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Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要：

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词： malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

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Molecular classification and molecular targeted therapy of cancer

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 147-149 doi: 10.1007/s11684-013-0274-2

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Molecular classification and precision therapy of cancer: immune checkpoint inhibitors

null

《医学前沿（英文）》 2018年 第12卷 第2期   页码 229-235 doi: 10.1007/s11684-017-0581-0

摘要：

On May 23, 2017, the US Food and Drug Administration (FDA) approved a treatment for cancer patients with positive microsatellite instability-high (MSI-H) markers or mismatch repair deficient (dMMR) markers. This approach is the first approved tumor treatment using a common biomarker rather than specified tumor locations in the body. FDA previously approved Keytruda for treatment of several types of malignancies, such as metastatic melanoma, metastatic non-small-cell lung cancer, recurrent or metastatic head and neck cancer, refractory Hodgkin lymphoma, and urothelial carcinoma, all of which carry positive programmed death-1/programmed death-ligand 1 biomarkers. Therefore, indications of Keytruda significantly expanded. Several types of malignancies are disclosed by MSI-H status due to dMMR and characterized by increased neoantigen load, which elicits intense host immune response in tumor microenvironment, including portions of colorectal and gastric carcinomas. Currently, biomarker-based patient selection remains a challenge. Pathologists play important roles in evaluating histology and biomarker results and establishing detection methods. Taking gastric cancer as an example, its molecular classification is built on genome abnormalities, but it lacks acceptable clinical characteristics. Pathologists are expected to act as “genetic interpreters” or “genetic translators” and build a link between molecular subtypes with tumor histological features. Subsequently, by using their findings, oncologists will carry out targeted therapy based on molecular classification.

关键词： molecular classification     precision medicine     pembrolizumab     PD-1/PD-L1     MSI-H    

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Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 157-171 doi: 10.1007/s11684-013-0272-4

摘要：

Non-small-cell lung cancer (NSCLC) is the most common cause of premature death among the malignant diseases worldwide. The current staging criteria do not fully capture the complexity of this disease. Molecular biology techniques, particularly gene expression microarrays, proteomics, and next-generation sequencing, have recently been developed to facilitate effectively its molecular classification. The underlying etiology, pathogenesis, therapeutics, and prognosis of NSCLC based on an improved molecular classification scheme may promote individualized treatment and improve clinical outcomes. This review focuses on the molecular classification of NSCLC based on gene expression microarray technology reported during the past decade, as well as their applications for improving the diagnosis, staging and treatment of NSCLC, including the discovery of prognostic markers or potential therapeutic targets. We highlight some of the recent studies that may refine the identification of NSCLC subtypes using novel techniques such as epigenetics, proteomics, or deep sequencing.

关键词： non-small-cell lung cancer     molecular typing     individualized medicine     molecular-targeted therapy     gene expression profiling    

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Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma

《医学前沿（英文）》 2023年 第17卷 第2期   页码 240-262 doi: 10.1007/s11684-022-0936-z

摘要： Detailed characterizations of genomic alterations have not identified subtype-specific vulnerabilities in adult gliomas. Mapping gliomas into developmental programs may uncover new vulnerabilities that are not strictly related to genomic alterations. After identifying conserved gene modules co-expressed with EGFR or PDGFRA (EM or PM), we recently proposed an EM/PM classification scheme for adult gliomas in a histological subtype- and grade-independent manner. By using cohorts of bulk samples, paired primary and recurrent samples, multi-region samples from the same glioma, single-cell RNA-seq samples, and clinical samples, we here demonstrate the temporal and spatial stability of the EM and PM subtypes. The EM and PM subtypes, which progress in a subtype-specific mode, are robustly maintained in paired longitudinal samples. Elevated activities of cell proliferation, genomic instability and microenvironment, rather than subtype switching, mark recurrent gliomas. Within individual gliomas, the EM/PM subtype was preserved across regions and single cells. Malignant cells in the EM and PM gliomas were correlated to neural stem cell and oligodendrocyte progenitor cell compartment, respectively. Thus, while genetic makeup may change during progression and/or within different tumor areas, adult gliomas evolve within a neurodevelopmental framework of the EM and PM molecular subtypes. The dysregulated developmental pathways embedded in these molecular subtypes may contain subtype-specific vulnerabilities.

关键词： glioma progression     molecular classification     EM/PM subtyping     intratumor heterogeneity    

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Molecular alterations and clinical relevance in esophageal squamous cell carcinoma

null

《医学前沿（英文）》 2013年 第7卷 第4期   页码 401-410 doi: 10.1007/s11684-013-0286-y

摘要：

Esophageal squamous cell carcinoma (ESCC) is one of the most common types of gastrointestinal cancers, and the fourth leading cause of cancer-related deaths in China. Early detection and intervention in time may dramatically increase the survival of the patients by initiating treatment regimens during earlier stages of ESCC or even during precancerous stages. Molecular classification will be useful for subtyping esophageal tumors or precancerous lesions to improve current therapeutics or early intervention of the disease. In this review, we summarize the findings in investigating the molecular alterations and clinical relevance of ESCC.

