紫色球杆菌视紫红质光谱特性的机器学习研究

近年来，机器学习等人工智能技术被应用于蛋白质工程，其在蛋白质结构、功能预测、催化活性等研究中具有独特优势。在未知蛋白质结构的情况下，将蛋白质序列和功能特性与机器学习相结合，基于序列-活性关系（innovative sequence-activity relationship，ISAR）算法，将蛋白质氨基酸序列数字化，用快速傅里叶变换（fast four transform，FFT）进行预处理，再进行偏最小二乘回归建模，可在数据集较少情况下拟合得到最佳模型。通过机器学习对紫色球杆菌视紫红质（gloeobacter violaceus rhodopsin，GR）的突变体蛋白质氨基酸序列与光谱最大吸收波长进行建模，获得了最佳模型。用最佳索引LEVM760106建模得到的确定系数R² 为0.944，均方误差E为11.64。用小波变换进行的预处理，其R² 虽也约为0.944，但E大于11.64，不及FFT进行的预处理。方法较好地解决了蛋白质序列与功能特性之间的数学建模问题，在蛋白质工程中可为预测更优的突变体提供支持。     

Generalized gradient approximation adjusted to transition metals properties: Key roles of exchange and local spin density

Perdew-Burke-Ernzerhof (PBE) and PBE adapted for solids (PBEsol) are exchange-correlation (xc) functionals widely used in density functional theory simulations. Their differences are the exchange, μ, and correlation, β, coefficients, causing PBEsol to lose the Local Spin Density (LSD) response. Here, the μ/β two-dimensional (2D) accuracy landscape is analyzed between PBE and PBEsol xc functional limits for 27 transition metal (TM) bulks, as well as for 81 TM surfaces. Several properties are analyzed, including the shortest interatomic distances, cohesive energies, and bulk moduli for TM bulks, and surface relaxation degree, surface energies, and work functions for TM surfaces. The exploration, comparing the accuracy degree with respect experimental values, reveals that the found xc minimum, called VV, being a PBE variant, represents an improvement of 5% in mean absolute percentage error terms, whereas this improvement reaches ~11% for VVsol, a xc resulting from the restoration of LSD response in PBEsol, and so regarded as its variant.     

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The novel heteronuclear complexes [{cis-PtCl (NH₃)(μ-pyrazine)ZnCl (terpy)}](ClO₄)₂ (Pt-L1-Zn) and [{cis-PtCl (NH₃)(μ-4,4′-bipyridyl)ZnCl (terpy)}](ClO₄)₂ (Pt-L2-Zn) (where terpy = 2,2′:6′,2′′-terpyridine, L1 = pyrazine, L2 = 4,4′-bipyridyl) were synthesized and characterized. The pK_a values were determined, and based on them it was established that the π-acceptor ability of the pyrazine bridging ligand is more affective on lower pK_a values. The kinetic measurements of the substitution reactions with biologically relevant ligands, such as guanosine-5′-monophosphate (5′-GMP), inosine-5′-monophosphate (5′-IMP) and glutathione (GSH), were studied at pH 7.4. The reactions were followed under pseudo-first-order conditions by UV–Vis spectrophotometry. The order of reactivity of the investigated biomolecules for the first reaction is 5′-GMP > 5′-IMP > GSH, while for the second is 5′-IMP > GSH. Pt-L1-Zn complex is more reactive than Pt-L2-Zn. The cytotoxic activity of heteronuclear Pt-L1-Zn and Pt-L2-Zn complexes was determined on human colorectal cancer cell line (HCT-116) and human breast cancer cell line (MDA-MB-231). Both complexes significantly reduced cell viability on tested cell lines and exerted significant cytotoxic effects, with better effect on HCT-116 cells than cisplatin, especially after 72 hr (IC₅₀ < 0.52 μM). The Pt-L2-Zn complex showed higher activity against human breast cancer cells (MDA-MB-231) than cisplatin after 72 hr. The higher reactivity toward DNA constituent and significant cytotoxic activity may be attributed to the different geometry, Lewis acidity of different metal centers, as well as, to choice of bridging ligands.     

The double deflating technique for irreducible singular M-matrix algebraic Riccati equations in the critical case

As is known, Alternating-Directional Doubling Algorithm (ADDA) is quadratically convergent for computing the minimal nonnegative solution of an irreducible singular M-matrix algebraic Riccati equation (MARE) in the noncritical case or a nonsingular MARE, but ADDA is only linearly convergent in the critical case. The drawback can be overcome by deflating techniques for an irreducible singular MARE so that the speed of quadratic convergence is still preserved in the critical case and accelerated in the noncritical case. In this paper, we proposed an improved deflating technique to accelerate further the convergence speed – the double deflating technique for an irreducible singular MARE in the critical case. We proved that ADDA is quadratically convergent instead of linearly when it is applied to the deflated algebraic Riccati equation (ARE) obtained by a double deflating technique. We also showed that the double deflating technique is better than the deflating technique from the perspective of dimension of the deflated ARE. Numerical experiments are provided to illustrate that our double deflating technique is effective.     

