Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies

Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino acid frequencies. These frequencies determine the maximum dissimilarity expected for highly diverged but functionally and structurally conserved sequences, and hence are crucial for estimating long distances. We introduce a codon- level model of coding sequence evolution in which position-specific amino acid frequencies are free parameters. In our implementation, these are estimated from an alignment using methods described previously. We use simulations to demonstrate the importance and feasibility of modeling such behavior; our model produces linear distance estimates over a wide range of distances, while several alternative models underestimate long distances relative to short distances. Site-to-site differences in rates, as well as synonymous/nonsynonymous and first/second/third-codon-position differences, arise as a natural consequence of the site-to-site differences in amino acid frequencies.      

High-level expression of the Endo-beta-N-acetylglucosaminidase F2 gene in E.coli: one step purification to homogeneity

The Endo F2gene was overexpressed in E.coli as a fusion protein joined to the maltose-binding protein. MBP-Endo F2was found in a highly enriched state as insoluble, inactive inclusion bodies. Extraction of the inclusion bodies with 20% acetic acid followed by exhaustive dialysis rendered the fusion protein active and soluble. MBP-Endo F2was digested with Factor Xaand purified on Q-Sepharose. The enzyme was homogeneous by SDS-PAGE, and appeared as a single symmetrical peak on HPLC. Analysis of the amino-terminus demonstrated conclusively that recombinant Endo F2was homogeneous and identical to the native enzyme.      

Design and analysis of a replicated server architecture for supporting IP–host mobility

Mobility support in IP networks requires servers to forward packets to mobile hosts and to maintain information pertaining to a mobile host's location in the network. In the mobile Internet Protocol (mobile-IP), location and packet forwarding functions are provided by servers referred to as home agents. These home agents may become the bottleneck when there are a large number of mobile hosts in the network. In this paper, we consider the design and analysis of a replicated server architecture in which multiple home agents are used to provide mobility support. In order to minimize the delay across the home agents, one of the key aspects is the design of load balancing schemes in which a home agent may transfer the control of a mobile host to another home agent in the same network. The methods for triggering the transfer and the policy for selecting the next home agent define various load balancing schemes which have different performance characteristics. In this paper, we design a protocol that forms the building block for implementing such load balancing schemes, and we then study the performance characteristics of three selection schemes, namely, random, round-robin, and join the shortest queue (JSQ), and three transfers policies, namely, timer-, counter- and threshold-based. The key results of this study are as follows: (1) The results show that both random and round-robin selection policies can yield modest load balancing gains, and that these gains increase when the traffic is more bursty (burstiness is defined as the ratio of the peak arrival rate to the mean arrival rate) as well as when there are more home agents. (2) The threshold-based transfer policy performs better than timer-based and counter-based policies, since in threshold-based policies transfers are made only when the queue is overloaded, unlike counter- and timer-based policies in which transfers can be made from an unloaded home agent to an overloaded home agent. This revised version was published online in August 2006 with corrections to the Cover Date.     

High Mean Water Vapour Pressure Promotes the Transmission of Bacillary Dysentery

Bacillary dysentery is an infectious disease caused by Shigella dysenteriae, which has a seasonal distribution. External environmental factors, including climate, play a significant role in its transmission. This paper identifies climate-related risk factors and their role in bacillary dysentery transmission. Harbin, in northeast China, with a temperate climate, and Quzhou, in southern China, with a subtropical climate, are chosen as the study locations. The least absolute shrinkage and selectionator operator is applied to select relevant climate factors involved in the transmission of bacillary dysentery. Based on the selected relevant climate factors and incidence rates, an AutoRegressive Integrated Moving Average (ARIMA) model is established successfully as a time series prediction model. The numerical results demonstrate that the mean water vapour pressure over the previous month results in a high relative risk for bacillary dysentery transmission in both cities, and the ARIMA model can successfully perform such a prediction. These results provide better explanations for the relationship between climate factors and bacillary dysentery transmission than those put forth in other studies that use only correlation coefficients or fitting models. The findings in this paper demonstrate that the mean water vapour pressure over the previous month is an important predictor for the transmission of bacillary dysentery.     

Comparison of Short- and Medium-Term Clinical Outcomes between Transradial Approach and Transfemoral Approach in a High-Volume PCI Heart Center in China

Background

Transradial approach (TRA) outweighed transfemoral approach (TFA) in acute coronary syndrome patients because the former has better short-term outcomes in high-volume percutaneous coronary intervention (PCI) centers. Our study was one of the limited studies specifically in comparing the short- and medium-term effects of TRA and those of TFA in patients undergoing elective PCIs.

