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  • 文章类型: Journal Article
    本研究的目的是系统分析其发展趋势,研究热点,通过文献计量学方法对脊髓刺激治疗神经性疼痛(NP)的未来发展方向进行了展望。我们从WebofScience数据库中提取了2004年1月至2023年12月与脊髓刺激治疗NP相关的文献。因此,共检索到264篇。通过分析每年发表的文章,作者,国家,机构,期刊,共同引用的文献,和关键词,我们发现该领域的出版物数量一直在总体增长,过去5年的出版物占总产量的42%。美国和英国的专家在这一领域做出了重大贡献,建立了稳定的协作团队,初步建立国际合作网络。疼痛是该领域经常被引用的期刊。脊髓刺激治疗NP的研究尤其是脊髓刺激治疗背部手术失败综合征(FBSS)的研究及其潜在机制是该领域的研究热点。而高频脊髓刺激和脊髓爆裂刺激等新范式的研究代表了未来的发展方向。总之,脊髓刺激已成为治疗NP的有效方法。脊髓刺激的新范式是该领域未来研究的重点。
    The purpose of this study is to systematically analyze the development trend, research hotspots, and future development direction on the treatment of neuropathic pain (NP) with spinal cord stimulation through bibliometric method. We extracted the literature related to the treatment of NP with spinal cord stimulation from January 2004 to December 2023 from the Web of Science database. As a result, a total of 264 articles were retrieved. By analyzing the annual published articles, authors, countries, institutions, journals, co-cited literature, and keywords, we found that the count of publication in this field has been experiencing an overall growth, and the publications within the past 5 years accounted for 42% of the total output. Experts from the United States and the UK have made significant contributions in this field and established a stable collaborative team, initially establishing an international cooperation network. Pain is the frequently cited journal in this field. The study on spinal cord stimulation therapy for NP especially the study on spinal cord stimulation therapy for back surgery failure syndrome (FBSS) and its potential mechanisms are the research hotspots in this field, while the study on novel paradigms such as high-frequency spinal cord stimulation and spinal cord burst stimulation represents the future development directions. In short, spinal cord stimulation has been an effective treatment method for NP. The novel paradigms of spinal cord stimulation are the key point of future research in this field.
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  • 文章类型: Journal Article
    偏头痛是全球公共卫生问题,影响社会和个人福祉。降钙素基因相关肽(CGRP),一种关键的神经肽,对理解偏头痛的发病机制具有重要的研究价值。CGRP受体拮抗剂和靶向CGRP或其受体的单克隆抗体已显示出降低偏头痛频率和严重程度的功效。提出了一种有希望的治疗方法。本研究旨在进行全面的文献计量分析,以分析现状,研究趋势,以及CGRP在偏头痛中的未来方向。
    文献计量工具,包括CiteSpace,VOSviewer,等。,用于从2004年至2023年12月31日的WebofScience核心收藏数据库(WOSCC)中提取和总结与偏头痛中CGRP相关的出版物。分析的重点是年度出版物的趋势,领先的国家/地区和机构,著名的期刊和参考文献,有影响力的作家,和领域中的高频关键词。
    这项研究共纳入1,821篇文章和评论,涉及来自64个国家/地区的1,315个组织的5,180名作者。到2023年12月31日,这些出版物分布在362种期刊上,累计引用56,999篇。在偏头痛CGRP的年度出版物中观察到了增加的趋势。美国在出版物和引文方面都是领先的国家,学术PeterGoadsby贡献了最多的出版物。哥本哈根大学是出版物最多的机构,而脑痛症成为最有影响力的期刊。被引用最多的论文是JesOlesen的“降钙素基因相关肽受体拮抗剂BIBN4096BS用于偏头痛的急性治疗”,发表在《新英语医学杂志》上。关键词频率分析揭示了流行的术语,如“偏头痛,\"\"CGRP,“和”发作性偏头痛,“以及由包括“试用”在内的关键字代表的新兴主题,单克隆抗体,预防性治疗,\"和\"安全。\"
    CGRP在偏头痛发病机制中至关重要,有一个强大的研究基础来探索它的作用。美国在偏头痛CGRP方面的研究成果处于领先地位。研究CGRP及其受体在偏头痛中的作用机制仍然是人们关注的关键领域,特别关注信号通路。未来的研究应着眼于确定用于偏头痛治疗的CGRP拮抗剂途径中的关键治疗靶标。
    UNASSIGNED: Migraine is a global public health concern, affecting both social and individual well-being. Calcitonin gene-related peptide (CGRP), a crucial neuropeptide, holds important research value in understanding migraine pathogenesis. CGRP receptor antagonists and monoclonal antibodies that target CGRP or its receptors have shown efficacy in reducing migraine frequency and severity, presenting a promising therapeutic approach. This study aimed to conduct a comprehensive bibliometric analysis to analyze the current state, research trends, and future directions of CGRP in migraine.
