The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

Influence of ambient temperature on the CO_(2)emitted of light-duty vehicle

Because of global warming,people have paid more attention to greenhouse gas emitted by vehicles.To quantify the impact of temperature on vehicle CO_(2)emissions,this study was conducted using the world light vehicle test cycle on two light-duty E10 gasoline vehicles a ambient temperatures of-10,0,23,and 40℃,and found that CO_(2)emission factors of Vehicle1 in the low-speed phase were 22.07%and 20.22%higher than those of Vehicle 2 at cold star and hot start under-10℃.The reason was vehicle 1 had a larger displacement and more friction pairs than vehicle 2.There was the highest CO_(2)emission at the low-speed phase due to low average speed,frequent acceleration,and deceleration.The CO_(2)temperature factor and the ambient temperature had a strong linear correlation(R2=0.99).According to CO_(2)temperature factors and their relationships,CO_(2)emission factors of other ambien temperatures could be calculated when the CO_(2)emission factor of 23℃was obtained,and the method also could be used to obtain the CO_(2)temperature factors of different vehicles.To separate the effect of load setting and temperature variation on CO_(2)emission quantitatively a method was proposed.And results showed that the load setting was dominant for the CO_(2)emission variation.Compared with 23℃,the CO_(2)emission for vehicle 1 caused by load setting variation were 62.83 and 47.42 g/km,respectively at-10 and 0℃,while those fo vehicle 2 were 45.01 and 35.63 g/km,respectively.

革兰氏阴性菌膜间质蛋白酶DegP研究进展

膜间质蛋白酶(DegP),是一种广泛存在于真核生物和原核生物细胞中的蛋白。DegP同时具有酶活性和分子伴侣活性,并通过多聚体构成胶囊状结构执行其分子伴侣功能。DegP的酶活性依赖酶切位点与PDZ1结构域双重识别方式识别底物,这种识别模式被称为"分子量尺"。在革兰氏阴性菌中,DegP主要位于膜间质,通过分子伴侣活性与酶活性帮助保护错误折叠蛋白或降解变性蛋白。DegP也参与外膜蛋白的转运,是DegP胞内活性的研究重点。DegP也可以被分泌到胞外,帮助宿主对抗恶劣环境,并参与调节生物被膜的形成。本文将从DegP的结构与活性、胞内功能与胞外功能三大方面对DegP的研究进展进行总结,为革兰氏阴性菌周质中蛋白质质量控制与DegP体外功能的进一步研究提供参考。

Adjuvant chemotherapy versus adjuvant concurrent chemoradiotherapy after radical surgery for early-stage cervical cancer:a randomized,non-inferiority,multicenter trial

We conducted a prospective study to assess the non-inferiority of adjuvant chemotherapy alone versus adjuvant concurrent chemoradiotherapy (CCRT) as an alternative strategy for patients with early-stage (FIGO 2009 stage IB–IIA) cervical cancer having risk factors after surgery. The condition was assessed in terms of prognosis, adverse effects, and quality of life. This randomized trial involved nine centers across China. Eligible patients were randomized to receive adjuvant chemotherapy or CCRT after surgery. The primary end-point was progression-free survival (PFS). From December 2012 to December 2014, 337 patients were subjected to randomization. Final analysis included 329 patients, including 165 in the adjuvant chemotherapy group and 164 in the adjuvant CCRT group. The median follow-up was 72.1 months. The three-year PFS rates were both 91.9%, and the five-year OS was 90.6% versus 90.0% in adjuvant chemotherapy and CCRT groups, respectively. No significant differences were observed in the PFS or OS between groups. The adjusted HR for PFS was 0.854 (95% confidence interval 0.415–1.757;P = 0.667) favoring adjuvant chemotherapy, excluding the predefined non-inferiority boundary of 1.9. The chemotherapy group showed a tendency toward good quality of life. In comparison with post-operative adjuvant CCRT, adjuvant chemotherapy treatment showed non-inferior efficacy in patients with early-stage cervical cancer having pathological risk factors. Adjuvant chemotherapy alone is a favorable alternative post-operative treatment.

A NOTE ON THE GRADIENT PROJECTION METHOD WITH EXACT STEPSIZE RULE

In this paper, we give some convergence results on the gradient projection method with exact stepsize rule for solving the minimization problem with convex constraints. Especially, we show that if the objective function is convex and its gradient is Lipschitz continuous, then the whole sequence of iterations produced by this method with bounded exact stepsizes converges to a solution of the concerned problem.

