Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

the trustworthiness metric model of software process quality based-on life circle

Communication University of China; Wuhan University; James Madison University; Institute of Policy and Management, Chinese Academy of Sciences; IEEE Wuhan Section

A Video Quality Assessment Metric Based on Human Visual System

It is important for practical application to design an effective and efficient metric for video quality. The most reliable way is by subjective evaluation. Thus, to design an objective metric by simulating human visual system (HVS) is quite reasonable and available. In this paper, the video quality assessment metric based on visual perception is proposed. Three-dimensional wavelet is utilized to decompose video and then extract features to mimic the multichannel structure of HVS. Spatio-temporal contrast sensitivity function (S-T CSF) is employed to weight coefficient obtained by three-dimensional wavelet to simulate nonlinearity feature of the human eyes. Perceptual threshold is exploited to obtain visual sensitive coefficients after S-T CSF filtered. Visual sensitive coefficients are normalized representation and then visual sensitive errors are calculated between reference and distorted video. Finally, temporal perceptual mechanism is applied to count values of video quality for reducing computational cost. Experimental results prove the proposed method outperforms the most existing methods and is comparable to LHS and PVQM.

Self-similarity limits of genomic signatures

It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display genomic signature in chaos game representation is obtained by eliminating effects of the finite sequence. The optimal string length is further shown as a self-similarity limit in computing information dimension. By using the method, self-similarity limits of bacteria complete genomic signatures are further determined.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Optimized phase pupil masks for extended depths of field

By properly designing a phase pupil mask to modulate or encode the optical images and then digitally restoring them, one can greatly extend the depth of field and improve image quality. The original works done by Dowski and Cathey introduce the use of a cubic phase pupil mask to extend the depth of field. The theoretical and experimental researches all verified its effectiveness. In this paper, we suggest the use of an exponential phase pupil mask to extend the depth of field. This phase mask has two variable parameters for designing to control the shape of the mask so as to modulate the wave-front more flexible. We employ an optimization procedure based on the Fisher information metric to obtain the optimum values of the parameters for the exponential and the cubic masks, respectively. A series of performance comparisons between these two optimized phase masks in extending the depth of field are then done. The results show that the exponential phase mask provide slight advantage to the cubic one in several aspects. (c) 2006 Elsevier B.V. All rights reserved.

Spatial distribution of benthic algae in the Gangqu River, Shangrila, China

This study consisted of sampling benthic algae at 32 sites in the Gangqu River, an important upstream tributary of the Yangtze River. Our aims were to characterize the benthic algae communities and relationships with environmental variables. Among the 162 taxa observed, Achnanthes linearis and Achnanthes lanceolata var. elliptica were the dominant species (17.10% and 14.30% of the total relative abundance, respectively). Major gradients and principal patterns of variation within the environmental variables were detected by principal component analysis (PCA). Then non-metric multidimensional scaling (NMS) divided all the sites into three groups, which were validated by multi-response permutation procedures (MRPP). Canonical correspondence analysis (CCA) indicated that three environmental variables (TN, TDS, and TP) significantly affected the distribution of benthic algae. Weighted averaging regression and cross-calibration produced strong models for predicting TN and TDS concentration, which enabled selection of algae taxa as potentially sensitive indicators of certain TN and TDS levels: for TN, Achnanthes lanceolata, Achnanthes lanceolata var. elliptica, and Cymbella ventricosa var. semicircularis; for TDS, Cocconeis placentula, Cymbella alpina var. minuta, and Fragilaria virescens. The present study represents an early step in establishing baseline conditions. Further monitoring is suggested to gain a better understanding of this region.

使用容量指标的安全实时数据库信道限制方法

依据可信计算机系统评测标准(TCSEC)要求,提出一种使用信道容量指标的安全实时数据库中数据竞争信道的限制方法(CUCCMM),给出了限制过程中信道容量度量算法和限制参数计算方法。为了保证系统的信道容量限制标准的准确执行,提出了一种基于多概率的并发控制协议选择策略(MPBPSP)。实验结果证明CUCCMM方法可以有效地、准确地实施对隐蔽信道容量的限制,并且通过使用MPBPSP策略显著降低了信道限制操作对系统实时性能的影响。

基于度量工具的软件成本估算模型使用方法

输入的主观性以及输入过多是妨碍软件成本估算模型实际应用效果的重要影响因素.针对以上问题,提出了一种基于度量工具的软件成本估算模型使用方法.该方法通过引入统计理论中的工具变量,将度量工具所采集的度量元数据自动转换为软件成本估算模型的输入.这一方面可以避免模型校准和估算过程中输入的主观性与不一致性,提高了估算结果的准确性与可靠性;另一方面能减少估算人员的手工操作,提高工作效率,增加了软件成本估算模型的可用性.结合具体实例说明了所提出方法的可行性与有效性.