    UNASSIGNED: Bibliometric tools including CiteSpace, VOSviewer, etc., were utilized to extract and summarize publications related to CGRP in migraine from the Web of Science Core Collection Database (WOSCC) between 2004 and 2023, as of December 31, 2023. The analysis focused on trends in annual publications, leading countries/regions and institutions, prominent journals and references, influential authors, and high-frequency keywords in the field.
    UNASSIGNED: A total of 1,821 articles and reviews involving 5,180 authors from 1,315 organizations across 64 countries were included in the study. These publications were distributed across 362 journals and accumulated 56,999 citations by December 31, 2023. An increasing trend was observed in annual publications on CGRP in migraine. The United States emerged as the leading nation in both publications and citations, with academic Peter Goadsby contributing the highest number of publications. The University of Copenhagen stood out as the institution with the most publications, and Cephalalgia emerged as the most influential journal. The most cited paper identified was \"Calcitonin gene-related peptide receptor antagonist BIBN4096BS for the acute treatment of migraine\" by Jes Olesen, published in the New Engl Med. Keyword frequency analysis revealed prevalent terms such as \"migraine,\" \"CGRP,\" and \"episodic migraine,\" along with emerging topics represented by keywords including \"trial,\" \"monoclonal antibodies,\" \"preventive treatment,\" and \"safety.\"
    UNASSIGNED: CGRP is pivotal in migraine pathogenesis, and there is a robust research foundation exploring its role. The US leads in research output on CGRP in migraine. Investigating the mechanism of CGRP and its receptor in migraine remains a key area of interest, particularly focusing on signaling pathways. Future research should target identifying critical therapeutic targets in CGRP antagonist pathways for migraine treatment.
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  • 文章类型: Journal Article
    治疗性单克隆抗体(mAb)在不同的临床适应症中显示出有希望的结果,包括但不限于移植排斥,癌症,和最近的自身免疫性疾病。认识到科学界迫切需要快速,轻松地获取有关单克隆抗体(mAb)的可靠信息,IMGT®,国际ImMunoGeneTics信息系统®,提供了独特而宝贵的资源:IMGT/mAb-DB,一个全面的治疗性单克隆抗体数据库,可通过用户友好的Web界面访问。然而,这种方法限制了更复杂的查询,并将信息与其他数据库隔离。
    要将IMGT/mAb-DB与其余IMGT数据库连接,我们创建了IMGT/mAb-KG,连接到IMGT结构和基因组学数据库的治疗性单克隆抗体的知识图谱。IMGT/mAb-KG使用最有效的语义网方法和标准开发,并从IMGT/mAb-DB获取数据。关于互操作性,IMGT/mAb-KG重复使用来自生物医学资源的术语,并连接到相关资源。
    2024年2月,IMGT/mAb-KG,包括总共139,629个三胞胎,提供对1,489单克隆抗体的访问,大约500个目标,和500多个临床适应症。它提供了对单克隆抗体作用机制的详细见解,他们的建筑,以及他们的各种产品和相关研究。链接到其他资源,如Thera-SAbDab(治疗性结构抗体数据库),PharmGKB(关于遗传变异对药物反应影响的综合资源管理知识),PubMed,和HGNC(HUGO基因命名委员会),IMGT/mAb-KG是mAb开发的重要资源。用户友好的Web界面有助于探索和分析IMGT/mAb-KG的内容。
    UNASSIGNED: Therapeutic monoclonal antibodies (mAbs) have demonstrated promising outcomes in diverse clinical indications, including but not limited to graft rejection, cancer, and autoimmune diseases lately.Recognizing the crucial need for the scientific community to quickly and easily access dependable information on monoclonal antibodies (mAbs), IMGT®, the international ImMunoGeneTics information system®, provides a unique and invaluable resource: IMGT/mAb-DB, a comprehensive database of therapeutic mAbs, accessible via a user-friendly web interface. However, this approach restricts more sophisticated queries and segregates information from other databases.
