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Calculating Linkage Intensities from F(3) Data 总被引:1,自引:0,他引:1
Immer FR 《Genetics》1934,19(2):119-136
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Angel Soto-Hermida Mercedes Fernández-Moreno Natividad Oreiro Carlos Fernández-López Sonia Pértega Estefania Cortés-Pereira Ignacio Rego-Pérez Francisco J. Blanco 《PloS one》2014,9(11)
Objective
To evaluate the influence of the mtDNA haplogroups on knee osteoarthritis progression in Osteoarthritis Initiative (OAI) participants through longitudinal data from radiographs and magnetic resonance imaging (MRI).Methods
Four-year knee osteoarthritis progression was analyzed as increase in Kellgren and Lawrence (KL) grade, in addition to increase in OARSI atlas grade for joint space narrowing (JSN), osteophytes and subchondral sclerosis in the tibia medial compartment of 891 Caucasian individuals from the progression subcohort. The influence of the haplogroups on the rate of structural progression was also assessed as the four-year change in minimum joint space width (mJSW in millimetres) in both knees of (n = 216) patients with baseline unilateral medial-tibiofemoral JSN. Quantitative cartilage measures from longitudinal MRI data were those related to cartilage thickness and volume with a 24 month follow-up period (n = 381).Results
During the four-year follow-up period, knee OA patients with the haplogroup T showed the lowest increase in KL grade (Hazard Risk [HR] = 0.499; 95% Confidence Interval [CI]: 0.261–0.819; p<0.05) as well as the lowest cumulative probability of progression for JSN (HR = 0.547; 95% CI: 0.280–0.900; p<0.05), osteophytes (HR = 0.573; 95% CI: 0.304–0.893; p<0.05) and subchondral sclerosis (HR = 0.549; 95% CI: 0.295–0.884; p<0.05). They also showed the lowest decline in mJSW (standardized response means (SRM) = −0.39; p = 0.037) in those knees without baseline medial JSN (no-JSN knees). Normalized cartilage volume loss was significantly lower in patients carrying the haplogroup T at medial tibia femoral (SRM = −0.33; p = 0.023) and central medial femoral (SRM = −0.27; p = 0.031) compartments. Cartilage thickness loss was significantly lower in carriers of haplogroup T at central medial tibia-femoral (SRM = −0.42; p = 0.011), medial tibia femoral (SRM = −0.32; p = 0.018), medial tibia anterior (SRM = +0.31; p = 0.013) and central medial femoral (SRM = −0.19; p = 0.013) compartments.Conclusions
Mitochondrial genome seems to play a role in the progression of knee osteoarthritis. mtDNA variation could improve identification of patients predisposed to faster or severe progression of the disease. 相似文献9.
Nicholas P. Tippery Karolina Fučíková Paul O. Lewis Louise A. Lewis 《Journal of phycology》2012,48(6):1482-1493
Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms. 相似文献
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A list of 29 species of Thysanoptera belonging to three families from Central Yakutia is given. 相似文献
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使用高通量方法学来检测基因表达情况在最近几年已非常普遍。微集芯片技术可同时定量成千上万的基因转录本。基因表达综合数据库(Gene Expression Omnibus 简称GEO)是目前最大的而且完全公开的高通量分子丰度数据库,主要储存基因表达数据。该数据库以一个灵活开放的设计理念,允许用户或科研人员来递呈,保存和检索多种不同类型的数据。本文综合描述一下近年来该数据库在基因表达数据挖掘中的应用,同时介绍一些通过使用用户友好网络界面能有效探索、查询和再现数百个实验和数百万个基因表达谱的工具,以方便数据进行挖掘和可视化。登录GEO公用数据库的网址为:http://www.ncbi.nlm.nih.gov/geo. 相似文献
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The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year. This is mainly due to large-scale submissions from Japanese sequencing teams on mouse, rice, chimpanzee, nematoda and other organisms. The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD). Our complete genome sequence database, Genome Information Broker (GIB), has been improved by incorporating XML. It is now possible to perform a more sophisticated database search against the new GIB than the ordinary BLAST or FASTA search. 相似文献
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Megha Mohan Sau Lee Changning Guo S. Prasad Peri William H. Doub 《AAPS PharmSciTech》2017,18(5):1585-1594