Methods

A total of 21,242 patients who underwent elective PCI with stent implantation were included. Using propensity score methodology, 1,634 patient pairs were matched. Major clinical outcomes and PCI-related complications between TRA and TFA were compared.

Results

In the propensity score-matched patients, the rates of in-hospital net adverse clinical events, which included death, myocardial infarction (MI), target vessel revascularization (TVR), stroke, and major bleeding, were much lower with TRA than with TFA (1.8% vs. 3.9%, P < 0.001). This difference was mainly due to the lower rate of major bleeding (0.6% vs. 1.8%, P < 0.001) and the decreased rate of MI (1.1% vs. 1.9%, P = 0.060). PCI-related dissection and thrombosis were similar between the TRA and TFA groups (both P > 0.05). Meanwhile, one-year incidence rates of major adverse cardiovascular events, which included death, MI, and TVR, were also similar (4.1% vs. 4.9%, P = 0.272) in TRA and TFA. Multivariable regression analyses showed that TRA was an independent predictor of the low rate of in-hospital net adverse clinical events (odds ratio, 0.53; 95% confidence interval, 0.40 to 0.71), but not of major adverse cardiovascular events at one-year follow-up (hazard ratio, 1.01; 95% confidence interval, 0.96 to 1.06).

Conclusions

In patients undergoing elective PCI, TRA patients had lower rates of in-hospital net adverse clinical outcomes compared with TFA patients. TRA might be recommended as a routine approach in high-volume PCI hospitals for elective PCIs.     

Predictors and Treatments of Proglide-Related Complications in Percutaneous Endovascular Aortic Repair

Purpose

To investigate the predictors and treatment of the 6-Fr Perclose Proglide-related complications (PRC) in percutaneous endovascular aortic repair (pEVAR).

Methods

We retrospectively analyzed the PRC after pEVAR for the treatment of aortic aneurysm or dissection in our center from December 2012 to November 2013. Procedure success was defined as effective functioning of the two devices and local hemostasis. Access-related adverse events included vascular complications and device failures. Operative data and angiographic and computed tomography images were collected to assess the complications and treatment strategy.

Results

A total of 198 patients with 275 puncture sites underwent pEVAR with the 6-Fr Perclose Proglide. The procedure was successful in 178 patients (89.9%), whereas PRC occurred in 20 cases (10.1%), including 10 device failures and 10 vascular complications. An extra manual ancillary compression was conducted in 7 patients, one more device was used in 8 patients, and surgical repair of the femoral artery was performed in 5 patients. PRC had a tendency to occur in patients with body mass index (BMI)>30 kg/m² (p = 0.021), thoracic stent grafts (p = 0.038), common femoral artery (CFA) calcification (p = 0.001), CFA depth>4 cm (p = 0.001), and sheath size>20Fr (p = 0.005). Device failure-related mortality was zero. None of the access sites had complications during the midterm follow-up.

Conclusions

The pre-close technique with 6-Fr Perclose Proglide devices for pEVAR appears to be safe and effective with low technical failure and complication rates. Careful patient selection and proficiency in device manipulation might reduce the device related complications.     

微卫星技术在大耳白黑眼兔近交系培育中的监测分析

利用微卫星技术监测大耳白黑眼兔(white hair black eyes rabbits,WHBE兔)近交培育中第五代(F5)、第六代(F6)和第七代(F7)的遗传多样性.选取21个微卫譬座位,筛选出扩增产物稳定并且具有多态性的11对微卫星引物用于本研究.结果表明,F5代WHBE兔在每个座位上的等位基因数(Na)为3～9个不等,11个座位的平均有效等位基因数(Ne)为1.81个,平均观察杂合度(Ho)和平均多态信息含量(PIC)分别为0.381和0.524,累积个体识别率(CDP)达到100%,累积非父排除概率(CPE)在双亲信息都是未知情况下的为0.926,而在得知任一亲本信息的情况F,CPE值为0.993.F6代WHBE兔在每个座位上的Na为3～8个不等,11个座位的平均Ne为1.68个,平均Ho和PIC值分别为0.356和0.548,CDP达到100%,CPE在双亲信息都是未知情况下的为0.931,而在得知任一亲本信息的情况下,CPE值为0.994.F7代WHBE兔在每个座位上的Na为2～6个不等,11个座位的Ne为1.51个,平均Ho和PIC值分别为0.287和0.498,CDP达到100%,CPE在双亲信息都是未知情况下的为0.891,而在得知任一亲本信息的情况下,CPE值为0.986.在近交系培育过程中,从F5代到F7代,WHBE兔的平均Ne和平均Ho 都呈下降趋势,提示随着近交代数的增加,WHBE兔的基因纯合度越来越高.