    UNASSIGNED: To connect IMGT/mAb-DB with the rest of the IMGT databases, we created IMGT/mAb-KG, a knowledge graph for therapeutic monoclonal antibodies connected to IMGT structures and genomics databases. IMGT/mAb-KG is developed using the most effective methodologies and standards of semantic web and acquires data from IMGT/mAb-DB. Concerning interoperability, IMGT/mAb-KG reuses terms from biomedical resources and is connected to related resources.
    UNASSIGNED: In February 2024, IMGT/mAb-KG, encompassing a total of 139,629 triplets, provides access to 1,489 mAbs, approximately 500 targets, and over 500 clinical indications. It offers detailed insights into the mechanisms of action of mAbs, their construction, and their various products and associated studies. Linked to other resources such as Thera-SAbDab (Therapeutic Structural Antibody Database), PharmGKB (a comprehensive resource curating knowledge on the impact of genetic variation on drug response), PubMed, and HGNC (HUGO Gene Nomenclature Committee), IMGT/mAb-KG is an essential resource for mAb development. A user-friendly web interface facilitates the exploration and analyse of the content of IMGT/mAb-KG.
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  • 文章类型: Journal Article
    基于单细胞测序探索淋巴结癌的不同分子和临床病理特征可以揭示癌症的肿瘤间异质性,为早期诊断提供新思路,癌症的治疗和预后分析。
    热点,全球科学产出的特点,并使用我们的文献计量分析确定了2011年至2024年与癌症相关的单细胞序列的前沿。搜索2011年至2024年之间发表的与癌症相关的单细胞序列的WebofScienceCoreCollection(WOSCC)数据库。根据期刊,关键词,记录数,从属关系,引文,和国家,我们进行了文献计量分析。通过使用从WOSCC收集的数据,地理分布是可视化的,关键字,从属关系,并进行了作者聚类分析,和共同引用的参考文献进行了审查,并进行了描述性分析。
    从分析来看,得出的结论是,共发现了2011年至2024年间发表的6189篇文章。免疫学前沿是该研究领域出版物最多的领先期刊。为热点确定的五个集群包括免疫疗法,单细胞RNA测序,肝细胞癌,扩散,基因表达最频繁。Journals,国家,组织,提取了全球贡献最大和引用最多的出版物的学者。研究主要集中在空间转录组学上,泛癌症分析,肝细胞癌等。
    单细胞测序在肿瘤诊断中起着重要作用,治疗和预后。
    UNASSIGNED: Exploring the different molecular and clinicopathological features of nodal cancer based on single cell sequencing can reveal the intertumoral heterogeneity in cancer, and provide new ideas for early diagnosis, treatment and prognosis analysis of cancer.
    UNASSIGNED: The hotspots, the features of worldwide scientific output, and the frontiers concerning single cell sequence related to cancer from 2011 to 2024 were determined using our bibliometric analysis. Web of Science Core Collection (WOSCC) database was searched for publications on single cell sequence associated with cancer that were published between 2011 and 2024. According to the journals, keywords, number of records, affiliations, citations, and countries, we conducted a bibliometric analysis. With the use of the data gathered from the WOSCC, geographic distribution was visualized, keyword, affiliation, and author cluster analyses were conducted, and co-cited references were reviewed and a descriptive analysis was also performed.
    UNASSIGNED: From the analysis, it was concluded that 6189 articles that were published between 2011 and 2024 in total were identified. Frontiers in immunology is the leading journal with the most publications in field of the research. The five clusters that were identified for hotspots included immunotherapy, single-cell RNA sequencing, hepatocellular carcinoma, proliferation, gene expression appeared the most frequently. Journals, nations, organizations, scholars with most contribution and most referenced publications globally were extracted. Studies have mostly concentrated on the spatial transcriptomics, pan-cancer analysis, hepatocellular carcinoma et al.
    UNASSIGNED: Single-cell sequencing plays a significant role in tumor diagnosis, treatment and prognosis.
