Can environmental constraints determine random patterns of plant species co-occurrence?

Plant community ecologists use the null model approach to infer assembly processes from observed patterns of species co-occurrence. In about a third of published studies, the null hypothesis of random assembly cannot be rejected. When this occurs, plant ecologists interpret that the observed random pattern is not environmentally constrained - but probably generated by stochastic processes. The null model approach (using the C-score and the discrepancy index) was used to test for random assembly under two simulation algorithms. Logistic regression, distance-based redundancy analysis, and constrained ordination were used to test for environmental determinism (species segregation along environmental gradients or turnover and species aggregation). This article introduces an environmentally determined community of alpine hydrophytes that presents itself as randomly assembled. The pathway through which the random pattern arises in this community is suggested to be as follows: Two simultaneous environmental processes, one leading to species aggregation and the other leading to species segregation, concurrently generate the observed pattern, which results to be neither aggregated nor segregated - but random. A simulation study supports this suggestion. Although apparently simple, the null model approach seems to assume that a single ecological factor prevails or that if several factors decisively influence the community, then they all exert their influence in the same direction, generating either aggregation or segregation. As these assumptions are unlikely to hold in most cases and assembly processes cannot be inferred from random patterns, we would like to propose plant ecologists to investigate specifically the ecological processes responsible for observed random patterns, instead of trying to infer processes from patterns

外来入侵种紫茎泽兰竞争策略与扩散动态

紫茎泽兰（Eupatorium adenophorum Spreng.）作为重要的外来入侵种之一，已严重破坏了入侵地生态系统的结构与功能，同时使当地农林业生产蒙受巨大的损失。因此，明确紫茎泽兰的竞争策略与扩散潜力，对制定合理的控制措施具有重要意义。 土壤氮素增加常常有助于外来种的入侵，那么降氮能否抵制入侵呢？向土壤中添加碳素，增强微生物对氮素的吸收，从而降低土壤中可被植物吸收的氮素是目前常用的降氮方法。为检验这一假说对入侵种紫茎泽兰的适用性，选取入侵种紫茎泽兰和本地种禾本科雀麦（Bromus japonicus）、菊科鱼眼草（Dichrocephala integrifolia），分别单栽或与紫茎泽兰混栽，向各植物组合中添加碳素（按1650克有机质/平方米计）或氮素（按30克氮素/平方米计），并设立对照进行盆栽实验。在碳素添加条件下，紫茎泽兰地上与地下生物量分别比对照降低了71.9% 和 74.9%，而本地种的生物量却没有受到显著影响。同时，碳素添加导致紫茎泽兰对本地种的竞争强度（RII）明显下降。氮素添加则减弱或逆转了上述碳素的作用。因此，向土壤中添加碳素有助于抵抗氮沉降对外来种入侵的促进作用，特别对抵御那些与氮素有亲和力的入侵种更为有效。在不同氮素条件下，紫茎泽兰对本地种竞争中，资源竞争强度均明显大于化感作用。尽管在紫茎泽兰发育早期化感作用较小，但是，碳素添加使紫茎泽兰可利用氮素减少，激发了化感作用在竞争中占有更大的比例，说明资源竞争与化感是相互结合、共同发挥作用的。 去叶作为模拟采食方法之一，至少可以通过两种方式影响植物竞争。一是去叶对目标种生长产生负面影响，二是邻种去叶有利于目标种生长，进而改变种间竞争关系。基于以上假定，对紫茎泽兰与相邻本地种分别单栽、同种合栽和异种混栽，进行去叶处理。结果恰与假定相悖：在整个生长季内，去叶增加目标株生物量的1.0 – 198.9%。对于入侵种而言，当邻居本地种去叶时，紫茎泽兰能完全弥补竞争产生的负面效应，即它与未去叶的单栽紫茎泽兰生长无显著差异;而紫茎泽兰去叶降低了相邻本地种的生长，加剧了原本由于竞争给对本地种带来的负面影响。因此，去叶效应与邻种的存在与否及邻种的类型均有关。在应用生物控制对目标株采食时，特别是在没有造成严重伤害或致死情况下，可以使本来具有竞争优势的入侵种变得更具强势。竞争与去叶之间存在复杂的相互作用，采食带来的间接效应可能比预想的更为复杂。因此，在生物控制措施实施之前，充分地估计生物控制的间接作用至关重要。 为检验反应—扩散模型（reaction–diffusion model）能否正确模拟紫茎泽兰小尺度扩散速率，本研究调查了四川攀枝花山区5个不同的生境的紫茎泽兰群落。对各样地内紫茎泽兰定位和年龄确定，基于克里金插值法做出其入侵格局的等年线图，通过等年线之间的垂直距离即可得到紫茎泽兰扩散速率的经验值。同时，计算内禀增长率和扩散系数，根据模型计算得到扩散速率的预测值。结果表明：紫茎泽兰扩散速率经验值明显小于模型预测值。因此，尽管反应—扩散模型已在大尺度扩散预测方面得到广泛的应用和验证，但在小尺度上，由于没有借助于复杂的生活史模型和分层模型，单凭反应—扩散模型不足以得到准确的预测。另外，在没有遭受干扰的生境中，可以发现紫茎泽兰扩散早期存在明显的时滞期。倘若这种时滞效应在入侵扩散中是频繁发生的，那么在判定物种是否具有入侵性时，很可能由于物种处于时滞期而被误认为非入侵种。 基于紫茎泽兰入侵至中国60年来所收集到的441已知分布记录和23个环境变量，采用GARP模型对其潜在分布范围做出了预测，并通过Kappa和ROC（receiver–operator characteristic）对预测结果进行检验。结果表明紫茎泽兰目前分布以云贵高原为主体，逐渐向四川盆地东部、山东半岛、东南沿海、台湾沿海以及海南岛等地扩散。冷季降水量、年极端低温和年均最高温对分布影响较大。RDA（Redundancy Analysis）分析结果显示温度和降水是限制紫茎泽兰扩散的重要因素。在过去的20年里，紫茎泽兰已经从温度较高、天气波动较小的亚热带气候逐渐向气候温凉、降水减少的高海拔地区扩散。紫茎泽兰可以适应相对较宽的温度和降水梯度，年均温度在10—22 ˚C，年降水量在800—2000 mm区间均有分布。本研究结果为发展早期预警工作、防止紫茎泽兰在中国进一步入侵提供了科学依据。

