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Journal of Behavioral and Brain Science 2014年第1期4卷 1-10页

作者： Yongning Song Yuji Hakoda Faculty of Human-Environment Studies Kyushu University Fukuoka Japan Key Laboratory of Brain Functional genomics (MOE & STCSM) School of Psychology and Cognitive Science East China Normal University Shanghai China

Objective: This study examined the hypothesis that individuals with attention deficit hyperactivity disorder, predominantly inattentive type (ADHD-I), show both executive function (EF) deficits and non-EF deficits. Method: A group with ADHD-I (n = 16) and a paired control group (n = 21) completed a battery of tasks covering the major domains of EF (planning, working memory, flexibility and inhibition) and non-EF (alertness, divided attention, flexibility, sustained attention, visual field and visual scanning). Results: EF impairments in planning, spatial working memory, flexibility, and inhibition as well as non-EF impairments in divided attention, flexibility, sustained attention and visual scanning were observed in the ADHD-I group. Conclusion: Our results do not support the traditional model of ADHD. Given that neither EF nor non-EF tests typically distinguish ADHD-I from ADHD-C, alternative methodologies are required to confirm the validity of ADHD subtypes in the Diagnostic and statistical Manual of Mental Disorders, Fourth Edition.

关键词： ADHD-I Executive Function Non-Executive Function Cognitive Profile

Identification of Conserved Regulatory Elements in Mammalian Promoter Regions:A Case Study Using the PCK1 Promoter

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genomics, Proteomics & Bioinformatics 2008年第3期6卷 129-143页

作者： George E. Liui Matthew T. Weirauch Curtis P. Van Tassell Robert W. Li Tad S. Sonstegard LakshmiK. Matukumal Erin E. Connor Richard W. Hanson Jianqi Yang Bovine Functional genomics Laboratory Beltsville Agricultural Research Center Beltsville MD 20705 USA Department of Biomolecular Engineering University of California Santa Cruz Santa Cruz CA 95064 USA Department of Bioinformatics and Computational Biology George Mason University Manassas VA 20110 USA Department of Biochemistry Case Western Reserve University School of Medicine Cleveland OH 44106 USA.

A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http：//***/tfbsConsSites.

关键词： phylogenetic footprinting phosphoenolpyruvate carboxykinase transcription factor binding sites mammalian gene promoters

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GMATA:a comprehensive software for exploring microsatellites toward molecular breeding in whole genome sequences

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GMATA:a comprehensive software for exploring microsatellites...

Influence of DAP1 Genotype and Psychosocial Factors on Posttraumatic Stress Disorder in Thai Tsunami Survivors: A GxE Approach

中国遗传学会第九次全国会员代表大会暨学术研讨会

作者：王学文 Jeffrey Bennetzen Plant Germplasm and genomics Center Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of Sciences Department of genetics University of Georgia

Simple Sequence Repeats(SSR),also called microsatellite,is important genome feature and very useful for genetic marker based genome *** increasing whole sequences of large genomes provide informative resources for SSR marker developing and applied genetic *** currently it lacks of efficient software for the above purpose at whole large genome ***-wide Microsatellite Analyzing Tool Package(GMATA) is a novel software for SSR mining,statistical analysis and plotting,SSR loci viewing,marker designing,electronic mapping,and marker transferability investigation at whole genome *** from any other software,GMATA provides multiple and comprehensive statistical data for SSRs,markers, e-mapping,statistical figure plotting and graphically browsing SSR loci with other genome sequence features in Gbrowse for any large *** one input file is required which contains genome sequences in fasta *** software runs super-faster and more accurate than existed tools SSR Locator and *** was programmed in Java,R and Perl languages with both graphic and command line interface,either executable alone in platform independent manner with full parameters *** GMATA is a powerful tool package for complete SSR characterization,marker development and transferability analyzing in any genome at any size, which speeds up the applied genomic research.

关键词： genome microsatellite SSR marker development e-mapping statistics plotting Gbrowse

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Open Journal of Genetics 2019年第3期9卷 65-75页