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  • 文章类型: Journal Article
    通过查阅T细胞与变应性鼻炎领域的相关文献,我们确定了发展状况,研究热点,研究前沿观点,为研究者和临床工作者提供参考。
    方法:应用WebofScienceCoreCollection(WoSCC)获得了2003年至2023年与T细胞和过敏性鼻炎(AR)相关的研究,并使用CiteSpace6.1分析了从这些研究中提取的信息。R6和VOSviewer1.6.18。
    结果:总计,从WoSCC收集了1585篇文章,时间定在2003年至2023年之间。总的来说,越来越多的文章每年都在发表。出版物数量最多的国家和机构是中国(370,23.34%)和中山大学(34,2.15%)。这个领域最大的贡献者是达勒姆,来自英国的斯蒂芬·R(22,1.39%)。《过敏与临床免疫学杂志》发表了该领域最相关的论文(88,5.54%)。免疫疗法,Th细胞,炎症是近年来T细胞和过敏性鼻炎的研究热点。Pathway,模型,调节性T细胞(Treg细胞),调节性B细胞,免疫球蛋白E,先天淋巴样细胞是目前该领域的研究热点。
    结论:T细胞与变应性鼻炎领域发展迅速,许多国家在这一领域做出了重大贡献。该领域的大多数研究人员主要集中在免疫疗法上,Th细胞,和炎症。Pathway,模型,Treg细胞,调节性B细胞,免疫球蛋白E,先天淋巴细胞是当前研究的主要课题,预计该领域将有未来的发展。
    By reviewing the relevant literature in the field of T cell and allergic rhinitis, we determined the development status, study hotspots, and research frontiers viewpoints of this field to provide a reference for researchers and clinical workers.
    METHODS: Web of Science Core Collection (WoSCC) was applied to obtain the studies related to T cells and allergic rhinitis (AR) from 2003 to 2023, and the information extracted from these studies was analyzed using CiteSpace 6.1. R6 and VOSviewer 1.6.18.
    RESULTS: In total, 1585 articles were collected from WoSCC, with the time set between 2003 and 2023. Overall, a growing number of articles are being published annually. The countries and institutions with the maximum publications volume are China (370, 23.34 %) and Sun Yat-sen University (34, 2.15 %). The biggest contributor to the field was Durham, Stephen R. from the UK (22, 1.39 %). The Journal of Allergy and Clinical Immunology published the most related papers in the field (88, 5.54 %). Immunotherapy, Th cells, and inflammation were found to be the research hotspots in this area of T cells and allergic rhinitis in recent years. Pathway, model, Regulatory T cells (Treg cells), regulatory B cells, immunoglobulin E,and innate lymphoid cells were the current research hotspots in this field.
    CONCLUSIONS: The field of T cell and allergic rhinitis is developing rapidly, and many countries significantly contributed to this field. Most researchers in this field mainly focused on immunotherapy, Th cell, and inflammation. Pathway, model, Treg cell, regulatory B cell, immunoglobulin E,and innate lymphoid cells were the main subject of current research, and future development is expected to occur in this field.
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  • 文章类型: Journal Article
    背景:非酒精性脂肪性肝病(NAFLD)越来越被认为是一个重要的健康问题。新兴的研究集中在肠道微生物群在NAFLD中的作用,强调肠-肝轴。这项研究旨在确定关键的研究趋势,并指导未来在这一不断发展的领域的研究。
    方法:本文献计量研究利用Scopus分析了有关肠道菌群与NAFLD之间联系的全球研究。该方法涉及一种专注于文章标题中相关关键词的搜索策略,通过只包括同行评审的期刊文章来完善。数据分析包括文献计量指标,如出版物数量和趋势,使用VOSviewer软件版本1.6.20进行网络和共现分析,突出关键研究集群和新兴主题。
    结果:在关于肠道菌群和NAFLD的479篇出版物中,大多数是原创文章(n=338;70.56%),其次是评论(n=119;24.84%)。年度出版物数量从2010年的1个增加到2022年的118个,从2017年开始进入显著的增长阶段(R2=0.9025,p<0.001)。该研究在全球范围内分布,并以中国(n=231;48.23%)和美国(n=90;18.79%)为主。加州大学,圣地亚哥,主导机构捐款(n=18;3.76%)。资金是突出的,62.8%的文章得到支持,特别是国家自然科学基金(n=118;24.63%)。平均引文计数为43.23,h指数为70,每篇文章的引文范围为0至1058。研究热点在2020年后将重点转向高脂肪饮食对NAFLD发病率的影响。
    结论:这项研究有效地绘制了有关肠道微生物群与NAFLD关系的研究,自2017年以来,出版物大幅增加。对肠道微生物群和NAFLD研究有很大的兴趣,主要由中国和美国领导,具有不同的重点领域。最近,该领域已经开始探索饮食之间的相互联系,生活方式,和肠-肝轴。我们假设有了先进的技术,个性化医疗的新机会和对NAFLD的全面理解将会出现。
    BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is increasingly recognized as a significant health issue. Emerging research has focused on the role of the gut microbiota in NAFLD, emphasizing the gut-liver axis. This study aimed to identify key research trends and guide future investigations in this evolving area.
