Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Molecular cloning, characterization and expression analysis of a putative C-type lectin (Fclectin) gene in Chinese shrimp Fenneropenaeus chinensis

Lectin is regarded as a potential molecule involved in immune recognition and phagocytosis through opsonization in crustacean. Knowledge on lectin at molecular level would help us to understand its regulation mechanism in crustacean immune system. A novel C-type lectin gene (Fclectin) was cloned from hemocytes of Chinese shrimp Fenneropenaeus chinensis by 3' and 5' rapid amplification of cDNA ends (RACE) PCR. The full-length cDNA consists of 1482 bp with an 861 bp open reading frame, encoding 287 amino acids. The deduced amino acid sequence contains a putative signal peptide of 19 amino acids. It also contains two carbohydrate recognition domains/C-type lectin-like domains (CRD1 and CRD2), which share 78% identity with each other. CRD1 and CRD2 showed 34% and 30% identity with that of mannose-binding lectin from Japanese lamprey (Lethenteron japonicum), respectively. Both CRD1 and CRD2 of Fclectin have I I amino acids residues, which are relatively invariant in animals' C-type lectin CRDs. Five residues at Ca2+ binding site I are conserved in Fclectin. The potential Ca2+/carbohydrate-binding (site 2) motif QPD, E, NP (Gln-Pro-Asp, Glu, Asn-Pro) presented in the two CRDs of Fclectin may support its ability to bind galactose-type sugars. It could be deduced that Fclectin is a member of C-type lectin superfamily. Transcripts of Fclectin were found only in hemocytes by Northern blotting and RNA in situ hybridization. The variation of mRNA transcription level in hemocytes during artificial infection with bacteria and white spot syndrome virus (WSSV) was quantitated by capillary electrophoresis after RT-PCR. An exploration of mRNA expression variation after LPS stimulation was carried out in primarily cultured hemocytes in vitro. Expression profiles of Fclectin gene were greatly modified after bacteria, LPS or WSSV challenge. The above-stated data can provide us clues to understand the probable role of C-type lectin in innate immunity of shrimp and would be helpful to shrimp disease control. (c) 2006 Elsevier Ltd. All rights reserved.

AiC1qDC-1, a novel gC1q-domain-containing protein from bay scallop Argopecten irradians with fungi agglutinating activity

The globular C1q-domain-containing (C1qDC) proteins are a family of versatile pattern recognition receptors via their globular C1q (gC1q) domain to bind various ligands including several PAMPs on pathogens. In this study, a new gC1q-domain-containing protein (AiC1qDC-1) gene was cloned from Argopecten irradians by rapid amplification of cDNA ends (RACE) approaches and expressed sequence tag (EST) analysis. The full-length cDNA of AiC1qDC-1 was composed of 733 bp, encoding a signal peptide of 19 residues and a typical gC1q domain of 137 residues containing all eight invariant amino acids in human C1qDC proteins and seven aromatic residues essential for effective packing of the hydrophobic core of AiC1qDC-1. The gC1q domain of AiC1qDC-1, which possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, showed high homology not only to those of Cl qDC proteins in mollusk but also to those of C1qDC proteins in human. The AiC1qDC-1 transcripts were mainly detected in the tissue of hepatopancreas and also marginally detectable in adductor, heart, mantle, gill and hemocytes by fluorescent quantitative real-time PCR. In the microbial challenge experiment, there was a significant up-regulation in the relative expression level of AiC1qDC-1 in hepatopancreas and hemocytes of the scallops challenged by fungi Pichia pastoris GS115, Gram-positive bacteria Micrococcus luteus and Gram-negative bacteria Listonella anguillarum. The recombinant AiC1qDC-1 (rAiC1qDC-1) protein displayed no obvious agglutination against M. luteus and L. anguillarum, but it aggregated P. pastoris remarkably. This agglutination could be inhibited by D-mannose and PGN but not by LPS, glucan or D-galactose. These results indicated that AiC1qDC-1 functioned as a pattern recognition receptor in the immune defense of scallops against pathogens and provided clues for illuminating the evolution of the complement classical pathway. (C) 2010 Elsevier Ltd. All rights reserved.