DSA、CTA联合MR影像评估AIS患者脑支循环及预后性关系

探讨数字减影血管成像(DSA)、计算机断层扫描血管成像(CTA)联合磁共振(MR)影像评估急性缺血性卒中(AIS)患者脑支循环及预后性关系。选取60例大脑中动脉M1段急性闭塞所致AIS患者为研究对象,根据DSA、CTA与MR影像对其脑侧支循环评估,比较患者基线资料、结局指标等,并分析预后性。结果发现:基于DSA、CTA与MR影像对AIS患者脑侧支循环评估结果一致性良好;3种影像模式下脑侧支循环良好组与不良组结局资料差异显著(P<0.05);多因素分析显示,FVH-ASPECTS评分、rLMC评分、ASITN/SIR分级量表均为AIS患者神经功能预后的独立影响因素。总之,DSA、CTA、MR影像对AIS患者脑侧支循环评估具有一致性,且FVH-ASPECTS评分、rLMC评分、ASITN/SIR分级量表均为AIS患者神经功能预后的独立影响因素。     

Media pressures on Welsh language preservation

Despite compulsory school instruction in the Welsh language and strong cultural incentives to acquire the language, the most recent UK Census showed a downward trend in the number of speakers. The asymmetry in explicit language acquisition incentives is here considered to be offset by the media dominance of the English language. This dominance is modeled by the introduction of time-dependent connectivity and infectivity among English speakers into an adapted epidemiological model. Extrapolations up to 2050 are made, this being the announced date of a Welsh Assembly language-planning target of one million Welsh speakers.     

Assessing the nucleophilic character of 2-amino-4-arylthiazoles through coupling with 4,6-dinitrobenzofuroxan: Experimental and theoretical approaches based on structure-reactivity relationships

A kinetic study of the reactions of potentially bioactive 2-amino-4-arylthiazoles with highly reactive 4,6-dinitrobenzofuroxan (DNBF) is reported herein in acetonitrile solution. The complexation reaction was followed by recording the UV–vis spectra with time at λ_max = 482 nm. Electronic effects of substituents influencing the rate of reaction have been studied using structure-reactivity relationships. It is shown that the Hammett plot relative to the reaction of DNBF with 2-amino-4-(4-chlorophenyl)thiazole exhibit positive deviation from the log k₁ versus σ correlation, while it showed excellent linear correlation in terms of Yukawa–Tsuno equation. It has be noticed that the nonlinear Hammett plot observed for 2-amino-4-(4-chlorophenyl) thiazole is not attributed to a change in rate-determining step but is due to nature of electronic effect of substituent caused by the resonance of stabilization of substrates. The second-order rate constant (k₁) relating to the bond C–C and C-N forming step of the complexation processes of DNBF with 4-substituted-aminothiazoles and 2-amino-5-methyl-4-phenylthiazole, respectively, is fit into the linear relationship log k = s_N (N + E), thereby permitting the assessment of the nucleophilicity parameter (N) of the 2-amino-4-arylthiazoles of the range (4.90 < N < 6.85). 2-amino-4-arylthiazoles is subsequently ranked by positioning its reactivity on the general nucleophilicity scale developed recently by Mayr and coworkers (2003) leading an interesting and a direct comparison over a large domain of π-, σ -, and n-nucleophiles. The global electrophilicity/nucleophilicity reactivity indexes of the 2-amino-4-arylthiazoles have been investigated by means of a density functional theory (DFT) method. .     

Time-dependent Ginzburg–Landau equations for multi-gap superconductors

We numerically solve the time-dependent Ginzburg–Landau equations for two-gap superconductors using the finite-element technique. The real-time simulation shows that at low magnetic field, the vortices in small-size samples tend to form clusters or other disorder structures. When the sample size is large, stripes appear in the pattern. These results are in good agreement with the previous experimental observations of the intriguing anomalous vortex pattern, providing a reliable theoretical basis for the future applications of multi-gap superconductors.     

Identifying the viscoelastic properties of soft matter from the indentation response of a hard film-soft substrate system

The indentation technique is widely used in measuring the mechanical properties of soft matter at the microscale or nanoscale,but still faces challenges by these unique properties as well as the consequent strong surface adhesion, including the strong nonlinear effect, unclear judgment of the contact point, difficulties in estimating the contact area, and the risk of the indenter piercing the sample. Here we propose a two-step method to solve these problems: lay a hard film on a soft matter, and obtain the viscoelastic properties of this soft matter through the indentation response of this composite structure. We first establish a theoretical indentation model of the hard film-soft substrate system based on the theory of plates, elastic-viscoelastic correspondence principle and Boltzmann superposition principle. To verify the correctness of this method, we measure the mechanical properties of the methyl vinyl silicone rubber(MVSR) covered by a Cu nanofilm. Finally, we test the effectiveness and error sensitivity of this method with the finite element method(FEM). The results show that our method can accurately measure the mechanical properties of soft matter, while effectively circumventing the problems of the traditional indentation technique.