    METHODS: This bibliometric study utilized Scopus to analyze global research on the link between the gut microbiota and NAFLD. The method involved a search strategy focusing on relevant keywords in article titles, refined by including only peer-reviewed journal articles. The data analysis included bibliometric indicators such as publication counts and trends, which were visualized using VOSviewer software version 1.6.20 for network and co-occurrence analysis, highlighting key research clusters and emerging topics.
    RESULTS: Among the 479 publications on the gut microbiota and NAFLD, the majority were original articles (n = 338; 70.56%), followed by reviews (n = 119; 24.84%). The annual publication count increased from 1 in 2010 to 118 in 2022, with a significant growth phase starting in 2017 (R2 = 0.9025, p < 0.001). The research was globally distributed and dominated by China (n = 231; 48.23%) and the United States (n = 90; 18.79%). The University of California, San Diego, led institutional contributions (n = 18; 3.76%). Funding was prominent, with 62.8% of the articles supported, especially by the National Natural Science Foundation of China (n = 118; 24.63%). The average citation count was 43.23, with an h-index of 70 and a citation range of 0 to 1058 per article. Research hotspots shifted their focus post-2020 toward the impact of high-fat diets on NAFLD incidence.
    CONCLUSIONS: This study has effectively mapped the growing body of research on the gut microbiota-NAFLD relationship, revealing a significant increase in publications since 2017. There is significant interest in gut microbiota and NAFLD research, mainly led by China and the United States, with diverse areas of focus. Recently, the field has moved toward exploring the interconnections among diet, lifestyle, and the gut-liver axis. We hypothesize that with advanced technologies, new opportunities for personalized medicine and a holistic understanding of NAFLD will emerge.
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  • 文章类型: Journal Article
    背景:非酒精性脂肪性肝病(NAFLD)是一种在全球范围内普遍存在的肝脏疾病,与重大的健康风险和经济负担相关。由于它与胰岛素抵抗(IR)有关,本研究旨在进行文献计量学分析,直观地呈现关于IR和NAFLD的科学文献.
    目标:绘制研究图景,强调重点领域,有影响力的研究,以及NAFLD和IR的未来方向。
    方法:本研究对1999年至2022年在SciVerseScopus数据库中索引的IR和NAFLD的文献进行了文献计量分析。搜索策略使用文献和医学主题词中的术语,专注于与IR和NAFLD相关的术语。VOSviewer软件用于可视化研究趋势,合作,和关键主题领域。分析检查了出版物类型,年度研究成果,作出贡献的国家和机构,资助机构,期刊影响因素,引文模式,和高度引用的参考文献。
    结果:此分析确定了关于NAFLD的23124份文件,揭示了1999年至2022年间出版物数量的显著增加。搜索检索到715篇关于IR和NAFLD的论文,包括573篇(80.14%)文章和88篇(12.31%)评论。生产率最高的国家是中国(n=134;18.74%),美国(n=122;17.06%),意大利(n=97;13.57%),日本(n=41;5.73%)。领先的机构包括都灵大学,意大利(n=29;4.06%),和纳西亚拉·德尔·里切,意大利(n=19;2.66%)。最高的资助机构是美国国立糖尿病,消化和肾脏疾病研究所(n=48;6.71%),国家自然科学基金(n=37;5.17%)。该领域最活跃的期刊是肝病学(27种出版物),肝病学杂志(17种出版物),和临床内分泌学和代谢杂志(13种出版物)。主要研究热点是“IR和NAFLD的治疗方法”和“炎症和高脂饮食对NAFLD的影响”。
    结论:这是第一个研究IR和NAFLD之间关系的文献计量分析。为了应对NAFLD不断升级的全球健康挑战,这项研究强调迫切需要更好地了解这种情况并制定干预策略.政策制定者需要优先考虑和解决日益流行的NAFLD。
    BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a liver condition that is prevalent worldwide and associated with significant health risks and economic burdens. As it has been linked to insulin resistance (IR), this study aimed to perform a bibliometric analysis and visually represent the scientific literature on IR and NAFLD.
