溃疡性结肠炎差异表达基因及中药预测的生物信息学分析

通过生物信息学技术分析比较溃疡性结肠炎(UC)患者与健康人的基因芯片数据,初步筛选UC的差异表达基因,进而预测治疗UC的潜在中药药物。从基因表达数据库(GEO)下载GSE36807基因芯片,使用R语言分析得到上调和下调的差异表达基因,通过String数据库、Cytoscape软件及其插件分析得到差异表达基因的核心基因,对核心基因进行基因本体及京都基因与基因组百科全书分析,通过核心基因与医学本体信息检索平台(Coremine Medical)相互映射,筛选治疗UC的中药。筛选出648个差异表达基因,包括251个下调基因和397个上调基因。上调差异表达基因共得出15个核心基因,包括CXCL8,IL1B,MMP9,CXCL1,CXCL10,CXCL9,CXCL2,CXCL5,TIMP1,CXCL11,STAT1,LCN2,IL1RN,MMP1,IDO1;其生物过程与通路主要富集在白细胞介素、趋化因子配体和细胞因子、趋化因子介导的信号通路,与炎症反应、防御反应、细胞趋化性、分泌颗粒、IL17信号通路、Toll样受体信号通路、NOD样受体信号通路、TNF信号通路等密切相关。治疗UC的潜在中药药物有姜黄、黄连、黄芩、石斛、地榆、黄柏、白及、苍术等。差异表达基因和核心基因的分析促进了对UC发病机制的理解,该研究为UC中药干预的新药开发提供了潜在基因靶标与研发思路。     

A unified software framework for deriving,visualizing, and exploring abstraction networks for ontologies

Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT’s relational format). A Protégé plugin for deriving “live partial-area taxonomies” is demonstrated.     

Concurrence of Myelodysplastic syndromes and large granular lymphocyte leukemia: clinicopathological features,mutational profile and gene ontology analysis in a single center

The concurrence of Myelodysplastic syndromes (MDS) and large granular lymphocyte leukemia (LGLL) has been reported in a small group of patients and might suggest an etiologic relationship rather than a simple coincidence. In this present study, clinicopathological features were detailed in ten cases of MDS concurrent with LGLL (MDS-LGLL). These cases included seven patients with T-LGLL, two with mixed-phenotype LGLL, and one with CLPD-NK. Subsequently, gene mutation screening for commonly myeloid-related or lymphoid-related genes was performed in MDS-LGLL patients by using next generation sequencing (NGS). The genes with the highest frequency of mutations were ASXL1 (3/10, 30%) and STAG2 (3/10, 30%) among a panel of 114 genes. LGLL-associated mutations of STAT3 (2/10, 20%) and STAT5b (1/10, 10%) were also detected. Moreover, whole-exome sequencing (WES) and gene ontology (GO) analysis for one patient in his different phases revealed increased enrichment of histone H3 lysine 4 (H3K4) mono-methylation (GO:0097692) pathway and decreased enrichment of translocation of ZAP-70 to immunological synapse (R-HAS-202430) pathway upon progression from MDS to MDS-LGLL.     

基于网络药理学研究肝复方治疗肝癌的分子机制

目的:基于网络药理学方法,探究肝复方有效活性物质治疗肝癌的相关作用靶点及潜在分子机制。方法:通过检索中药系统药理学数据库与分析平台(TCMSP)及国内外文献筛选出肝复方药味中的化合物以及相关靶点蛋白。通过GeneCards数据库获取肝癌相关疾病靶点。运用Cytoscape 3.2.1软件构建"药物-有效成分-靶点"网络、蛋白相互作用(PPI)网络,并通过网络拓扑分析筛选出核心靶点。最后,通过DAVID进行基因本体(GO)和KEGG信号通路富集分析。结果:通过口服生物利用度(OB)≥30%,类药性(DL)≥0.18的筛选获得有效成分104种,药物对应的靶点1135个,肝癌相关靶点16490个;豆甾醇、人参皂苷、β-谷甾醇为主要核心成分;白细胞介素6(IL-6)、表皮生长因子受体(EGFR)、胱天蛋白酶3(CASP3)为关键靶点。结论:肝复方治疗肝癌具有多成分、多靶点、多通路的作用特点,其作用机制可能是通过IL-6、血管内皮生长因子(VEGF)A、EGFR、CASP3等核心靶点来调节,涉及VEGF、PI3K-Akt与p53等相关信号通路。本研究应用网络药理学预测肝复方治疗肝癌的分子机制,为其临床应用提供了理论依据。     