关键词： esophageal squamous cell carcinoma (ESCC)     early detection     molecular classification     molecular markers    

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Translational medicine in hepatocellular carcinoma

null

《医学前沿（英文）》 2012年 第6卷 第2期   页码 122-133 doi: 10.1007/s11684-012-0193-7

摘要：

Hepatocellular carcinoma (HCC) is a highly complex disease that is generally resistant to commonly used chemotherapy and radiotherapy. Consequently, there is an urgent need for the development of new treatment strategies for this devastating disease. In the past decade, tremendous progress has been achieved in the molecular stratification of HCCs for diagnosis, prognosis, and therapeutic decision-making. To date, the molecular classification of HCCs has been carried out through transcriptomic, genetic and epigenetic profiling of tumors. Such research has led to identification of several potential molecular targets in HCC, and subsequently, development of novel systemic agents for the treatment of HCC has begun in earnest. In this article, we review the current knowledge of the molecular pathogenesis of HCC and outline potential areas for application of this knowledge in a clinical setting. As a typical virus and inflammation-associated cancer, both host immune response and tumor microenvironment have crucial roles in HCC pathogenesis. In addition, we examine the potential of immunotherapy and strategies targeting various components of the tumor microenvironment, as well as novel molecular and cellular targets in HCC such as cancer stem cells.

关键词： hepatocellular carcinoma     molecular classification     molecular targeted therapies     tumor microenvironment     immunotherapy    

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Development of a new method for RMR and Q classification method to optimize support system in tunneling

Asghar RAHMATI,Lohrasb FARAMARZI,Manouchehr SANEI

《结构与土木工程前沿（英文）》 2014年 第8卷 第4期   页码 448-455 doi: 10.1007/s11709-014-0262-x

摘要： Rock mass classification system is very suitable for various engineering design and stability analysis. classification method is confirmed by Japan Highway Public Corporation that this method can figure out either strength or deformability of rock mass, further appropriating the amount of rock bolts, thickness of shotcrete, and size of pitch of steel ribs just after the blasting procedure. Based on these advantages of method, in this study, according to data of five deep and long tunnels in Iran, two equations for estimating the value of method from and classification systems were developed. These equations as a new method were able to optimize the support system for and classification systems. From classification and its application in these case studies, it is pointed out that the method for the design of support systems in underground working is more reliable than the and classification systems.

关键词： JH classification     Q and RMR classification     new method    

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An approach for mechanical fault classification based on generalized discriminant analysis

LI Wei-hua, SHI Tie-lin, YANG Shu-zi

《机械工程前沿（英文）》 2006年 第1卷 第3期   页码 292-298 doi: 10.1007/s11465-006-0022-2

摘要： To deal with pattern classification of complicated mechanical faults, an approach to multi-faults classification based on generalized discriminant analysis is presented. Compared with linear discriminant analysis (LDA), generalized discriminant analysis (GDA), one of nonlinear discriminant analysis methods, is more suitable for classifying the linear non-separable problem. The connection and difference between KPCA (Kernel Principal Component Analysis) and GDA is discussed. KPCA is good at detection of machine abnormality while GDA performs well in multi-faults classification based on the collection of historical faults symptoms. When the proposed method is applied to air compressor condition classification and gear fault classification, an excellent performance in complicated multi-faults classification is presented.

关键词： generalized discriminant     non-separable     abnormality     classification     multi-faults classification    

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EAI-oriented information classification code system in manufacturing enterprises

WANG Junbiao, DENG Hu, JIANG Jianjun, YANG Binghong, WANG Bailing

《机械工程前沿（英文）》 2008年 第3卷 第1期   页码 81-85 doi: 10.1007/s11465-008-0011-8

摘要： Although the traditional information classification coding system in manufacturing enterprises (MEs) emphasizes the construction of code standards, it lacks the management of the code creation, code data transmission and so on. According to the demands of enterprise application integration (EAI) in manufacturing enterprises, an enterprise application integration oriented information classification code system (EAIO-ICCS) is proposed. EAIO-ICCS expands the connotation of the information classification code system and assures the identity of the codes in manufacturing enterprises with unified management of codes at the view of its lifecycle.