基于仿射不变特征的图像匹配

图像匹配是计算机视觉中的一个重要研究领域，无论在民用还是军用上都有着重要的应用价值。本文以研究室国防重点预研究项目自动目标识别为背景，采用图像匹配方法，实现飞行器定位导航。具体工作流程是：事先利用侦察手段获取飞行器途经下方的地物景象(基准图)并存于飞行器载计算机中，然后当携带相应传感器的飞行器飞过预定的位置范围时，拍摄当地的地物景象(实时图)，将实时图和基准图在飞行器载计算机中进行匹配比较，可确定当前飞行器的准确位置，完成定位导航功能。 由于对同一场景使用相同或不同的传感器(成像设备)，以及在不同条件下(天候、照度、摄像位置和角度等)成像的复杂性和多样性等困难的存在，传统的相关匹配方法对上述困难的克服在方法原理上存在先天不足，所以无法胜任。故本文采用的方法是基于局部不变量特征的图像匹配。局部不变量特征因为能更灵活地描述图像，有效地处理图像复杂和遮挡问题，所以基于局部不变量特征的图像匹配方法对于视点的大变化，图像背景变化，以及目标场景识别等都有较好的效果。 基于局部不变量特征的图像匹配方法的步骤通常分为三部分：(1)用图像区域检测算子提取图像相关区域，(2)构造合适的特征描述区域，(3)选择特征相似度度量准则实现图像区域特征的匹配。本文详细研究了最大稳定极值区域 (MSER)方法，在此基础上进行了改进，具体工作如下：(1)利用高斯核函数对图像平滑采样，建立图像的高斯尺度空间，(2)在图像的高斯尺度空间中，利用MSER检测算子检测出图像在不同尺度下的所有仿射相关区域，(3)由于区域不规则，再用仿射不变的椭圆拟合并归一化，这时所有的区域仅存在旋转的不同，(4)用SIFT特征描述图像区域，得到所有区域的128维特征向量集。(5)采用欧式距离度量特征间的相似度，以最近邻和次近邻的比值作为特征匹配准则进行匹配。 本论文的主要研究工作在于把图像的高斯尺度空间引入到MSER算法中，进而大大改善了MSER算法对于图像的尺度变换、仿射变换以及图像模糊的性能。由于建立了高斯尺度空间，增加了MSER检测算子检测的范围，所以使得改进算法的性能得到了改善。论文第四章给出四组实验，分别为尺度变换，仿射变换，图像模糊和大视点变换。最后通过对匹配结果正确数量和错误数量的统计，论证了改进方法的性能要好于MSER算法。通过对算法复杂度的分析，得出虽然在改进算法引入了图像的高斯尺度空间，但是算法复杂度却并未增加，与MSER算法相同，为O(nloglogn)。

Robust Guaranteed Cost Control for Yaw Control of Helicopter

针对具有时变不确定性且不确定性界为椭球的线性系统提出了一种新的具有自适应机制的鲁棒保性能控制器设计方法。首先,引入一个具有可由自适应律在线调整的可调参数的目标模型,通过该参数来保证由目标模型与被控模型所获得的误差系统渐近稳定。结合保证目标模型稳定性的设计,最终形成保证闭环系统稳定且控制器增益仿射依赖于可调参数的鲁棒保性能跟踪控制器。应用于安装在试验平台上的小型直升机航向控制中,仿真试验表明了该方法的有效性。