在本体中如何表达对象特征的运算框架

本体的对象特征（ObjectProperty，OP）的运算语境在《生物医学知识整合论》一书中被称为“概念的语境变量框架”（FrameofContextualVariableofConcept，FCVC），简称为对象特征的“运算框架”（ComputingFrame，CF）。当用Prot6g6建立本体时，一般只能根据对象特征的数学特征加以定义，这些数学特征包括定义域，值域，反关系，是否为函数，是否具有对称性，反对称性，自返性和传递性等，因而事实上用传统的Protege方法是无法表达CF的。根据这类定义，计算机和应用程序是无法理解和处理一个OP的运算语境，因而只能对由该OP驱动的相应的断言“一知半解”。探索的一种新方法引入一种新型的认知和操作类0bjectPropertyEntityConcept—OPEC作为0P的对应体，并放置于实体类树结构中：借助这种新型类，就能利用Protege对实体类的强大的定义功能（与对0P类的定义功能相比较而言）对相应的OP的CF作定义，从而使计算机和应用程序获得阅读和理解0P的运算语境的机会，并进而对由该0P驱动的断言获得更深的理解。     

The Head and Neck Muscles of the Serval and Tiger: Homologies,Evolution, and Proposal of a Mammalian and a Veterinary Muscle Ontology

Here we describe the head and neck muscles of members of the two extant felid subfamilies (Leptailurus serval: Felinae; Panthera tigris: Pantherinae) and compare these muscles with those of other felids, other carnivorans (e.g., domestic dogs), other eutherian mammals (e.g., rats, tree‐shrews and modern humans), and noneutherian mammals including monotremes. Another major goal of the article is to discuss and help clarify nomenclatural discrepancies found in the Nomina Anatomica Veterinaria and in veterinary atlases and textbooks that use cats and dogs as models to understand the anatomy of domestic mammals and to stress differences with modern humans. We propose a unifying nomenclature that is expanded to all the head and neck muscles and to all mammalian taxa in order to help build veterinary and mammalian muscle ontologies. Our observations and comparisons and the specific use of this nomenclature point out that felids such as tigers and servals and other carnivorans such as dogs have more facial muscle structures related to the mobility of both the auricular and orbital regions than numerous other mammals, including modern humans, which might be the result of an ancient adaptation related to the remarkable predatory capacities of carnivorans. Interestingly, the skeletal differences, mainly concerning the hyoid apparatus, pharynx, and larynx, that are likely associated with the different types of vocalizations seen in the Felinae (mainly purring) and Pantherinae (mainly roaring) are not accompanied by clear differences in the musculature connected to these structures in the feline L. serval and the pantherine P. tigris. Anat Rec, 2012. © 2012 Wiley Periodicals, Inc.     