关键词： EAI     EAIO-ICCS     management     classification     connotation    

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Fault classification and reconfiguration of distribution systems using equivalent capacity margin method

K. Sathish KUMAR, T. JAYABARATHI

《能源前沿（英文）》 2012年 第6卷 第4期   页码 394-402 doi: 10.1007/s11708-012-0211-0

摘要： This paper investigates the capability of support vector machines (SVM) for prediction of fault classification and the use of the concept of equivalent capacity margin (ECM) for restoration of the power system. The SVM, as a novel type of machine learning based on statistical learning theory, achieves good generalization ability by adopting a structural risk minimization (SRM) induction principle aimed at minimizing a bound on the generalization error of a model rather than the minimization of the error on the training data only. Here, the SVM has been used as a classification. The inputs of the SVM model are power and voltage values. An equation has been developed for the prediction of the fault in the power system based on the developed SVM model. The next steps of this paper are the restoration and reconfiguration by using the ECM concept, the development of a code, and the testing of the results with various load outages, which have been executed for a 12 load system.

关键词： support vector machines (SVM)     structural risk minimization (SRM)     equivalent capacity margin (ECM)     restoration     fault classification    

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 1-3 doi: 10.1007/s11705-021-2134-y

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Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿（英文）》 2022年 第16卷 第2期   页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要： Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词： computer-aided molecular design     bio-oil additives     molecular signature descriptor    

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Multiclass classification based on a deep convolutional

Ying CAI,Meng-long YANG,Jun LI

《信息与电子工程前沿（英文）》 2015年 第16卷 第11期   页码 930-939 doi: 10.1631/FITEE.1500125

摘要： Head pose estimation has been considered an important and challenging task in computer vision. In this paper we propose a novel method to estimate head pose based on a deep convolutional neural network (DCNN) for 2D face images. We design an effective and simple method to roughly crop the face from the input image, maintaining the individual-relative facial features ratio. The method can be used in various poses. Then two convolutional neural networks are set up to train the head pose classifier and then compared with each other. The simpler one has six layers. It performs well on seven yaw poses but is somewhat unsatisfactory when mixed in two pitch poses. The other has eight layers and more pixels in input layers. It has better performance on more poses and more training samples. Before training the network, two reasonable strategies including shift and zoom are executed to prepare training samples. Finally, feature extraction filters are optimized together with the weight of the classification component through training, to minimize the classification error. Our method has been evaluated on the CAS-PEAL-R1, CMU PIE, and CUBIC FacePix databases. It has better performance than state-of-the-art methods for head pose estimation.

关键词： Head pose estimation     Deep convolutional neural network     Multiclass classification    

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Modular design of typical rigid links in parallel kinematic machines: Classification and topology optimization

Xinjun LIU, Xiang CHEN, Zhidong LI

《机械工程前沿（英文）》 2012年 第7卷 第2期   页码 199-209 doi: 10.1007/s11465-012-0315-6

摘要：

Due to the demand of reconfigurable system in parallel kinematic machines (PKMs), modular design technology is significant and necessary. However, in earlier research, the core joint modules have been concerned about rather than the customized link modules. The modular design to the typical customized links from the point of seeking optimal structures with best mechanical performances is analyzed and processed in two steps: classification and optimization. Firstly, a brief introduction to the current research status and the aims of this paper are outlined. And then, how the typical customized links classified is proposed. Next, the technology method and the iterative formula derivation process of topology optimization are described in detail. Finally, calculation models for each group of classified ones are set up and their optimal structures are achieved through topology optimization technique. The results provide useful references for reconfigurable and modular design in engineering cases.

关键词： parallel kinematic machines (PKMs)     modular design     classification     topology optimization and improved Guide-Weight method    

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标题 作者 时间 类型 操作

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文

Molecular classification and precision therapy of cancer: immune checkpoint inhibitors

null

期刊论文

Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

null

期刊论文

Temporal and spatial stability of the EM/PM molecular subtypes in adult diffuse glioma

期刊论文

Molecular alterations and clinical relevance in esophageal squamous cell carcinoma

null

期刊论文

Translational medicine in hepatocellular carcinoma

null

期刊论文

Development of a new method for RMR and Q classification method to optimize support system in tunneling

Asghar RAHMATI,Lohrasb FARAMARZI,Manouchehr SANEI

期刊论文

An approach for mechanical fault classification based on generalized discriminant analysis

LI Wei-hua, SHI Tie-lin, YANG Shu-zi

期刊论文

EAI-oriented information classification code system in manufacturing enterprises

WANG Junbiao, DENG Hu, JIANG Jianjun, YANG Binghong, WANG Bailing

期刊论文

Fault classification and reconfiguration of distribution systems using equivalent capacity margin method

K. Sathish KUMAR, T. JAYABARATHI

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

期刊论文

Multiclass classification based on a deep convolutional

Ying CAI,Meng-long YANG,Jun LI

期刊论文

Modular design of typical rigid links in parallel kinematic machines: Classification and topology optimization

Xinjun LIU, Xiang CHEN, Zhidong LI

期刊论文