    OBJECTIVE: To map the research landscape to underscore critical areas of focus, influential studies, and future directions of NAFLD and IR.
    METHODS: This study conducted a bibliometric analysis of the literature on IR and NAFLD indexed in the SciVerse Scopus database from 1999 to 2022. The search strategy used terms from the literature and medical subject headings, focusing on terms related to IR and NAFLD. VOSviewer software was used to visualize research trends, collaborations, and key thematic areas. The analysis examined publication type, annual research output, contributing countries and institutions, funding agencies, journal impact factors, citation patterns, and highly cited references.
    RESULTS: This analysis identified 23124 documents on NAFLD, revealing a significant increase in the number of publications between 1999 and 2022. The search retrieved 715 papers on IR and NAFLD, including 573 (80.14%) articles and 88 (12.31%) reviews. The most productive countries were China (n = 134; 18.74%), the United States (n = 122; 17.06%), Italy (n = 97; 13.57%), and Japan (n = 41; 5.73%). The leading institutions included the Università degli Studi di Torino, Italy (n = 29; 4.06%), and the Consiglio Nazionale delle Ricerche, Italy (n = 19; 2.66%). The top funding agencies were the National Institute of Diabetes and Digestive and Kidney Diseases in the United States (n = 48; 6.71%), and the National Natural Science Foundation of China (n = 37; 5.17%). The most active journals in this field were Hepatology (27 publications), the Journal of Hepatology (17 publications), and the Journal of Clinical Endocrinology and Metabolism (13 publications). The main research hotspots were \"therapeutic approaches for IR and NAFLD\" and \"inflammatory and high-fat diet impacts on NAFLD\".
    CONCLUSIONS: This is the first bibliometric analysis to examine the relationship between IR and NAFLD. In response to the escalating global health challenge of NAFLD, this research highlights an urgent need for a better understanding of this condition and for the development of intervention strategies. Policymakers need to prioritize and address the increasing prevalence of NAFLD.
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    文章类型: Journal Article
    包括个性化疫苗在内的新抗原靶向疗法在癌症治疗中显示出希望。新抗原的准确识别/优先排序与设计临床试验高度相关,预测治疗反应,了解抵抗机制。随着大规模平行测序技术的出现,现在可以根据患者特异性变异信息预测新抗原.然而,在将新抗原优先用于个性化治疗时,必须考虑多种因素.复杂性,如替代转录本注释,各种绑定,表达和免疫原性预测算法,和可变的肽长度/寄存器都潜在地影响新抗原选择过程。虽然计算工具为新抗原表征生成了许多算法预测,这些管道的结果很难导航,需要对底层工具的广泛了解才能准确解释。由于复杂的性质和数量的突出的新抗原特征,提供所有相关信息以促进下游应用程序的候选选择是当前工具无法解决的难题。我们已经创建了pVACview,第一个交互式工具,旨在帮助个性化新抗原治疗的新抗原候选物的优先排序和选择。pVACview具有用户友好和直观的界面,用户可以上传,探索,选择并输出他们的新抗原候选物。该工具允许用户使用变体可视化候选人,转录物和肽信息。pVACview将允许研究人员在基础和翻译设置中以更高的效率和准确性分析和优先考虑新抗原候选物。该应用程序可作为pVACtools管道的一部分在pvactools.org和作为在线服务器在pvacview.org。
    UNASSIGNED: Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies are underway globally. Accurate identification and prioritization of neoantigens is highly relevant to designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address.
    UNASSIGNED: We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select and export their neoantigen candidates. The tool allows users to visualize candidates across three different levels, including variant, transcript and peptide information.
    UNASSIGNED: pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings The application is available as part of the pVACtools pipeline at pvactools.org and as an online server at pvacview.org.