作者： Nuntika Thavichachart Prathan Rutchatajumroon Taisei Mushiroda Anchalee Prasansuklab Sookjaroen Tangwongchai Puangsoi Worakul Buranee Kanchanatawan Siriluck Suppapitiporn Atapol Sughondhabirom Chutima Roomruangwong Ongart Charoensook Wasun Chantratita Atsushi Takahashi Michiaki Kubo Naoyuki Kamatani Yusuke Nakamura Department of Psychiatry Faculty of Medicine Chulalongkorn University Bangkok Thailand Thailand Center of Excellence for Life Sciences (Public Organization) Ministry of Science and Technology Bangkok Thailand Laboratory for Pharmacogenetics RIKEN Center for Genomic Medicine Kanagawa Japan College of Public Health Sciences Chulalongkorn University Bangkok Thailand Center for Medical genomics Ramathibodi Hospital Mahidol University Bangkok Thailand Laboratory for statistical Analysis RIKEN Center for Genomic Medicine Kanagawa Japan Laboratory for Genotyping Development RIKEN Center for Genomic Medicine Kanagawa Japan Laboratory of Molecular Medicine Human Genome Center Institute of Medical Science The University of Tokyo Tokyo Japan

Background: Posttraumatic Stress Disorder (PTSD) is a psychiatric disorder found in individuals afflicted by a traumatic event including the natural disaster. “Tsunami” occurred in Andaman coast of Thailand on December 26, 2004, in which 33.6% of survivors were diagnosed as PTSD. This study aimed to explore the single nucleotide polymorphism (SNP). rs267943 genotype is located on chromosome 5 in the intron of the death-associated protein 1 (DAP1) gene and psychosocial factors for PTSD. Methods: Participants (N = 1970) were recruited from volunteers who have complete data both of DAP1 gene and psychosocial factor. Results: Using a binary logistic regression model, significant gene-environment interactions were found for the single nucleotide polymorphism (SNP) rs267943 and psychosocial factors including depression (adj. OR = 6.0, 95% CI = 4.29 - 8.39), neurotic personality (adj. OR = 2.73, 95% CI = 2.18 - 3.42), planning (adj. OR = 1.52, 95% CI = 1.20 - 1.93), use of emotional support (adj. OR = 1.32, 95% CI = 1.21 - 1.94) with statistical significant p Conclusion: This study demonstrated that GxE studies can be utilized to shed light on the origins of PTSD.

关键词： Death-Associated Protein 1 Gene (DAP1) Gene-by-Environment Interaction (GxE) Genetype Posttraumatic Stress Disorder (PTSD) Psychosocial Factors Tsunami

A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia

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Chinese Medical Journal 2016年第2期129卷 181-186页

作者： Fang Wang Ran Li Ying Shang Can Wang Guo-Qing Wang DeXun Zhou Dong-Hong Yang Wen Xi Ke-QiangWang Jing Bao Yu Kang Zhan-Cheng Gao Department of Respiratory and Critical Care Medicine Peking University People's Hospital Beijing 100044 China Department of Assay Development CapitalBio Corporation Beijing 102206 China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

Background： It is important to achieve the definitive pathogen identification in hospital-acquired pneumonia （HAP）, but the traditional culture results always delay the target antibiotic therapy. We assessed the method called quantitative loop-mediated isothermal amplification （qLAMP） as a new implement for steering of the antibiotic decision-making in HAP. Methods： Totally, 76 respiratory tract aspiration samples were prospectively collected from 60 HAP patients. DNA was isolated from these samples. Specific DNA fragments for identifying 11 pneumonia-related bacteria were amplified by qLAMP assay. Culture results of these patients were compared with the qLAMP results. Clinical data and treatment strategies were analyzed to evaluate the effects of qLAMP results on clinical data. McNemar test and Fisher＇s exact test were used for statistical analysis. Results： The detection of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Stenotrophomonas maltophilia, Streptococcus pneumonia, and Acinetobacter baumannii by qLAMP was consistent with sputum culture （P 〉 0.05）. The qLAMP results of 4 samples for Haemophilus influenzae, Legionella pneumophila, or Mvcoplasma pneumonia （MP） were inconsistent with culture results; however, clinical data revealed that the qLAMP results were all reliable except 1 MP positive sample due to the lack of specific species identified in the final diagnosis. The improvement of clinical condition was more significant （P 〈 0.001） in patients with pathogen target-driven therapy based on qLAMP results than those with empirical therapy. Conclusion： qLAMP is a more promising method for detection of pathogens in an early, rapid, sensitive, and specific manner than culture.

关键词： Hospital-acquired Pneumonia Sputum Culture Target-driven Therapy Quantitative Loop-mediated Isothermal Amplification

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Title-2(in revise article):Adaptive K-nearest neighbors AUC Test:an efficient method for nonlinear dependence between one continuous variable and one binary variable

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Title-2(in revise article):Adaptive K-nearest neighbors AUC ...