The full-resolution next generation impactor (NGI) and three abbreviated impactor systems were used to obtain the apparent aerodynamic particle size distribution (APSD) and other quality measures for marketed dry powder inhalers (DPIs) using the compendial method and efficient data analysis (EDA). APSD for the active pharmaceutical ingredient (API) in Spiriva® Handihaler®, Foradil® Aerolizer®, and Relenza® Diskhaler® was obtained using a full-resolution NGI at 39, 60, and 90 L/min, respectively. Two reduced NGI (rNGI) configurations, the filter-only configuration (rNGI-f) and the modified-cup configuration (rNGI-mc), and the fast-screening impactor (FSI) with appropriate inserts to provide a 5-μm cut size were evaluated. The fine particle dose (FPD) obtained using the FSI for Spiriva was statistically similar to that obtained using the full NGI. However, the FPD for both Foradil and Relenza obtained using the FSI was significantly different from that obtained using the full NGI. Despite this, no significant differences were observed for the fine particle fraction (FPF) obtained using the FSI relative to that obtained from the full NGI for any of the DPIs. The use of abbreviated impactor systems appears promising with good agreement observed with the full-resolution NGI, except for small differences observed for the rNGI-mc configuration. These small differences may be product- and/or flow rate-specific, and further evaluation will be required to resolve these differences. 相似文献
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Biology Bulletin - At present, in Central Yakutia on the right bank of the Lena River, the northern border of the distribution of the Siberian musk deer has advanced to the mouth and lower reaches... 相似文献
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Konstantinos Mavromatis Ken Chu Natalia Ivanova Sean D. Hooper Victor M. Markowitz Nikos C. Kyrpides 《PloS one》2009,4(11)
Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG''s regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov. 相似文献
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This article deals with the results of the study of diatom algae of Lake Shira. The list of found algae contains 95 species
(126, including infraspecific taxa). A brief ecological and geographical analysis of the algal flora is made. 相似文献
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采用DNA分子测序技术对梧桐科5个族30个代表种的rbcL基因及核糖体DNA的内转录间隔区ITS序列(包括ITS1、ITS2和5.8srRNA基因)进行了序列分析。使用PAUP4.0b10软件对序列进行统计和分支分析。用启发式搜索方法寻找最简约树。从严格一致性树来看,梧桐科的全部代表类群主要被分为4支,一支仅为Sterculieae所构成;一支包括Helictereae的全部代表种;一支由Byttnerieae代表种所构成;最后一支由Dombeyeae和单属族翅子树族Pterospermeae所构成。rbcL和ITS系统树的不同仅表现在族内个别代表类群的位置和族的分支方式上。分析结果表明,与Helictereae相比,翅子树属,Pterospermum与Dombeyeae有更近的亲缘关系。然而,在外部形态、内部解剖和胚胎学方面,二者之间又存在诸多差异.故支持将Pterospermum另立为Ptcrospermeae的观点。 相似文献
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《遗传、选种与进化》2007,39(6):621-631
Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses. 相似文献
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Paleontological Journal - The Oxfordian–Kimmeridgian Cerithiopsidae, represented by two genera Cosmocerithium Cossmann, 1906 and Dragonia gen. nov. are re-investigated. Three species (C.... 相似文献
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世界秋海棠属侧膜组植物新资料 总被引:2,自引:0,他引:2
记述了秋海棠属侧膜组11新种,即星果草叶秋海棠(BegoniaasteropyrifoliaY.M.ShuietW.H.Chen)、耳托秋海棠(B.auritistipulaY.M.ShuietW.H.Chen)、桂南秋海棠(B.austroguangxiensisY.M.ShuietW.H.Chen)、水晶秋海棠(B.crystallinaY.M.ShuietW.H.Chen)、须苞秋海棠(B.fimbribracteataY.M.ShuietW.H.Chen)、巨叶秋海棠(B.gigaphyllaY.M.ShuietW.H.Chen)、黄氏秋海棠(B.huangiiY.M.ShuietW.H.Chen)、长柱秋海棠(B.longistylaY.M.ShuietW.H.Chen)、扁果秋海棠(B.platycarpaY.M.ShuietW.H.Chen)、喙果秋海棠(B.rhynchocarpaY.M.ShuietW.H.Chen)、多变秋海棠(B.variifoliaY.M.ShuietW.H.Chen);并报道了3新变种及1新名称,即疏毛越南秋海棠(B.boniiGagnep.var.remotisetulosaY.M.ShuietW.H.Chen)、密毛龙州秋海棠(B.morseiIrmsch.var.myriotrichaY.M.ShuietW.H.Chen)、簇毛伞叶秋海棠(B.umbr-aculifoliaY.WanetB.N.Changvar.flocculosaY.M.ShuietW.H.Chen)及彩纹秋海棠(B.variegataY.M.ShuietW.H.Chen)。 相似文献