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  • 文章类型: Journal Article
    随着机器学习的发展,神经网络等技术,决策树,支持向量机越来越多地应用于医学领域,特别是对于涉及大型数据集的任务,如细胞检测,认可,分类,和可视化。在骨髓细胞形态学分析领域,深度学习由于其鲁棒性而提供了实质性的好处,自动特征学习的能力,和强大的图像表征能力。深度神经网络是专门为图像处理应用量身定制的机器学习范例。人工智能是支持临床骨髓细胞形态学诊断过程的有力工具。尽管人工智能具有增强该领域临床诊断的潜力,手动分析骨髓细胞形态仍然是黄金标准和必不可少的工具,诊断,并评估血液病的疗效。然而,传统的手工方法并不是没有限制和缺点,有必要,探索用于检查和分析骨髓细胞形态学的自动化解决方案。这篇综述提供了六个骨髓细胞形态学过程的多维描述:自动骨髓细胞形态学检测,自动骨髓细胞形态学分割,自动骨髓细胞形态学鉴定,自动骨髓细胞形态学分类,自动骨髓细胞形态学计数,和自动骨髓细胞形态学诊断。突出了基于骨髓细胞形态学的机器学习系统的吸引力和潜力,这篇综述综合了机器学习在这一领域应用的最新研究和最新进展。这篇综述的目的是为血液学家提供建议,以选择最合适的机器学习算法来自动化骨髓细胞形态学检查,能够快速精确地分析骨髓细胞病变趋势,以便早期识别和诊断疾病。此外,这篇综述试图描述基于机器学习的骨髓细胞形态学分析应用的潜在未来研究途径.
    As machine learning progresses, techniques such as neural networks, decision trees, and support vector machines are being increasingly applied in the medical domain, especially for tasks involving large datasets, such as cell detection, recognition, classification, and visualization. Within the domain of bone marrow cell morphology analysis, deep learning offers substantial benefits due to its robustness, ability for automatic feature learning, and strong image characterization capabilities. Deep neural networks are a machine learning paradigm specifically tailored for image processing applications. Artificial intelligence serves as a potent tool in supporting the diagnostic process of clinical bone marrow cell morphology. Despite the potential of artificial intelligence to augment clinical diagnostics in this domain, manual analysis of bone marrow cell morphology remains the gold standard and an indispensable tool for identifying, diagnosing, and assessing the efficacy of hematologic disorders. However, the traditional manual approach is not without limitations and shortcomings, necessitating, the exploration of automated solutions for examining and analyzing bone marrow cytomorphology. This review provides a multidimensional account of six bone marrow cell morphology processes: automated bone marrow cell morphology detection, automated bone marrow cell morphology segmentation, automated bone marrow cell morphology identification, automated bone marrow cell morphology classification, automated bone marrow cell morphology enumeration, and automated bone marrow cell morphology diagnosis. Highlighting the attractiveness and potential of machine learning systems based on bone marrow cell morphology, the review synthesizes current research and recent advances in the application of machine learning in this field. The objective of this review is to offer recommendations to hematologists for selecting the most suitable machine learning algorithms to automate bone marrow cell morphology examinations, enabling swift and precise analysis of bone marrow cytopathic trends for early disease identification and diagnosis. Furthermore, the review endeavors to delineate potential future research avenues for machine learning-based applications in bone marrow cell morphology analysis.
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  • 文章类型: Journal Article
    我们开发了一系列基于课程的本科研究经验,让学生融入课程课程,围绕使用3D可视化和虚拟现实进行科学可视化。一个项目涉及创建和使用超栈图像的体积渲染器,与共聚焦显微镜的生物学项目配对。学生们致力于开发和测试支持VR的工具,用于跨基于耳机和基于CAVE的VR平台的共聚焦显微镜可视化。介绍了该工具的两种应用:果蝇原始生殖细胞的绘制以及自动检测和计数,和开发花粉粒3D渲染的数据库。另一个项目涉及点云渲染器的开发和测试。学生的工作重点是在一系列2D和3D硬件上进行性能测试和增强,包括原生Quest应用程序。通过开发这些工具的过程,向学生介绍科学的可视化概念,在获得编程实践经验的同时,软件工程,图形,着色器编程,和跨平台设计。
    We have developed a series of course-based undergraduate research experiences for students integrated into course curriculum centered around the use of 3D visualization and virtual reality for science visualization. One project involves the creation and use of a volumetric renderer for hyperstack images, paired with a biology project in confocal microscopy. Students have worked to develop and test VR enabled tools for confocal microscopy visualization across headset based and CAVE based VR platforms. Two applications of the tool are presented: a rendering of Drosophila primordial germ cells coupled with automated detection and counting, and a database in development of 3D renderings of pollen grains. Another project involves the development and testing of point cloud renderers. Student work has focused on performance testing and enhancement across a range of 2D and 3D hardware, including native Quest apps. Through the process of developing these tools, students are introduced to scientific visualization concepts, while gaining practical experience with programming, software engineering, graphics, shader programming, and cross-platform design.
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