MRI-SNAP序列诊断CAP患者的影像学技术分析

目的研究磁共振(MRI)-同步非对比剂血管成像和斑块内出血成像(SNAP)序列诊断颈动脉粥样硬化斑块(CAP)患者的影像学技术。方法选择2017年5月—2019年5月本院收治的CAP患者70例进行研究。所有患者均予以3.0T MRI-SNAP序列诊断以及传统多对比序列血管成像诊断,完成斑块内钙化(CA)、出血(IPH)、溃疡(UL)、脂质(LRNC)等成分的检测。且以术后病理结果作为金标准,比较MRI-SNAP序列与传统多对比序列诊断CA、IPH、UL、LRNC的能效。结果除了LRNC敏感度与准确度外,SNAP序列诊断敏感度、特异度、准确度均高于传统序列,且其诊断IPH的准确度显著高于传统序列(P<0.05)。经ROC曲线分析可得:SNAP序列诊断CA、IPH、UL的曲线下面积均显著高于传统序列诊断(均P<0.05)。结论 MRI-SNAP序列诊断CAP患者的敏感度、特异度、准确度较高。

Fast algorithm for constructing neighbor-joining phylogenetic trees

To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.

Phylogenetic Analysis of Cystatin

[Objective] The molecular weight,isoelectric point,signal peptide,domain and other properties of the encoding protein of the known cystatin genes were analyzed.[Method] Cystatin genes were searched in NCBI and the related amino acids sequences were downloaded.SMART software was used to predict the domain.SingalP program was used to search signal peptide.TMHMM program was used to search and predict the transmembrane domain.CLUSTAL W program was used to make multiple sequence alignment.Using MEGA3.1 software,...

Molecular Studies on Heat Shock Protein 70 Gene （Hsp70） Using ClustalW Multiple Sequence Alignment Analysis

Degenerate primers are particularly useful in amplifying homologous genes from different organisms. This paper describes a method for designing degenerate primers for a given multiple alignment of DNA sequences of Hsp70 gene family using ClustalW algorithm. The authors used an in silico approach to find a homology between more than one accession numbers of DNA sequences, X67711.2 was for Oryza sativa Hsp70, AY372071.1 was for Nicotiana tabacum Hsp70 and L41253.2 was for Lycopersicon esculentum Hsc70. The three accession numbers which were retrieved by the BLASTn program depend on their expected value （E-value）. Multiple sequence alignment was performed by ClustalW algorithm to produce a conserved blocks and determine the consensus region which had been used to produce the forward and reverse primer by the primer select module of DNAStar Lasergene V7 and In-Silco PCR module of FASTPCR program ver.4.0.8 was performed to detect the melting temperatures （Tm） and predict the PCR product size, The results of designed degenerate primer showed that there was a homology found between the designed primers and the DNA templates for the three accession numbers with at least 80% identity. The result of degenerate PCR showed that the three bands of the amplified PCR products of the three accession numbers were detected at the same molecular weight of marker （400 bp） with a difference about 15 pb compared to the in silco PCR product （385 pb）. In conclusion, this study focused on the importance of using the clustalW algorithm for designing the degenerate primer.

Cultivable Bacterial Diversity of the East China Sea

Bacterial diversity of 14 sites of the East China Sea was investigated by culture-dependent methods. The impact of human activities on marine bacteria was primarily studied and characteristics of bacteria communities in different areas were analyzed. A total of 396 strains were obtained. These strains belong to 4 phyla, 9 classes and 146 species according to 16S rDNA sequences alignment. For 32 strains, the 16S rDNA sequences similarities between isolated strains and their most closely related species were lower than 98%. The result indicated that there are abundant microbial diversity and a large number of unknown microbial resources in the East China Sea. Isolated strains were dominated byy-proteobacteria （64%）, ct-proteobacteria （18%） and Firmicutes （15%）. Actinobacteria and Bacteroidetes were less than 3%. Microbial community composition, diversity and abundance among areas with varies distances from land were different. The far the regions from the land, the lower the Shannon index （H＇） and the Margalef index （DMg） values were.

Fast vectorized distance matrix computation for multiple sequence alignment on multi-cores

Although high quality multiple sequence alignment is an essential task in bioinforma- tics, it becomes a big dilemma nowadays due to the gigantic explosion in the amount of molecular data. The most consuming time and space phase is the distance matrix computation. This paper addresses this issue by proposing a vectorized parallel method that accomplishes the huge number of similarity comparisons faster in less space. Per- formance tests on real biological datasets using core-iT show superior results in terms of time and space.