A New Model for a Carpool Matching Service

Carpooling is an effective means of reducing traffic. A carpool team shares a vehicle for their commute, which reduces the number of vehicles on the road during rush hour periods. Carpooling is officially sanctioned by most governments, and is supported by the construction of high-occupancy vehicle lanes. A number of carpooling services have been designed in order to match commuters into carpool teams, but it known that the determination of optimal carpool teams is a combinatorially complex problem, and therefore technological solutions are difficult to achieve. In this paper, a model for carpool matching services is proposed, and both optimal and heuristic approaches are tested to find solutions for that model. The results show that different solution approaches are preferred over different ranges of problem instances. Most importantly, it is demonstrated that a new formulation and associated solution procedures can permit the determination of optimal carpool teams and routes. An instantiation of the model is presented (using the street network of Guangzhou city, China) to demonstrate how carpool teams can be determined.     

宏蛋白质组学:研究微生物群落的一种新策略

宏蛋白质组学是一种运用蛋白质组技术对特定微生物群落所产生的全部蛋白质进行大规模研究与分析的新技术。简要概述宏蛋白组学的产生、研究策略及其应用情况,并对其应用前景进行展望。     

The Disturbed Resource-Flux Invasion Matrix: A New Framework for Patterns of Plant Invasion

Attempts to classify certain habitats as vulnerable to invasion or plant traits as invasive have met with limited success and applicability. Clearly, not all plant invaders are able to exploit all habitats and not all habitats are equally susceptible to invasion. Here we argue that it is critical for a successful model for invasions to incorporate both environmental and species traits and present just such a framework. Although disturbance has been targeted as a crucial event which renders habitats vulnerable to invasion, disturbances are often integral parts of ecosystems (e.g. floods, tree-falls, fire, etc.) and are not always associated with invasion events. We argue that disturbances that are associated with invasions alter historical patterns of turnover, or flux, of resources in an ecosystem. Given this perspective on the relationship between invasions and disturbances, and the need to integrate species traits with those of invaded ecosystems, we have developed an approach to characterize plant invasion patterns that we call the Disturbed Resource-Flux Invasion Matrix or DRIM. This is a 16-cell matrix that classifies habitats by the quality of changes in physical and chemical resource flux either increasing or decreasing flux relative to historical patterns. Within each matrix cell, it is then possible to apply basic ecological principles to target species traits that can facilitate successful invasion of habitats experiencing that particular kind of disturbance. We present examples from the literature of how habitats and species can be classified according to the DRIM, and demonstrate the application of this theoretical model.     

宏基因组学:土壤微生物研究的新策略

土壤中多数微生物不可培养,这限制了微生物资源的开发利用。宏基因组学方法在开发和利用不可培养微生物资源方面有巨大潜力,可以将其运用到土壤微生物学研究中。对土壤宏基因组DNA的提取、宏基因组文库的构建和筛选等方面的研究现状和进展进行了简要综述。     

Controlled Enzymatic Hydrolysis: A New Strategy for the Discovery of Antimicrobial Peptides

The use of antimicrobial peptides (AMPs) is an alternative to traditional antibiotics. AMPs are obtained using different methods such as bacterial synthesis, chemical synthesis and controlled enzymatic hydrolysis. The later is an interesting approach that deserves our attention because of the yields gathered and peptides engineered. Usually, activities of AMPs obtained in such a way are tightly dependent on the hydrolysis mechanism used. This paper deals with the hydrolysis of hemoglobin mechanism as a potential source of AMPs. Production of AMPs from hemoglobin using enzymatic controlled system is linked to hemoglobin structure. Further, we show that bovine hemoglobin, which is sensitive to peptic hydrolysis, results upon enzymatic digestion as a great source of AMPs. The hemoglobin in native and denatured states was hydrolyzed by “one-by-one” and “zipper” mechanisms, respectively. Nevertheless, a new mechanism named “semi-zipper” mechanism is obtained when protein is in molten globule structural state, constituting an original strategy for AMPs production. Seventy seven percentage of the peptides obtained by this new strategy showed antibacterial activity against nine strains.     