Gynecologic infections seen in ThinPrep cytological test in Wuhan, China

This study aimed to analyze the prevalence of bacterial, Candida, Trichomonas, and human papillomavirus （HPV） infections in ThinPrep cytological test （TCT） performed on women of Wuhan, China. ThinPrep smears were screened by two independent experienced pathologists and reported from 2008 to 2010. A total of 46 866 ThinPrep smears were studied, and smears with inflammation were analyzed. Of the 44 162 enrolled patients, inflammation changes were observed in 21 935 （49.7%） and specific infections in 6884 （31.4%）. The infections detected were as follows： bacteria, 5663 （82.3%）; Candida, 825 （12.0%）; Trichomonas, 273 （4.0%）; and HPV, 148 （2.1%）. Significant changes were found in the prevalence of bacteria and Candida among women who underwent TCT before and after 2010. Z2 revealed an increasing proportion of specific infections found in smears after 2010 （P = 0.000）. In conclusion, bacterial infection was the most detectable in the ThinPrep smears, followed by Candida and Trichomonas. The prevalence of infection identified by TCT was found to be similar in previous literature in China.

CONVERGENCE PROPERTIES OF THE DEPENDENT PRP CONJUGATE GRADIENT METHODS

In this paper, a new region of βk with respect to ;βk^PRP is given. With two Armijo-type line searches, the authors investigate the global convergence properties of the dependent PRP conjugate gradient methods, which extend the global convergence results of PRP conjugate gradient method proved by Grippo and Lucidi （1997） and Dai and Yuan （2002）.

GLOBAL CONVERGENCE OF A CLASS OF SMOOTH PENALTY METHODS FOR SEMI-INFINITE PROGRAMMING

For the semi-infinite programming （SIP） problem, the authors first convert it into an equivalent nonlinear programming problem with only one inequality constraint by using an integral function, and then propose a smooth penalty method based on a class of smooth functions. The main feature of this method is that the global solution of the penalty function is not necessarily solved at each iteration, and under mild assumptions, the method is always feasible and efficient when the evaluation of the integral function is not very expensive. The global convergence property is obtained in the absence of any constraint qualifications, that is, any accumulation point of the sequence generated by the algorithm is the solution of the SIP. Moreover, the authors show a perturbation theorem of the method and obtain several interesting results. Furthermore, the authors show that all iterative points remain feasible after a finite number of iterations under the Mangasarian-Fromovitz constraint qualification. Finally, numerical results are given.

GLOBAL CONVERGENCE OF THE DAI-YUAN CONJUGATE GRADIENT METHOD WITH PERTURBATIONS

In this paper, the authors propose a class of Dai-Yuan （abbr. DY） conjugate gradient methods with linesearch in the presence of perturbations on general function and uniformly convex function respectively. Their iterate formula is xk＋1 = xk ＋ αk（sk ＋ ωk）, where the main direction sk is obtained by DY conjugate gradient method, ωk is perturbation term, and stepsize αk is determined by linesearch which does not tend to zero in the limit necessarily. The authors prove the global convergence of these methods under mild conditions. Preliminary computational experience is also reported.

ON THE CONVERGENCE OF A NEW HYBRID PROJECTION ALGORITHM

For unconstrained optimization, a new hybrid projection algorithm is presented m the paper. This algorithm has some attractive convergence properties. Convergence theory can be obtained under the condition that Δ↓f（x） is uniformly continuous. If Δ↓f（x） is continuously differentiable pseudo-convex, the whole sequence of iterates converges to a solution of the problem without any other assumptions. Furthermore, under appropriate conditions one shows that the sequence of iterates has a cluster-point if and only if Ω＊ ≠ θ. Numerical examples are given at the end of this paper.

亚低温联合去骨瓣减压术治疗脑梗死后难治性高颅压一例

恶性大脑中动脉梗死(malignant middle cerebral artery infarct,MMI)是一种严重的脑血管缺血性疾病,可形成幕上占位性脑梗死,引起难治性高颅压,导致神经功能急剧恶化,致残率和死亡率高,严重影响患者生活质量和生命安全,预后极差。尽早开通血管在缺血性脑卒中领域的作用已得到肯定,而关于有效治疗大面积脑梗死血管开通后出现的脑水肿的研究却很少。近几年,越来越多的研究成果证实了亚低温治疗和去骨瓣减压术(decompressive craniectomy,DC)能够缓解MMI后出现的高颅压。本文报道1例亚低温联合去骨瓣减压术治疗MMI后出现的高颅压,预后良好。