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Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era

Quantitative Biology 2019年第4期7卷 278-292页

作者： Raffaella Rizzi Stefano Beretta murray patterson Yuri Pirola Marco Previtali Gianluca Della Vedova Paola Bonizzoni Department of Informatics Systems and CommunicationsUniversity of Milan-BicoccaMilanViale Sarca 33620126Italy

Background:De novo genome assembly relies on two kinds of graphs:de Bruijn graphs and overlap *** graphs are the basis for the Celera assembler,while de Bruijn graphs have become the dominant technical device in the last *** two kinds of graphs are collectively called assembly ***:In this review,we discuss the most recent advances in the problem of constructing,representing and navigating assembly graphs,focusing on very large *** will also explore some computational techniques,such as the Bloom filter,to compactly store graphs while keeping all functionalities ***:We complete our analysis with a discussion on the algorithmic issues of assembling from long reads(eg.,PacBio and Oxford Nanopore).Finally,we present some of the most relevant open problems in this field.

关键词： overlap graphs de Bruijn graphs genome assembly long reads string graphs

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循环饥饿激素加速糖尿病胃轻瘫患者胃排空:一项双盲、安慰剂、对照、交叉研究

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世界核心医学期刊文摘（胃肠病学分册） 2006年第4期2卷 40-40页

作者： murray C.D.R Martin N.M patterson M. A.V. Emmanuel 王志宇 Physiology Unit St. Mark‘s Hospital Harrow HA1 3UJ United KingdomDr.

Background: Diabetic gastroparesis is a disabling condition with no consistently effective treatment. In animals, ghrelin increases gastric emptying and reverses postoperative ileus. We present the results of a double blind, placebo controlled, crossover study of ghrelin in gastric emptying in patients with diabetic gastroparesis. Methods: Ten insulin requiring diabetic patients (fivemen, six type I) referred with symptoms indicative of gastroparesis received a two hour infusion of either ghrelin (5 pmol/kg/min) or saline on two occasions. Blood glucose was control led by euglycaemic clamp. Gastric emptying rate (GER) was calculated by real tim e ultrasound following a test meal. Blood was sampled for ghrelin, growth hormon e (GH), and pancreatic polypeptide (PP) levels. Cardiovagal neuropathy was asses sed using the Mayo Clinic composite autonomic severity score (range 0 (normal)- 3). Results: Baseline ghrelin levels were mean 445 (SEM 36) pmol/l. Ghrelin infu sion achieved a peak plasma level of 2786 (188) pmol/l at 90 minutes, correspond ing to a peak GH of 70.9 (19.8) pmol/l. Ghrelin increased gastric emptying in se ven of 10 patients (30 (6)%to 43 (5)%; p = 0.04). Impaired cardiovagal tone co rrelated inversely with peak postprandial PP values (p < 0.05) but did not corre late with GER. Conclusions: Ghrelin increases gastric emptying in patients with diabetic gastroparesis. This is independent of vagal tone. We propose that analo gues of ghrelin may represent a new class of prokinetic agents.

关键词：糖尿病胃轻瘫饥饿激素安慰剂对照胃排空率交叉研究实时超声显像术后肠梗阻迷走神经损伤致残

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