rhBNP治疗射血分数保留急性心力衰竭的临床研究

目的:探讨重组人脑利钠肽(rh BNP)对急性射血分数保留心力衰竭的临床治疗作用。方法:选择2008年6月至2014年6月间我院收治的20例急性射血分数保留心力衰竭患者为研究对象,其中10例予以硝普钠静脉注射48小时,10例予以rh BNP静脉注射48小时。48小时后,评估和比较两组患者心力衰竭的临床改善情况;72小时后,复查和比较两组患者血浆NT-pro BNP的下降值。结果:硝普钠组患者呼吸困难缓解积分(1.4±1.35)明显低于rh BNP组(3.5±0.71),rh BNP组呼吸困难缓解时间(3.68±1.69 h)显著短于硝普钠组(21.50±18.43 h),血浆NT-pro BNP浓度下降值(864.60±585.92 pg/ml)明显高于硝普钠组(423.30±284.06 pg/ml)。结论:rh BNP治疗急性射血分数保留心力衰竭的临床疗效优于硝普钠。     

The Nature of Expertise in Fingerprint Matching: Experts Can Do a Lot with a Little

Expert decision making often seems impressive, even miraculous. People with genuine expertise in a particular domain can perform quickly and accurately, and with little information. In the series of experiments presented here, we manipulate the amount of “information” available to a group of experts whose job it is to identify the source of crime scene fingerprints. In Experiment 1, we reduced the amount of information available to experts by inverting fingerprint pairs and adding visual noise. There was no evidence for an inversion effect—experts were just as accurate for inverted prints as they were for upright prints—but expert performance with artificially noisy prints was impressive. In Experiment 2, we separated matching and nonmatching print pairs in time. Experts were conservative, but they were still able to discriminate pairs of fingerprints that were separated by five-seconds, even though the task was quite different from their everyday experience. In Experiment 3, we separated the print pairs further in time to test the long-term memory of experts compared to novices. Long-term recognition memory for experts and novices was the same, with both performing around chance. In Experiment 4, we presented pairs of fingerprints quickly to experts and novices in a matching task. Experts were more accurate than novices, particularly for similar nonmatching pairs, and experts were generally more accurate when they had more time. It is clear that experts can match prints accurately when there is reduced visual information, reduced opportunity for direct comparison, and reduced time to engage in deliberate reasoning. These findings suggest that non-analytic processing accounts for a substantial portion of the variance in expert fingerprint matching accuracy. Our conclusion is at odds with general wisdom in fingerprint identification practice and formal training, and at odds with the claims and explanations that are offered in court during expert testimony.     

A New Protecting Group Strategy for Amino Groups in Oligonucleotide Chemistry: CEOC Group

Abstract

A new protecting group, 2-cyanoethyloxycarbonyl, or CEOC, has been developed for amino groups and utilized in synthesizing modified oligonucleotides. (CEOC)-oxy-succinimide reagent has been synthesized to introduce this protecting group. The protecting group is removed by standard oligonucleotide deprotection protocols. Using this approach, oligonucleotides have been synthesized with various types of alkylamine substituents.     

重组酶聚合酶扩增技术：一种新的核酸扩增策略

重组酶聚合酶扩增 (recombinase polymerase amplification, RPA)是近年来兴起的一种等温核酸扩增技术,它比聚合酶链式反应(polymerase chain reaction, PCR)及其它等温扩增技术更快速、便捷、高效。本文将详细介绍RPA这项新颖的技术,并对其在医疗诊断、农业、食品、生物安全等方面的研究及应用进展进行综述。期望这项技术得到更多的关注,使其发展更加完善,将来在更多的领域充分发挥作用,甚至书写核酸检测历史新篇章。     

A New Strategy for DNA Inhibition with Backbone Substituted DNA Analogues

Abstract

Methylphosphotriester DNA shows a number of unique (bio)chemical properties: formation of parallel right-handed, anti-parallel left- and right-handed duplexes, and a high sequence-specific affinity for natural DNA. The impact of (pro)chirality of phosphorus in natural and modified DNA is discussed.     

利用酵母展示系统确定空间构象性抗原表位的方法研究

酵母展示系统是研究可溶性蛋白间相互作用的有效系统.利用酵母展示系统可以简单快速地研究抗原与抗体相互作用.充分利用此系统的优势,在确定空间构象性的抗原决定簇方面发展出新的应用.利用酵母同源重组把巨噬细胞迁移抑制因子(macrophage migration inhibitory factor,MIF)序列中的不同肽段以及不同点突变体展示在酵母表面,并用3个抗MIF单克隆抗体10C3,2A12和4E10分别标记,流式细胞仪检测抗体与抗原突变体的结合.用酵母展示方法确定了MIF上与3个单克隆抗体结合的关键氨基酸序列,从而建立起一个简便可靠的确定空间构象性抗原决定簇的方法.     