A genome wide association study between copy number variation (CNV) and human height in Chinese population

2017中国长三角遗传学大会

作者： Yi Li Xiaoyu Liu Yanyun Ma Yi Wang Weichen Zhou Zhenghong Yuan Jie Liu Momiao Xiong Yin Yao Shugart Jiucun Wang Li Jin Ministry of Education Key Laboratory of Contemporary Anthropology Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan University State Key Laboratory of Genetic Engineering Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan University Department of Computational Medicine & Bioinformatics University of Michigan Shanghai Public Health Clinical Center Fudan University Key Laboratory of Medical Molecular Virology of MOE/MOH Shanghai Medical SchoolFudan University Department of Digestive Diseases of Huashan Hospital Collaborative Innovation Center for Genetics and DevelopmentFudan University Human Genetics Center School of Public HealthUniversity of Texas Houston Health Sciences Center unit on statistical genomics Division of Intramural Division ProgramsNational Institute of Mental HealthNational Institutes of Health

Background:Testing the dependence/correlation of two variables is one of the fundamental tasks in *** this work,we proposed an efficient method for the nonlinear dependence between one continuous variable X and one binary dependent variables Y(0 or 1).Results:We addressed this problem by using AKAT(Adaptive K-nearest neighbors AUC independence Test,the R package is made available at https://***/projects/akat/).In the AKAT framework,we first resampled a dataset to get the training and testing dataset according to the sample ratio(from 0 to 1),and then constructed an adaptive k-nearest neighbors algorithm classifier to get the yhat estimator(the probability of y=l) of *** we calculated the AUC estimator and tested whether the AUC estimator is greater than 0.5(alternative hypothesis).To evaluate the advantages of AKAT compared to seven other methods,we performed extensive simulations to explore the relationships between eight different methods and compared the false positive rates and statistical power using both simulated and real datasets(Chronic hepatitis B datasets and kidney cancer RNA-seq datasets).Conclusions:We concluded that AKAT is an efficient method to test non-linear dependence between continuous variables and binary dependent variables in real world applications.

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Journal of Genetics and genomics 2010年第12期37卷 779-785页

作者： Xi Li Lijun Tan Xiaogang Liu Shufeng Lei Tielin Yang Xiangding Chen Fang Zhang Yue Fang Yan Guo Liang Zhang Han Yan Feng Pan Zhixin Zhang Yumei Peng Qi Zhou Lina He Xuezhen Zhu Jing Cheng Lishu Zhang Yaozhong Liu Qing Tian Hongwen Deng Laboratory of Molecular and statistical Genetics College of Life Sciences Hunan Normal University Changsha 410081 China The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics School of Life Science and Technology Xi'an Jiaotong University Xi'an 710049 China National Engineering Research Center for Beijing Biochip Technology Beijing 102206 China Department of Basic Medical Science and Orthopedic Surgery School of Medicine University of Missouri - Kansas City Kansas City MO 64108 USA College of Life Sciences and Bioengineering Beijing Jiaotong University Beijing 100044 China

Copy number variation （CNV） is a type of genetic variation which may have important roles in phenotypic variability and disease susceptibility. To hunt for genetic variants underlying human height variation, we performed a genome wide CNV association study for human height in 618 Chinese unrelated subjects using Affymetrix 500K array set. After adjusting for age and sex, we found that four CNVs at 6p21.3, 8p23.3-23.2, 9p23 and 16p12.1 were associated with human height （with borderline significant p value： 0.013, 0.011, 0.024, 0.049; respectively）. However, after multiple tests correction, none of them was associated with human height. We observed that the gain of copy number （more than 2 copies） at 8p23.3-23.2 was associated with lower height （normal copy number vs. gain of copy number： 161.2 cm vs. 153.7 cm, p = 0.011）, which accounted for 0.9% of height variation. Loss of copy number （less than 2 copies） at 6p21.3 was associated with 0.8% lower height （loss of copy number vs. normal copy number： 154.5 cm vs. 161.1 cm, p = 0.013）. Since no important genes influencing height located in CNVs at loci of 8p23.3-23.2 and 6p21.3, the two CNVs may cause the structural rear- rangements of neighbored important candidate genes, thus regulates the variation of height. Our results expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.