VLSI architecture of a K-best detector for MIMO--OFDM wireless communication systems

The K-best detector is considered as a promising technique in the MIMO-OFDM detection because of its good performance and low complexity. In this paper, a new K-best VLSI architecture is presented. In the proposed architecture, the metric computation units (MCUs) expand each surviving path only to its partial branches, based on the novel expansion scheme, which can predetermine the branches' ascending order by their local distances. Then a distributed sorter sorts out the new K surviving paths from the expanded branches in pipelines. Compared to the conventional K-best scheme, the proposed architecture can approximately reduce fundamental operations by 50% and 75% for the 16-QAM and the 64-QAM cases, respectively, and, consequently, lower the demand on the hardware resource significantly. Simulation results prove that the proposed architecture can achieve a performance very similar to conventional K-best detectors. Hence, it is an efficient solution to the K-best detector's VLSI implementation for high-throughput MIMO-OFDM systems.

Approximate analytical optical transfer function for a wavefront-coded imaging system with two-dimensional rectangularly separable phase masks

Wavefront coding can be used to extend the depth of field of incoherent imaging systems and is a powerful system-level technique. In order to assess the performance of a wavefront-coded imaging system, defocused optical transfer function (OTF) is the metric frequently used. Unfortunately, to the best of our knowledge, among all types of phase masks, it is usually difficult to obtain the analytical OTF except the cubic one. Although numerical computation seems good enough for performance evaluation, the approximate analytical OTF is still indispensable because it can reflect the relationship between mask parameters and system frequency response in a clearer way. Thus, a method is proposed to derive the approximate analytical OTF for two-dimensional rectangularly separable phase masks. The analytical results are well consistent with the direct numerical computations, but the proposed method can be accepted only from engineering point of view and needs rigorous proof in future. (c) 2010 Society of Photo-Optical Instrumentation Engineers. [DOI: 10.1117/1.3485759]

Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.

Application of the characteristic CIP method to a shallow water model on the sphere

Semi-implicit algorithms are popularly used to deal with the gravitational term in numerical models. In this paper, we adopt the method of characteristics to compute the solutions for gravity waves on a sphere directly using a semi-Lagrangian advection scheme instead of the semi-implicit method in a shallow water model, to avoid expensive matrix inversions. Adoption of the semi-Lagrangian scheme renders the numerical model always stable for any Courant number, and which saves CPU time. To illustrate the efficiency of the characteristic constrained interpolation profile (CIP) method, some numerical results are shown for idealized test cases on a sphere in the Yin-Yang grid system.

