Genetic tuning of avian influenza A (H7N9) virus promotes viral fitness within different species

Since their emergence in eastern China, novel influenza A (H7N9) viruses have been continuously circulating in poultry and causing human infections and death. We have proposed a “genetic tuning” mechanism for the genesis and evolution of the novel H7N9 virus during interspecies transmission.     

Evolution and spectral tuning of visual pigments in birds and mammals

Variation in the types and spectral characteristics of visual pigments is a common mechanism for the adaptation of the vertebrate visual system to prevailing light conditions. The extent of this diversity in mammals and birds is discussed in detail in this review, alongside an in-depth consideration of the molecular changes involved. In mammals, a nocturnal stage in early evolution is thought to underlie the reduction in the number of classes of cone visual pigment genes from four to only two, with the secondary loss of one of these genes in many monochromatic nocturnal and marine species. The trichromacy seen in many primates arises from either a polymorphism or duplication of one of these genes. In contrast, birds have retained the four ancestral cone visual pigment genes, with a generally conserved expression in either single or double cone classes. The loss of sensitivity to ultraviolet (UV) irradiation is a feature of both mammalian and avian visual evolution, with UV sensitivity retained among mammals by only a subset of rodents and marsupials. Where it is found in birds, it is not ancestral but newly acquired.     

普通伏翼蝠下丘神经元基本声反应特性

自由声场条件下,采用单单位胞外微电极记录方法,研究了普通伏翼蝠(Pipistrellusabramus)下丘神经元基本声反应特性。结果发现,在所得的65个下丘神经元中:特征频率在18.9~76.7kHz(42.94±11.29)之间,最小阈值在29.1~80.1dBSPL(58.65±12.62)之间,潜伏期在3.1~10.4ms(6.10±1.47)之间;特征频率随记录深度的增加而增大,与最小阈值之间没有显著相关性;发放类型包括相位型(73.85%)、梳齿型(15.38%)和紧张型(10.77%)3种基本类型;频率调谐曲线均为开峰型,多数神经元(72.30%)调谐曲线较宽阔,少数(27.70%)较狭窄,并且多数神经元的频率调谐曲线高频边比低频边陡。     

Online automatic tuning and control for fed-batch cultivation

Performance of controllers applied in biotechnological production is often below expectation. Online automatic tuning has the capability to improve control performance by adjusting control parameters. This work presents automatic tuning approaches for model reference specific growth rate control during fed-batch cultivation. The approaches are direct methods that use the error between observed specific growth rate and its set point; systematic perturbations of the cultivation are not necessary. Two automatic tuning methods proved to be efficient, in which the adaptation rate is based on a combination of the error, squared error and integral error. These methods are relatively simple and robust against disturbances, parameter uncertainties, and initialization errors. Application of the specific growth rate controller yields a stable system. The controller and automatic tuning methods are qualified by simulations and laboratory experiments with Bordetella pertussis.     

Theoretical analysis of reverse-time correlation for idealized orientation tuning dynamics

A theoretical analysis is presented of a reverse-time correlation method used in experimentally investigating orientation tuning dynamics of neurons in the primary visual cortex. An exact mathematical characterization of the method is developed, and its connection with the Volterra–Wiener nonlinear systems theory is described. Various mathematical consequences and possible physiological implications of this analysis are illustrated using exactly solvable idealized models of orientation tuning.     

猫前内侧上雪氏区视神经元对运动随机线条的反应

对于运动信息在脑内的加工,一种观点认为分两阶段进行,低级视皮层只对运动图形内部成分的取向进行调谐,高级视皮层整合低级视皮层的输入,对图形整体的运动方向敏感。用网格（plaid）作为刺激的实验表明,在较低级皮层区,细胞多表现为成分方向选择性（Component-motion Selectivity),即对刺激中的取向因素敏感：而较高视皮层的细胞多表现为整体方向选择性（Pattern-motion Selecitivity),对运动整体的方向敏感,从而支持运动信息加工的“两阶段”理论。实验中,用一系列运动随机线条刺激（random line patterns)。研究猫前内侧上雪氏区（Anteriormedial lateral suprasylvian area,AMLS)神经元的方向调谐特性。结果表明多数细胞为整体方向选择性,且随线长增加此类细胞比例下降,而成分方向选择性细胞的比例有所增加,呈现由整体方向选择性向中间类型（Unclassified),由中间类型向成分方向选择性变化的趋势,提示整体或成分方向选择性可能并非细胞的固有特性,而是可以随刺激取向因素的变化而改变的。     