关键词： CNV human height GWAS Affymetrix 500K array

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Garcinia Cambogia attenuates diet-induced adiposity but exacerbates hepatic collagen accumulation and inflammation

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World Journal of Gastroenterology 2013年第29期19卷 4689-4701页

作者： Young-Je Kim Myung-Sook Choi Yong Bok Park Sang Ryong Kim Mi-Kyung Lee Un Ju Jung Department of Food Science and Nutrition Kyungpook National University Daegu 702-701 South Korea Center for Food and Nutritional genomics Research Kyungpook National University Daegu 702-701 South Korea School of Life Sciences and Biotechnology Kyungpook National University Daegu 702-701 South Korea Brain Science and Engineering Institute Kyungpook National University Daegu 702-701 South Korea Department of Food and Nutrition Sunchon National University Jeonnam 540-742 South Korea

AIM: To investigate long-term effects of Garcinia Cambogia (GC), weight-loss supplement, on adiposity and non-alcoholic fatty liver disease in obese mice. METHODS: Obesity-prone C57BL/6J mice were fed a high-fat diet (HFD, 45 kcal% fat) with or without GC (1%, w/w) for 16 wk. The HFD contained 45 kcal% fat, 20 kcal% protein and 35 kcal% carbohydrate. They were given free access to food and distilled water, and food consumption and body weight were measured daily and weekly, respectively. Data were expressed as the mean ± SE. statistical analyses were performed using the statistical package for the social science software program. Student's t test was used to assess the differences between the groups. statistical significance was considered at P < 0.05. RESULTS: There were no significant changes in body weight and food intake between the groups. However, the supplementation of GC significantly lowered visceral fat accumulation and adipocyte size via inhibition of fatty acid synthase activity and its mRNA expression in visceral adipose tissue, along with enhanced enzymatic activity and gene expression involved in adipose fatty acid β-oxidation. Moreover, GC supplementation resulted in significant reductions in glucose intolerance and the plasma resistin level in the HFD-fed mice. However, we first demonstrated that it increased hepatic collagen accumulation, lipid peroxidation and mRNA levels of genes related to oxidative stress (superoxide dismutase and glutathione peroxidase) and inflammatory responses (tumor necrosis factor-α and monocyte chemoattractant protein-1) as well as plasma alanine transaminase and aspartate transaminase levels, although HFD-induced hepatic steatosis was not altered. CONCLUSION: GC protects against HFD-induced obesity by modulating adipose fatty acid synthesis and β-oxidation but induces hepatic fibrosis, inflammation and oxidative stress.

关键词： Garcinia Cambogia Anti-adiposity Metabolic changes Hepatic collagen accumulation Hepatic inflammation Hepatic oxidative stress

关联分析定位水稻第4号染色体的芒性基因并结合连锁分析精细定位Awn4.1

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科学通报 2010年第Z2期55卷 2677-2681页

作者：胡广隆张冬玲潘慧乔李本吴建涛周雪崖张群远周雷姚国新李俊周李金杰张洪亮李自超中国农业大学农业部作物基因组学与遗传改良重点实验室北京市作物遗传改良重点实验室生物信息学教育部重点实验室信息国家实验室生物信息学研究部清华大学自动化系 Division of statistical genomics Washington University School of Medicine

芒性是水稻一个重要的驯化相关性状,但目前还没有其精细定位及关联分析的报道.利用303份栽培稻微核心种质材料和一个200株的BC5F2分离群体,考察其芒性表现和基因型,通过关联分析和连锁分析相结合的方法定位水稻第四号染色体的芒性基因.... 详细信息

芒性是水稻一个重要的驯化相关性状,但目前还没有其精细定位及关联分析的报道.利用303份栽培稻微核心种质材料和一个200株的BC5F2分离群体,考察其芒性表现和基因型,通过关联分析和连锁分析相结合的方法定位水稻第四号染色体的芒性基因.首先,运用logistic回归进行标记与性状的初步关联分析,在第4号染色体上发现了5个关联位点,包括了前人所发现的所有位点.然后,在其中一个位点Awn4.1的区间内加密标记,通过连锁分析与关联分析相结合的策略将芒基因Awn4.1精细定位在330kb的区间内,为克隆芒基因Awn4.1打下基础.结果表明,利用核心种质材料,结合连锁分析与关联分析方法能够更加高效和准确地定位水稻基因.

关键词：水稻芒关联分析连锁分析基因定位

关联分析定位水稻第4号染色体的芒性基因并结合连锁分析精细定位Awn4.1

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科学通报 2010年第27期55卷 2777-2781页

作者：胡广隆张冬玲潘慧乔李本吴建涛周雪崖张群远周雷姚国新李俊周李金杰张洪亮李自超中国农业大学农业部作物基因组学与遗传改良重点实验室北京市作物遗传改良重点实验室北京100193 生物信息学教育部重点实验室信息国家实验室生物信息学研究部清华大学自动化系北京100084 Division of statistical genomics Washington University School of Medicine

关键词：水稻芒关联分析连锁分析基因定位