integrates the functionality of similarity score computation derived by protein sequence alignment and Gene Ontology semantic similarity measures within a list of proteins, and calculates profile-based protein features based on position-specific scoring matrix. We also developed ProtrWeb, a user-friendly web server for calculating descriptors presented in the protr package. Availability and implementation: The protr package is freely available from CRAN: http://cran.r-project.org/package=protr, ProtrWeb, is freely available at http://protrweb.scbdd.com/.
MeSH term(s)	Amino Acids/chemistry ; Internet ; Peptides/chemistry ; Position-Specific Scoring Matrices ; Protein Conformation ; Proteins/chemistry ; Sequence Alignment ; Sequence Analysis, Protein/methods ; Software
Chemical Substances	Amino Acids ; Peptides ; Proteins
Language	English
Publishing date	2015-06-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv042
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Zs.A 2374: Show issues

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Article ; Online: Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.

Cao, Dong-Sheng / Xiao, Nan / Xu, Qing-Song / Chen, Alex F

Bioinformatics (Oxford, England)

2015 Volume 31, Issue 2, Page(s) 279–281

Abstract: Unlabelled: In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins ... ...

Abstract	Unlabelled: In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins and even complex interactions. To solve this problem, we developed a freely available R/Bioconductor package, called Compound-Protein Interaction with R (Rcpi), for complex molecular representation from drugs, proteins and more complex interactions, including protein-protein and compound-protein interactions. Rcpi could calculate a large number of structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of small molecules from their topology and protein-protein interaction and compound-protein interaction descriptors. In addition to main functionalities, Rcpi could also provide a number of useful auxiliary utilities to facilitate the user's need. With the descriptors calculated by this package, the users could conveniently apply various statistical machine learning methods in R to solve various biological and drug research questions in computational biology and drug discovery. Availability and implementation: Rcpi is freely available from the Bioconductor site (http://bioconductor.org/packages/release/bioc/html/Rcpi.html).
MeSH term(s)	Computational Biology/methods ; Databases, Pharmaceutical ; Drug Discovery ; Drugs, Investigational/chemistry ; Drugs, Investigational/metabolism ; Humans ; Protein Binding ; Proteins/chemistry ; Proteins/metabolism ; Software
Chemical Substances	Drugs, Investigational ; Proteins
Language	English
Publishing date	2015-01-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btu624
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Article ; Online: propy: a tool to generate various modes of Chou's PseAAC.

Cao, Dong-Sheng / Xu, Qing-Song / Liang, Yi-Zeng

Bioinformatics (Oxford, England)

2013 Volume 29, Issue 7, Page(s) 960–962

Abstract: Summary: Sequence-derived structural and physiochemical features have been frequently used for analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate extensive studies of proteins and ...

Abstract	Summary: Sequence-derived structural and physiochemical features have been frequently used for analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate extensive studies of proteins and peptides, we developed a freely available, open source python package called protein in python (propy) for calculating the widely used structural and physicochemical features of proteins and peptides from amino acid sequence. It computes five feature groups composed of 13 features, including amino acid composition, dipeptide composition, tripeptide composition, normalized Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors, composition, transition and distribution of various structural and physicochemical properties and two types of pseudo amino acid composition (PseAAC) descriptors. These features could be generally regarded as different Chou's PseAAC modes. In addition, it can also easily compute the previous descriptors based on user-defined properties, which are automatically available from the AAindex database. Availability: The python package, propy, is freely available via http://code.google.com/p/protpy/downloads/list, and it runs on Linux and MS-Windows. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Amino Acids/analysis ; Amino Acids/chemistry ; Peptides/chemistry ; Peptides/metabolism ; Protein Conformation ; Proteins/chemistry ; Proteins/metabolism ; Sequence Analysis, Protein ; Software ; Systems Biology/methods
Chemical Substances	Amino Acids ; Peptides ; Proteins
Language	English
Publishing date	2013-04-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btt072
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