Evolutionary analysis of rhodopsin and cone pigments: connecting the three-dimensional structure with spectral tuning and signal transfer

Extensive sequence data and structural sampling of expressed proteins from different species lead to the idea that entire molecules or specific domain folds belong to large superfamilies of proteins. A subset of G protein-coupled receptors, one of the largest families involved in cellular signaling, rod and cone opsins are involved in phototransduction in photoreceptor cells. Here, the evolutionary analysis of opsin sequences and structures predicts key residues involved in the transmission of the signal from the binding site of the chromophore to the cytoplasmic surface and residues that are involved in the spectral tuning of opsins to short wavelengths of light.     

Variable light environments induce plastic spectral tuning by regional opsin coexpression in the African cichlid fish,Metriaclima zebra

Critical behaviours such as predation and mate choice often depend on vision. Visual systems are sensitive to the spectrum of light in their environment, which can vary extensively both within and among habitats. Evolutionary changes in spectral sensitivity contribute to divergence and speciation. Spectral sensitivity of the retina is primarily determined by visual pigments, which are opsin proteins bound to a chromophore. We recently discovered that photoreceptors in different regions of the retina, which view objects against distinct environmental backgrounds, coexpress different pairs of opsins in an African cichlid fish, Metriaclima zebra. This coexpression tunes the sensitivity of the retinal regions to the corresponding backgrounds and may aid in detection of dark objects, such as predators. Although intraretinal regionalization of spectral sensitivity in many animals correlates with their light environments, it is unknown whether variation in the light environment induces developmentally plastic alterations of intraretinal sensitivity regions. Here, we demonstrate with fluorescent in situ hybridization and qPCR that the spectrum and angle of environmental light both influence the development of spectral sensitivity regions by altering the distribution and level of opsins across the retina. Normally, M. zebra coexpresses LWS opsin with RH2Aα opsin in double cones of the ventral but not the dorsal retina. However, when illuminated from below throughout development, adult M. zebra coexpressed LWS and RH2Aα in double cones both dorsally and ventrally. Thus, environmental background spectra alter the spectral sensitivity pattern that develops across the retina, potentially influencing behaviours and related evolutionary processes such as courtship and speciation.     

Systematic tuning of parameters in support vector clustering

Clustering algorithms divide a set of observations into groups so that members of the same group share common features. In most of the algorithms, tunable parameters are set arbitrarily or by trial and error, resulting in less than optimal clustering. This paper presents a global optimization strategy for the systematic and optimal selection of parameter values associated with a clustering method. In the process, a performance criterion for the optimization model is proposed and benchmarked against popular performance criteria from the literature (namely, the Silhouette coefficient, Dunn's index, and Davies-Bouldin index). The tuning strategy is illustrated using the support vector clustering (SVC) algorithm and simulated annealing. In order to reduce the computational burden, the paper also proposes an alternative to the adjacency matrix method (used for the assignment of cluster labels), namely the contour plotting approach. Datasets tested include the iris and the thyroid datasets from the UCI repository, as well as lymphoma and breast cancer data. The optimal tuning parameters are determined efficiently, while the contour plotting approach leads to significant reductions in computational effort (CPU time) especially for large datasets. The performance criteria comparisons indicate mixed results. Specifically, the Silhouette coefficient and the Davies-Bouldin index perform better, while the Dunn's index is worse on average than the proposed performance index.