Oro‐facial pain and temporomandibular disorders classification systems: A critical appraisal and future directions

It is a difficult undertaking to design a classification system for any disease entity, let alone for oro‐facial pain (OFP) and more specifically for temporomandibular disorders (TMD). A further complication of this task is that both physical and psychosocial variables must be included. To augment this process, a two‐step systematic review, adhering to PRISMA guidelines, of the classification systems published during the last 20 years for OFP and TMD was performed. The first search step identified 190 potential citations which ultimately resulted in only 17 articles being included for in‐depth analysis and review. The second step resulted in only 5 articles being selected for inclusion in this review. Five additional articles and four classification guidelines/criteria were also included due to expansion of the search criteria. Thus, in total, 14 documents comprising articles and guidelines/criteria (8 proposals of classification systems for OFP; 6 for TMD) were selected for inclusion in the systematic review. For each, a discussion as to their advantages, strengths and limitations was provided. Suggestions regarding the future direction for improving the classification process with the use of ontological principles rather than taxonomy are discussed. Furthermore, the potential for expanding the scope of axes included in existing classification systems, to include genetic, epigenetic and neurobiological variables, is explored. It is therefore recommended that future classification system proposals be based on combined approaches aiming to provide archetypal treatment‐oriented classifications.     

Nosology,ontology and promiscuous realism

Medics may consider worrying about their metaphysics and ontology to be a waste of time. I will argue here that this is not the case. Promiscuous realism is a metaphysical position which holds that multiple, equally valid, classification schemes should be applied to objects (such as patients) to capture different aspects of their complex and heterogeneous nature. As medics at the bedside may need to capture different aspects of their patients' problems, they may need to use multiple classification schemes (multiple nosologies), and thus consider adopting a different metaphysics to the one commonly in use.     

Building an Ontology for Identity Resolution in Healthcare and Public Health

Integration of disparate information from electronic health records, clinical data warehouses, birth certificate registries and other public health information systems offers great potential for clinical care, public health practice, and research. Such integration, however, depends on correctly matching patient-specific records using demographic identifiers. Without standards for these identifiers, record linkage is complicated by issues of structural and semantic heterogeneity.Objectives: Our objectives were to develop and validate an ontology to: 1) identify components of identity and events subsequent to birth that result in creation, change, or sharing of identity information; 2) develop an ontology to facilitate data integration from multiple healthcare and public health sources; and 3) validate the ontology’s ability to model identity-changing events over time.Methods: We interviewed domain experts in area hospitals and public health programs and developed process models describing the creation and transmission of identity information among various organizations for activities subsequent to a birth event. We searched for existing relevant ontologies. We validated the content of our ontology with simulated identity information conforming to scenarios identified in our process models.Results: We chose the Simple Event Model (SEM) to describe events in early childhood and integrated the Clinical Element Model (CEM) for demographic information. We demonstrated the ability of the combined SEM-CEM ontology to model identity events over time.Conclusion: The use of an ontology can overcome issues of semantic and syntactic heterogeneity to facilitate record linkage.     

Determination of concept technology – the ontology of the concept as a component of the knowledge development in caring science

The purpose of this study is to determine the ontology of the concept of technology from the perspective of caring science. The aim is to increase knowledge of the concept in caring science and to answer the research question concerning what the concept of technology is in caring science. In literature, the concept of technology is used diversely referring it to caring technology, nursing technology, wellbeing technology, information technology, telenursing and technology in care named by a specific device or an area of nursing or medicine. The definition of the concept of technology and its ontology has not been determined from the viewpoint of caring science. Eriksson's model of concept determination provides a method to explore the ontology of the concept. This includes an etymological and semantic analysis as well as a determination of essence and basic category of the concept. The results showed that the concept of technology is multidimensional. It has evolved and altered over the centuries. The origin of the concept formulated from the Greek word ‘techne’, which has wider ontological dimensions. It is universal, it can be taught and it depends on the substance. Subsequently, the concept was introduced an ethical dimension, and it also developed more to the direction of engineering, mechanics and technical know‐how. The semantic analysis revealed synonyms of the concept: art, equipment and knowledge. These introduced concepts such as craft, skill, treatment, engineering, science, study method and way. The nuances of the concept framed its nature. On the one hand, it stands out as practical and advanced, but on the other hand, it is difficult and conventional. The knowledge gained in this study will help to understand the phenomenon of technology in caring science.