输电线巡检机器人控制与实验研究

近年来，机器人的应用越来越广泛和深入，输电线巡检机器人是当前特种作业机器人的研究热点之一，具有广泛的应用前景和实用价值。本文的研究内容是围绕国家“863”计划支持项目“500KV超高压输电线巡检机器人的研究”展开的。本研究工作针对巡检机器人的关键控制问题，主要由三部分组成：设计了巡检机器人的体系结构，并应用离散事件理论对机器人的任务、行为和动作建模；对巡检机器人双轮同步驱动控制进行了分析，并应用奇异摄动理论设计了控制器；研究了基于单目视觉的输电线立体定位方法及通过视觉伺服完成机器人自主抓线控制。 第一，介绍了巡检机器人的作业环境，重点探讨了机器人机械系统和控制系统的设计与实现。在机械子系统中，详细介绍了巡检机器人的机构实现与越障方法。在控制系统中详细阐述了基于分层递阶的机器人控制系统硬件组成。另外介绍了供电系统、无线传输系统、传感系统的设计与实现。分析了输电线路周围的电磁环境，及其对机器人的影响，并根据分析结果完成了对机器人的电磁防护设计。 第二，开展了输电线巡检机器人体系结构及人机交互系统研究，针对巡检机器人工作特点设计了基于规划和感知行为的混合式体系结构。针对巡检机器人工作环境设计了以机器人为中心的人机交互方式。参考前人建立的离散事件动力系统的层次结构和并行结构，提出了顺序结构并证明了其无阻塞性、可控性和监控器存在性，并结合以上三种结构建立了巡检机器人作业行为的离散动力学模型，分别获得了任务层、行为层和动作层的监控器。 第三，进行了巡检机器人双轮驱动控制研究。巡检机器人双轮行走机构为过驱动系统，对双轮行走系统进行了运动学和动力学建模，将一行走轮设为主动轮另一行走轮设为从动轮。针对两行走轮之间弹性关节导致的控制中的振荡问题，采用奇异摄动理论将系统分为快慢两个子系统；针对巡检机器人系统参数的时变性采用PD自适应算法设计了慢系统控制器；应用最优控制理论设计了快系统控制器。仿真结果验证了该方法的有效性。 第四，进行了输电线视觉定位和视觉伺服抓线问题的研究。输电线巡检机器人的自主越障控制是实现机器人实用化的关键问题。为实现巡检机器人自主越障，采用视觉伺服控制机械手臂自动抓线。为提取输电线图像特征点，针对输电线投影图像特征改进了边缘提取算法，应用聚类算法提取了输电线上的像素点。提出在机械手运动过程中采用EKF（扩展卡尔曼滤波）来实现对输电线的立体定位。在分析了当前基于图像的视觉伺服研究现状，建立了基于图像雅克比矩阵的输电线视觉伺服抓线模型。针对非标定状况下图像雅可比矩阵中的不确定参数，应用I&I(Immersion Invariant)自适应算法来实现无标定图像视觉伺服。针对机器人的动力学不确定性，设计了模糊自适应控制器，并证明了稳定性。仿真验证该方法的有效性，实验验证了基于视觉伺服的抓线控制的有效性。

儿童汉字意识及精细辨认能力的发展研究

The important basis for the children to study chinese character is the Chinese character awareness, which means the understanding and extracting of the Chinese character combinatorial rule. The perceptual learning intrinsically is the direct perceive to the invariant rules. As the important mechanism to extract the abstract rule, the perceptual learning is the important mechanism of the development of the Chinese character awareness also. 4-6-year-old children's Chinese character awareness are tested by the degree of acceptance to the graphic words, inlaying words and pseudowords. The perceptual disintegration are tested by the perceptual learning experiment. Moreover, the development of the ability to finely-identify the Chinese character under the different level of attention condition is explored. The result suggests the quality to the development of the children's Chinese character awareness: The Chinese character awareness to 4-year-old children is in the rudiment stage, and it have different qualities as the change of the age. As the mechanism of the Chinese character awareness, the perceptual learning have an complex correlation to the awareness. The result indicates the following effects of the children perceptual disintegration: the level of the perceptual disintegration is transitive from three-dimension confusion to one-dimension falsity. It have correlation with the ability to finely-identify the Chinese character to a certain degree. The result also shows: the developmental specialties of the ability to finely-identify the Chinese character are different in the different age. The ability to finely-identify the Chinese character under the different level of attention condition have very similar processes.