基于RS和GIS的四川省土地利用/覆盖变化及可持续利用研究

LUCC是全球变化研究的核心主题之一，也是社会经济可持续发展的关键问题。改革开放后四川的社会经济发展非常快，在各种因素的驱动下，土地利用/覆盖发生了深刻变化。目前四川省缺乏基于实际调查数据的、全域性的、具有连续时间序列的LUCC和驱动力分析及土地可持续利用研究成果，这对我们从全局上把握全省土地利用现状、发展变化趋势，利用土地政策参与宏观调控，实现长期可持续发展目标，建设资源节约型、环境友好型社会极为不利。本研究针对这一问题，选取全川八大土地利用类型作为研究对象，研究了全省1996年到2006年的土地利用/覆盖格局和变化情况，分析了不同尺度的驱动因素，对全省农用地和建设用地的集约利用状况、潜力进行了分析评价，并提出相应的对策措施。 1．1996年-2006年10年来整个省域的土地利用/覆盖格局变化。 （1）1996年-2006年全省的土地利用/覆盖格局 1996年，全省是一个以农用地为主的土地利用/覆盖格局，林地和牧草地属于优势覆盖类型（合占69.17%），居民点及工矿用地和交通用地合占只有3%左右。 2000年的LUCC格局较为明显的特点是耕地所占比重下降0.4个百分点，水域和未利用土地所占比重有所下降，牧草地保持不变，其余地类所占比重有所上升。 与2000年相比，2004年林草地的优势格局进一步得到强化（合占比重达到70.23%）。耕地面积占幅员面积的比重下降0.83个百分点，略有下降的有未利用土地、水域和牧草地。值得关注的是在“退耕还林还草”的大背景下，牧草地占幅员面积的比重下降0.04个百分点。 到2006年，仍为林草地为主导优势的格局，二者合占上升0.15%。在城市化快速推进的背景下，居民点及工矿用地中的城市用地和建制镇用地占比重超过15%，农村居民点占比重降至76%。交通用地中农村道路占比重降至57.8%,公路用地占比重升至37.5%。五个地貌区的土地利用/覆盖格局与全省的变化基本一致。值得关注的是盆西平原区的交通用地上升幅度和盆地丘陵区的未利用土地的开发利用力度明显大于其它地貌区。 （2）1996-2006年10年间土地利用/覆盖格局的变化 1996-2000年4年间，耕地、水域和未利用地三个地类下降，年均减少0.75、0.19和0.32个百分点。其中耕地年均减少49229.0公顷，约一半流向林地，13.77%流向园地，约20%流向建设用地。另外5个地类面积增长，增长绝对量最大的是林地，年均增长40063.7公顷，交通用地增幅最大，4年年均增长达1.95%。 2001-2004年是西部大开发逐步推进、“退耕还林还草”项目全面展开和土地整理深入实施的关键期，LUCC更为深刻。耕地、未利用地、水域和牧草地四个地类面积下降，其余地类按增长幅度依次是园地、交通用地、居民点及工矿用地和林地。耕地加速下降，年均降幅达到1.59%，其减少去向主要是林地（占66.75%）和园地（占19.84%），其增加来源主要是未利用地、园地和水域。交通用地的增幅最大，为3.96%,其增加主要来源于耕地、未利用土地和林地，分别占49.96%、16.63%和13.09%。居民点及工矿用地增长幅度为3.12%。 从1996年到2006年的10年间，耕地、未利用地、水域和牧草地下降幅度分别为10.36%、3.61%、1.34%和0.26%。园地增幅达23.61%。绝对面积增长最大的则是林地，达630733.3公顷。交通用地和居民点及工矿用地增幅也较大，分别为15.00%和9.31%。 10年间年均总变化量为310326.6公顷，2000年-2004年之间变化最大（为356865.8公顷），高于平均变化量，而1996-2000年间和2004-2006年间都小于平均变化量。 （3）10年间不同地貌区的LUCC变化 盆西平原区的特点是园地大幅上升达77%，居民点及工矿用地和交通用地也大幅上升，耕地、未利用地下降幅度大，该区耕地、水域、未利用地的减少强度和园地、居民点及工矿用地、交通用地的上升强度均居五区第一；盆地丘陵区的特点是牧草地下降幅度大，为-36.89%,交通用地、园地和林地上升幅度较大，该区耕地减少、未利用地减少、林地增加、居民点及工矿用地和交通用地增加的变化强度均居五区相应地类增减的第二位；盆周山地区的特点是耕地减少较多，交通用地和园地增长较大，该区林地变化强度居各区第一位，牧草地和水域变化强度居各区第二位，耕地、居民点及工矿用地和未利用地居各区第三位；川西南山地区的特点是园地、耕地、交通用地和居民点及工矿用地变化幅度大，另外四个地类变化较小。该区减少的牧草地占全省牧草地减少的97.91%，变化强度居各个地貌区的第一位，园地相对变化强度居五区的第二位；川西北高山高原区的特点是耕地大幅下降、园地大幅上升，交通用地升幅也较大，其余地类变化不大。值得注意的是，该区牧草地和水域面积增加，与全省该地类的变化相反。其余地类的相对变化强度均是五个地貌区中最小的。 用变化强度分值考量变化强度，盆西平原区的变化强度最大，盆地丘陵区和盆周山地区的变化强度相当，川西北高山高原区的变化强度则要小得多。 （4）1996年及2006年全省土地利用/覆盖格局的景观生态学分析 全省是以自然景观占优势（占约70%）、农业景观为补充、建设用地景观居于从属地位的土地利用景观格局。景观多样性和均匀度不高。到2006年，全省总的景观格局并无大的改变。总体情况是随着时间的推移和人类活动的加强，区内景观优势度上升、多样性和均匀度变小。但斑块数减少，斑块面积和斑块孔隙度有所增大。斑块的形状指数和分维数均有所下降，表明受人为干扰有加剧的趋势。反映景观格局结构的破碎度指数有轻微下降。景观指数的变化表明全省土地利用有缓慢集中、规模聚集的趋势。 （5）三大生态建设工程对土地利用/覆盖变化的影响 1996-2006年间LUCC与三大生态建设工程实施的耦合分析，发现退耕工程对耕地、林地、牧草地等地类覆盖变化的影响最大，天保工程次之，长防工程最小。 2.四川省LUCC驱动力分析 （1）总体分析： 从整体上分析，人为因素对区域整体LUCC的影响从1996年的63.32%增加到2006年的66.99%，变得日益强烈。同时人为因素影响强度表现出明显的区域差异，地势平缓、经济区位条件好的区域其人为影响强度明显较高。 政策体制转变下的经济高速增长、快速的城市化、工业化过程和生态建设是四川省LUCC宏观尺度的驱动因素。区域的LUCC主要受到了由内向外(从城市到乡村)和由外向内(从山顶向平地)两种作用力的共同推动。局部尺度上，如距离交通线、水利线、中心城市的远近，地形凸起、大型独立项目落址、重污染项目的阻隔等，甚至一些乡规民俗等因素也会成为LUCC的驱动影响因素。在较小的尺度上,人类个体行为选择对LUCC的影响也是存在的。 　　根据驱动因子的特性作者将其划分为驱变、阻变、良性、惰性因子等类型。 （2）分地貌区的驱动因子分析 各地貌区都存在城市化、工业化、生态工程实施、自然灾害等驱动因子，但主次不一。对于盆西平原和盆地丘陵区，城市化、工业化是前两位的因子，而对另外三个地貌区，生态工程实施和产业结构调整则成为第第一、二位的驱动因子。 （3）分地类的驱动因子分析（以坡耕地为例） 分坡度的耕地变化分析发现，耕地减少主要集中在2°以下的平地、15°-25°和25°以上三个坡度级，是其它坡度级耕地减幅的三倍左右。这表明耕地减少受城市化进程和“退耕还林还草”工程驱动影响尤为巨大。 3.土地利用格局优化、集约利用评价和可持续利用及对策研究 （1）土地利用格局优化的战略选择及调整预测 土地利用格局调整的战略是农业生产用地、建设用地和生态及其他用地占幅员的比重分别稳定在13%、7%和80%左右，重点是三大类别内部二级和三级地类的合理调整。 （2）全省土地集约利用评价 全省农用地利用集约度为0.46，总体上集约度不高，处于较适度利用阶段。建设用地利用集约度为0.38，处于较适度利用阶段。集约利用提升空间较大。 农用地的潜力主要在于加强土地保育、完善利用制度、提高单产。城市建设用地的包括存量潜力、强度潜力、结构潜力，空间很大。农村居民点整理潜力可以逐步挖掘。 （3）新增建设用地集约利用的统筹安排 据测算，到2020年，四川省城市建设用地需求量在463850-492360hm2之间，城镇各业新增建设用地规模为361276.79hm2，占用耕地200565.94 hm2。2004-2020年间四川省农村居民点整理潜力33.86万hm2。农村居民点建设用地需求量为70.57万公顷。 （4）土地集约利用措施与坡耕地可持续利用战略 提出了土地集约利用的措施。在对坡耕地生态系统结构与功能分析的基础上，提出坡耕地可持续利用战略与生态恢复战略，并从技术和政策层面提出了坡耕地合理利用和生态退耕的措施和建议。 LUCC is one of the key questions of global change and sustainable development of society. After the opening and reform of China, the society and economy of Sichuan Province developed very fast ,the land-use/cover changed very strong droved by many factors .But nowadays we have no constant spatial-temporal study and driving force analysis about the whole province based on investigation. And it is lack of land sustainable utilization study based on correlative study. So we choose all the land resource in Sichuan, combine RS and GIS and field investigation, and take statistic-mathematic means and system analysis, to study the LUCC patterns and different scale driving force of different physiognomy regions, land cover types and periods; to analyze the current situation and potential of land resource intensive utilization, and gave out corresponding measurements. We found that forest and grassland are the dominant cover types of Sichuan provincial land –use/cover pattern, and becoming more and more stronger from 1996 to 2006,the natural landscape is the metric and occupy 70%,the diversity and evenness index are not high; the totally change quantity from 2000 to 2004 is the biggest; cultivated land especially steep cultivated land ,garden plot, forestry land ,settlement and industry land and traffic land changed relative stronger; among five physiognomy regions ,the changing intensity of PEN XI PING YUAN QU is the biggest, CHUAN XI BEI GAO SHAN GAO QU is smallest; under the background of policy system changing, the fast developing of economy, fast urbanization and industrialization and ecology construction are the macro-scale driving force of Sichuan provincial LUCC; to compare the impacts of “TUI GENG GONG CHENG” on LUCC especially to cultivated land ,forestry land and grassland is strongest, “TIAN BAO GONG CHENG ” is stronger,“ HANG FANG GONG CHENG” is smallest; the intensive utilization level of farmland and construction land of whole province is relative moderation, there is huge potential to excavate and fulfill the increasing demand of construction land；we must take synthetic measurements to accelerate the sustainable utilization of land resource, including administrative, economical ,technological and ecological policies.