货物装卸中的一个排序问题

本文考虑货物装卸管理中船主和港口之间的下述相互制约关系：有n条船在时刻零同时抵达同一码头装卸货物,因而也希望在同一时刻守成装卸货物。如某船的货物不能如期装卸守而延误了该船的离港,船主会向港方索取赔偿,反之如货物提前装卸完而使该船河提前投入运输,则船主会向港方付取奖金,加上正常装卸费用,从港方来说要适当考虑n条船的一个装卸顺序,使总费用减少,对这一NP-困难的排序问题,文中给出了几个多项式可解的特殊情形,一般情况下的一个快速下界估计方法以及相应的分支定界算法。     

Integrating Interval Estimates of Global Optima and Local Search Methods for Combinatorial Optimization Problems

The problem of estimating the global optimal values of intractable combinatorial optimization problems is of interest to researchers developing and evaluating heuristics for these problems. In this paper we present a method for combining statistical optimum prediction techniques with local search methods such as simulated annealing and tabu search and illustrate the approach on a single machine scheduling problem. Computational experiments show that the approach yields useful estimates of optimal values with very reasonable computational effort.     

A set of novel multi-allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

Massively parallel sequencing (MPS) technology allows to simultaneously type multitudinous molecular genetic markers for many samples in one run with the feature of high detection resolution, and thereby arouses the increasing attention from forensic science. Herein, multiple allelic single nucleotide polymorphisms (multi-allelic SNPs) were screened for personal identification and parentage testing, and then were genotyped using MPS platform. Unrelated individuals of Chinese Mongolian and Kazakh groups were investigated to further estimate forensic effectiveness and applicability of these multi-allelic SNPs. The results of sequencing efficiency estimations and forensic genetic statistical parameters demonstrated that this MPS panel of multi-allelic SNPs was expected to be work for forensic applications. Subsequently, the exploration of population genetic variation patterns among the two investigated groups and other 26 reference populations revealed that these Chinese Mongolian and Kazakh groups had the similar population genetic patterns with the populations from East Asian, but European ancestral composition in the Kazakh group was higher than that in the Mongolian group. Currently, the present results were the preliminary research to scrutinize genetic information of these two ethnic minority groups employing multi-allelic SNPs.     

Convexity in Scheduling Problems

凸性在连续性最优化理论中起着重要的作用．它在离散性最优化中的相应概念尚待研究．本文运用差分和次梯度的概念给出排序问题中离散凸性的描述，并指出凸性在构造最优排序中的重要性．     

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach

Massively parallel sequencing (MPS) technologies, also termed as next‐generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two‐round PCR that requires more steps, making it time‐consuming (about 2 days), laborious and expensive. In this study, a 16‐plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database‐type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS‐based STR typing and capillary electrophoresis (CE)‐based STR typing. The inconsistency might have been caused by off‐ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large‐scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation‐friendly process flow that saves labor, time and costs.     

RNA修饰分析方法研究进展

迄今为止,在RNA分子中发现150多个转录后修饰。研究表明RNA中大量动态、可逆的修饰具有多种生物学功能,能够参与真核生物基因表达的调控。因此,了解RNA修饰的动态分布、机制、调控和功能可以扩展人们对生命体调控机制的深入认识和理解。破译RNA修饰的生物学功能主要依赖于对这些修饰的精确检测、定量和定位分析。近10年来,用于RNA修饰的分析方法得到显著发展,促使RNA修饰领域发生了巨大变革。该文总结了RNA修饰分析方法的原理、优点和缺点,并对RNA修饰研究技术的发展进行了展望。     

Abiotic Sequence‐Coded Oligomers as Efficient In Vivo Taggants for the Identification of Implanted Materials

Sequence‐defined oligourethanes were tested as in vivo taggants for implant identification. The oligomers were prepared in an orthogonal solid‐phase iterative approach and thus contained a coded monomer sequence that can be unequivocally identified by tandem mass spectrometry (MS/MS). The oligomers were then included in small amounts (1 wt %) in square‐centimeter‐sized crosslinked poly(vinyl alcohol) (PVA) model films, which were intramuscularly and subcutaneously implanted in the abdomen of rats. After one week, one month, or three months of implantation, the PVA films were explanted. The rat tissues exposed to the implants did not exhibit any adverse reactions, which suggested that the taggants are not harmful and probably not leaching out from the films. Furthermore, the explanted films were immersed in methanol, as a solvent for oligourethanes, and the liquid extract was analyzed by mass spectrometry. In all cases, the oligourethane taggant was detected, and its sequence was identified by MS/MS.     

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry‐based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium–based isobaric tag for relative and absolute quantification of peptides (QAS‐iTRAQ 2‐plex). Upon collisional activation, the new stable benzylic‐type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS‐iTRAQ 2‐plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides.     

Cyclic and Lasso Peptides: Sequence Determination,Topology Analysis,and Rotaxane Formation

A broadly applicable chemical cleavage methodology to facilitate MS/MS sequencing was developed for macrocyclic and lasso peptides, which hold promise as exciting new therapeutics. Existing methods such as Edman degradation, CNBr cleavage, and enzymatic digestion are either limited in scope or completely fail in cleavage of constrained nonribosomal peptides. Importantly, the new method was utilized for synthesizing a unique peptide‐based rotaxane (both cyclic and threaded) from the lasso peptide, benenodin‐1 ΔC5.     

Cleavable Binary Dyads: Simplifying Data Extraction and Increasing Storage Density in Digital Polymers

Digital polymers are uniform macromolecules that store monomer‐based binary sequences. Molecularly stored information is usually extracted from the polymer by a tandem mass spectrometry (MS/MS) measurement, in which the coded chains are fragmented to reveal each bit (i.e. basic coded monomer unit) of the sequence. Here, we show that data‐extraction can be greatly simplified by favoring the formation of MS/MS fragments containing two bits instead of one. In order to do so, digital poly(alkoxyamine phosphodiester)s, containing binary dyads in each repeat unit, were prepared by an orthogonal solid‐phase approach involving successive phosphoramidite and radical‐radical coupling steps. Three different sets of monomers were considered to build these polymers. In all cases, four coded building blocks—two hydroxy‐nitroxides and two phosphoramidite monomers—were required to build the dyads. Among the three studied monomer sets, one combination allowed synthesis of uniform sequence‐coded polymers. The resulting polymers led to clear dyad‐containing fragments in MS/MS and could therefore be efficiently decoded. Additionally, an algorithm was created to detect specific dyad fragments, thus enabling automated sequencing.