Affine Matching with Bounded Sensor Error: A Study of Geometric Hashing and Alignment

Affine transformations are often used in recognition systems, to approximate the effects of perspective projection. The underlying mathematics is for exact feature data, with no positional uncertainty. In practice, heuristics are added to handle uncertainty. We provide a precise analysis of affine point matching, obtaining an expression for the range of affine-invariant values consistent with bounded uncertainty. This analysis reveals that the range of affine-invariant values depends on the actual $x$-$y$-positions of the features, i.e. with uncertainty, affine representations are not invariant with respect to the Cartesian coordinate system. We analyze the effect of this on geometric hashing and alignment recognition methods.

Green Theorems and Qualitative Properties of the Optical Flow

How can one compute qualitative properties of the optical flow, such as expansion or rotation, in a way which is robust and invariant to the position of the focus of expansion or the center of rotation? We suggest a particularly simple algorithm, well-suited to VLSI implementations, that exploits well-known relations between the integral and differential properties of vector fields and their linear behaviour near singularities.

Limitations of Non Model-Based Recognition Schemes

Different approaches to visual object recognition can be divided into two general classes: model-based vs. non model-based schemes. In this paper we establish some limitation on the class of non model-based recognition schemes. We show that every function that is invariant to viewing position of all objects is the trivial (constant) function. It follows that every consistent recognition scheme for recognizing all 3-D objects must in general be model based. The result is extended to recognition schemes that are imperfect (allowed to make mistakes) or restricted to certain classes of objects.

Viewer-Centered Object Recognition in Monkeys

How does the brain recognize three-dimensional objects? We trained monkeys to recognize computer rendered objects presented from an arbitrarily chosen training view, and subsequently tested their ability to generalize recognition for other views. Our results provide additional evidence in favor of with a recognition model that accomplishes view-invariant performance by storing a limited number of object views or templates together with the capacity to interpolate between the templates (Poggio and Edelman, 1990).

Relative Affine Structure: Canonical Model for 3D from 2D Geometry and Applications

We propose an affine framework for perspective views, captured by a single extremely simple equation based on a viewer-centered invariant we call "relative affine structure". Via a number of corollaries of our main results we show that our framework unifies previous work --- including Euclidean, projective and affine --- in a natural and simple way, and introduces new, extremely simple, algorithms for the tasks of reconstruction from multiple views, recognition by alignment, and certain image coding applications.

Spatial Reference Frames for Object Recognition: Tuning for Rotations in Depth

The inferior temporal cortex (IT) of monkeys is thought to play an essential role in visual object recognition. Inferotemporal neurons are known to respond to complex visual stimuli, including patterns like faces, hands, or other body parts. What is the role of such neurons in object recognition? The present study examines this question in combined psychophysical and electrophysiological experiments, in which monkeys learned to classify and recognize novel visual 3D objects. A population of neurons in IT were found to respond selectively to such objects that the monkeys had recently learned to recognize. A large majority of these cells discharged maximally for one view of the object, while their response fell off gradually as the object was rotated away from the neuron"s preferred view. Most neurons exhibited orientation-dependent responses also during view-plane rotations. Some neurons were found tuned around two views of the same object, while a very small number of cells responded in a view- invariant manner. For five different objects that were extensively used during the training of the animals, and for which behavioral performance became view-independent, multiple cells were found that were tuned around different views of the same object. No selective responses were ever encountered for views that the animal systematically failed to recognize. The results of our experiments suggest that neurons in this area can develop a complex receptive field organization as a consequence of extensive training in the discrimination and recognition of objects. Simple geometric features did not appear to account for the neurons" selective responses. These findings support the idea that a population of neurons -- each tuned to a different object aspect, and each showing a certain degree of invariance to image transformations -- may, as an assembly, encode complex 3D objects. In such a system, several neurons may be active for any given vantage point, with a single unit acting like a blurred template for a limited neighborhood of a single view.

Face Recognition from One Example View

If we are provided a face database with only one example view per person, is it possible to recognize new views of them under a variety of different poses, especially views rotated in depth from the original example view? We investigate using prior knowledge about faces plus each single example view to generate virtual views of each person, or views of the face as seen from different poses. Prior knowledge of faces is represented in an example-based way, using 2D views of a prototype face seen rotating in depth. The synthesized virtual views are evaluated as example views in a view-based approach to pose-invariant face recognition. They are shown to improve the recognition rate over the scenario where only the single real view is used.