提高Xa因子酶切效率的策略

为提高Xa因子对融合蛋白CBD-IGF和CBD-PACAP的酶切效率 ,以便高效释放非融合的重组多肽 ,利用基因工程技术在两个融合蛋白中Xa因子识别位点 (Ile-Glu-Gly-Arg↓ )前均引入 7个氨基酸组成的富含甘氨酸柔性短肽 (Gly-Thr-Gly-Gly-Gly-Ser-Gly)。纤维素亲和层析纯化各个融合蛋白 ,比较Xa因子对引入短肽前、后融合蛋白的酶切效率。比较结果表明 :短肽的引入不同程度地提高了融合蛋白CBD-IGF和CBD-PACAP对Xa因子的敏感性 ;但总体上CBD-IGF对Xa因子的敏感性比CBD-PACAP低。此研究结果提供了一种提高Xa因子酶切效率的策略。     

pepgrep: A Tool for Peptide MS/MS Pattern Matching

Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a compact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 fingerprint for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to-MS2 scoring algorithm. pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface (API) or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity purification techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http://bsproteomics.essex.ac.uk:8080/data/download/pepgrep-1.4.tgz.     

Expression and Purification of a Spider Silk Protein: A New Strategy for Producing Repetitive Proteins

Synthetic genes were constructed based on the known sequence of the spider dragline silk protein MaSp 2. The genes had 8, 16, or 32 contiguous units of the consensus repeat sequence of the protein. These artificial genes were constructed using a strategy involving compatible but nonregenerable restriction sites, which allowed construction of very large inserts in a precisely controlled manner. This strategy should have general utility in the controlled construction of repetitive proteins composed of identical or different repeat units. The protein from the 16-unit repeat was produced inEscherichia coliat levels up to 10 mg/g wet wt of cells although yields of 1–2 mg/g were more typical. The protein was easily purified with high recovery using an affinity column. The purified protein had the predicted amino acid composition and N-terminal sequence after cleavage of a leader sequence. The methodology described will allow production of sufficient quantities of protein for basic structure/function studies including production of synthetic fibers.     

A New Brain Drug Delivery Strategy: Focused Ultrasound-Enhanced Intranasal Drug Delivery

Central nervous system (CNS) diseases are difficult to treat because of the blood-brain barrier (BBB), which prevents most drugs from entering into the brain. Intranasal (IN) administration is a promising approach for drug delivery to the brain, bypassing the BBB; however, its application has been restricted to particularly potent substances and it does not offer localized delivery to specific brain sites. Focused ultrasound (FUS) in combination with microbubbles can deliver drugs to the brain at targeted locations. The present study proposed to combine these two different platform techniques (FUS+IN) for enhancing the delivery efficiency of intranasally administered drugs at a targeted location. After IN administration of 40 kDa fluorescently-labeled dextran as the model drug, FUS targeted at one region within the caudate putamen of mouse brains was applied in the presence of systemically administered microbubbles. To compare with the conventional FUS technique, in which intravenous (IV) drug injection is employed, FUS was also applied after IV injection of the same amount of dextran in another group of mice. Dextran delivery outcomes were evaluated using fluorescence imaging of brain slices. The results showed that FUS+IN enhanced drug delivery within the targeted region compared with that achieved by IN only. Despite the fact that the IN route has limited drug absorption across the nasal mucosa, the delivery efficiency of FUS+IN was not significantly different from that of FUS+IV. As a new drug delivery platform, the FUS+IN technique is potentially useful for treating CNS diseases.     

肿瘤新生血管及分子靶向治疗新策略

肿瘤血管靶向治疗是基于肿瘤新生血管与正常血管的不同,药物专一识别并阻断肿瘤新生血管,使肿瘤细胞“饿死”,而不影响正常细胞。从1971年Folkman提出“饿死肿瘤”的假说到2004年第一个血管靶向药物上市,记载着30多年领域发展的传奇经历。当今,肿瘤血管已成为生物医学和临床研究的热点,新的发现层出不穷。该文重点介绍肿瘤血管新靶点、新机制、新药物与未来发展。