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Screening analysis of candidate gene mutations in a kindred with polycystic liver disease

World Journal of Gastroenterology 2015年第8期21卷 2343-2351页

作者： Song Jin Kai Cui Zi-Qiang Sun Yang-Yang Shen Pang Li Zhen-Dan Wang Fei-Fei Li Ke-Nan Gong Sheng Li Department of Hepatobiliary and Vascular Surgery Affiliated Hospital of Jining Medical College Department of Hepatobiliary Surgery Shandong Cancer Hospital Laboratory of Disease Genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences Shandong Provincial Collaborative Innovation Center for Neurodegenerative Disorders Qingdao University

AIM:To find potential mutable sites by detecting mutations of the candidate gene in a kindred with polycystic liver disease(PCLD).METHODS:First,we chose a kindred with PCLD and obtained five venous blood samples of this kindred after the family members signed the informed consent form.In the kindred two cases were diagnosed with PCLD,and the left three cases were normal individuals.All the blood samples were preserved at-85?℃.Second,we extracted the genomic DNA from the venous blood samples of the kindred using a QIAamp DNA Mini Kit and then performed long-range polymerase chain reaction(PCR)with different primers.The exons of PKD1 were all sequenced with the forward and reverse primers to ensure the accuracy of the results.Next,we purified the PCR products and directly sequenced them using Big Dye Terminator Chemistry version 3.1.The sequencing reaction was conducted with Biomek FX(Beckman).Finally,we analyzed the results.RESULTS:A total of 42 normal exons were identified in detecting mutations of the PKD1 gene.A synonymous mutation occurred in exon 5.The mutation was a homozygous T in the proband and was C in the reference sequence.This mutation was located in the third codon and did not change the amino acid encoded by the codon.Missense mutations occurred in exons 11 and 35.These mutations were located in the second codon;they changed the amino acid sequence and existed in the db SNP library.A nonsense mutation occurred in exon 15.The mutation was a heterozygous CT in the proband and was C in the referencesequence.This mutation was located in the first codon and resulted in a termination codon.This mutation had an obvious influence on the encoded protein and changed the length of the protein from 4303 to 2246amino acids.This was a new mutation that was not present in the db SNP library.CONCLUSION:The nonsense mutation of exon 15existed in the proband and in the third individual.Additionally,the proband was heterozygous for this mutation,so the mutable site was a pathogenic mutation.

关键词： Gene mutation Polycystic liver disease kindred

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生物医学命名实体识别及关系提取的研究与系统构建

生物医学命名实体识别及关系提取的研究与系统构建

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作者：宁格林内蒙古农业大学

学位级别：硕士

生物医学文献数量巨大,并且每天仍以极快的速度增长。在同行评审的期刊上平均每天有3000篇新的文章发表,截至2019年,仅Pubmed就有2900万篇文章。包含有关新发现和新见解的有价值信息报告将不断添加到本已大量的文献中。因此,越来越需要... 详细信息

生物医学文献数量巨大,并且每天仍以极快的速度增长。在同行评审的期刊上平均每天有3000篇新的文章发表,截至2019年,仅Pubmed就有2900万篇文章。包含有关新发现和新见解的有价值信息报告将不断添加到本已大量的文献中。因此,越来越需要用于从文献中提取信息的精确的生物医学文本挖掘工具。生物医学命名实体数量巨大,命名规则不统一,实体构词复杂,给生物医学命名实体识别带来了很大的困难。传统机器学习算法对人工特征提取依赖很大,特征提取的好坏直接影响到实体识别的准确率。而在生物医学领域,人工提取特征以及标注数据集的成本都是非常巨大的。近年来,不依赖于人工特征的深度学习方法在许多领域都取得了很大的进步。本文提出一种Glove-字符级BLSTM-BLSTM-CRF的模型对生物医学命名实体进行识别。首先利用Glove模型训练单词具有语义特征的词向量,用BLSTM训练单词具有字符形态特征的词向量,两者结合作为单词的最终表示,输入BLSTM-CRF深度学习模型,对实体类别进行识别。实验结果表明,在不依赖任何人工特征及规则的前提下,该模型在JNLPBA2004生物医学命名实体识别任务中取得了较好的结果,F1值达到75.62%。本文引用kindred关系提取库,在Biocreative Ⅱ和Biocreative V两个数据集上训练出蛋白质相互作用关系提取模型以及化合物和疾病关系提取模型。基于Django搭建生物医学文本挖掘系统,将前两个模型嵌入到系统当中为用户提供文献挖掘服务。

关键词：生物医学命名实体识别关系提取 Glove BLSTM CRF kindred Django

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Mapping of a dominantly inherited spinocerebellar ataxia with azoospermia to chromosome 7q32.3

Mapping of a dominantly inherited spinocerebellar ataxia wit...

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中国神经科学学会第四次会员代表大会暨第八届全国学术会议

作者： Nancy J.Cox Christopher M.Gomez Section of Genetic Medicine Department of MedicineUniversity of ChicagoChicago60637USA Department of Neurology University of Chicago Medical CenterChicagoIllinois 60637USA

＜正＞The dominantly inherited spinocerebellar ataxias（SCA） are a clinically and genetically heterogeneous group of neurodegenerative disorders characterized by progressive imbalance,dysarthria and motor incoordination.Etiologically distinct SCA subtypes can only be distinguished consistently by genetic analysis.We identified a five-generation kindred of french ancestry inherited as an autosomal dominant trait that is associated with a novel form of progressive ataxia and cognitive impairment,in which all affected males are infertile.The disorder is inherited only from affected or presymptomatic females.The affected individuals including 9 females and 11 males,particularly females,have a broad range of age of onset, which is significantly much later than male patients.Detailed neuropsychological evaluations demonstrated cognitive impairment with borderline IQ scores for those with onset of ataxia before 40 years age.Brain magnetic resonance imaging demonstrates cerebellar atrophy.Affected males had testicular atrophy and azoospermia.Testicular biopsy from one sterile male demonstrated complete absence of germ cells and progenitors.After exclusion of mutations in or linkage to known SCA loci and genes,fragile X,X-linkage,Y-chromosome microdeletion,we carried out a genome-wide genetic linkage scan and located the disease locus to chromosome 7q32.3 by two-point analysis（a maximal two-point LOD score of 3.59,9=0） and haplotype-based analysis.Sequencing of one candidate disease-causing gene（transiently secret） within the region using a recombinant DNA sequencing approach including TA clone method,which carried（ATTCT）n pentanucleotide repeat units in intron 31,revealed an interesting small difference in the size of repeat between affected and normal individuals in the pedigree,for which more normal controls should be detected and confirmed for co-segregation in the disease.Identification of the gene responsible for this complex phenotype may shed additional light into the pathogenesis of ataxia,male infertility,and mental

关键词： dominantly inherited spinocerebellar ataxia kindred clinical characteristics mapping

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