玉米新老品种生理生态特征与竞争力差异研究

本文以中国不同年代主要的玉米品种为试验材料，深入研究了玉米品种更替过程中新老品种的生理生态特征和竞争力差异，分析了差异形成的原因并进行了理论探讨。 玉米新老品种竞争力差异的研究采用了单作和混作两种方式，设高低两个密度。生长过程中全面测量了生物量、形态、生理和群体指标，运用了生长分析的方法来研究竞争，整合了各水平参数来解释竞争结果，并用本研究数据检验了生长冗余理论。 玉米新老品种对比研究发现新品种的生理生态特征普遍优于老品种。这些优势不仅体现在较高的生物量积累、较大的籽粒库容和较强的再分配能力上，而且体现在高的叶面积指数、衰老过程中仍维持较高的叶绿素含量、可溶性蛋白含量和光合效率上，同时新品种的群体特性还具有更低的感病率和更少的无效分蘖。玉米新老品种竞争结果表明在混作条件下，相对总产量这一指标反映出新老品种间明显的互利效应，且这种效应随发育阶段而降低。新品种对老品种的相对竞争力则随着发育阶段波动，并且密度和发育阶段两因子对品种竞争力的影响有明显的相互作用。相对于新品种，老品种的确存在叶片和根系的生长冗余部分，但老品种并没有在混作竞争中获得明显的竞争优势，即玉米品种选育并不完全符合生长冗余理论，因此在理解植物竞争力方面仍需要其他层面更深入的探讨。 同时，玉米品种选育不完全符合生长冗余理论的结论在农学实践上并非毫无价值。因为新品种总生物量的提高，不仅增加了籽粒产量，而且增加了秸秆产量，提供了更多可利用的生物质资源。相对于仅仅关注粮食产量，综合利用中国农村巨大的生物质资源具有更重要的生态意义。

Designing MPC controllers by reverse-engineering existing LTI controllers

This technical report presents a method for designing a constrained output-feedback model predictive controller (MPC) that behaves in the same way as an existing baseline stabilising linear time invariant output-feedback controller when constraints are inactive. The baseline controller is cast into an observer-compensator form and an inverse-optimal cost function is used as the basis of the MPC controller. The available degrees of design freedom are explored, and some guidelines provided for the selection of an appropriate observer-compensator realisation that will best allow exploitation of the constraint-handling and redundancy management capabilities of MPC. Consideration is given to output setpoint tracking, and the method is demonstrated with three different multivariable plants of varying complexity.

Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey

Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti)

We constructed a high redundancy bacterial artificial chromosome library of a seriously endangered Old World Monkey, the Yunnan snub-nosed monkey (Rhinopithecus bieti) from China. This library contains a total of 136 320 BAC clones. The average insert size of BAC clones was estimated to be 148 kb. The percentage of small inserts (50-100 kb) is 2.74%, and only 2.67% non-recombinant clones were observed. Assuming a similar genome size with closely related primate species, the Yunnan snub-nosed monkey BAC library has at least six times the genome coverage. By end sequencing of randomly selected BAC clones, we generated 201 sequence tags for the library. A total of 139 end-sequenced BAC clones were mapped onto the chromosomes of Yunnan snub-nosed monkey by fluorescence in-situ hybridization, demonstrating a high degree of synteny conservation between humans and Yunnan snub-nosed monkeys. Blast search against human genome showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the BAC library. This library and the mapped BAC clones will serve as a valuable resource in comparative genomics studies and large-scale genome sequencing of nonhuman primates. The DNA sequence data reported in this paper were deposited in GenBank and assigned the accession number CG891489-CG891703.

Antihemostatic molecules from saliva of blood-feeding arthropods

The ability to feed on vertebrate blood has evolved many times in various arthropod clades. Consequently, saliva of blood-feeding arthropods has proven to be a rich source of antihemostatic molecules. A variety of platelet aggregation inhibitors antagonize platelet responses to wound-generated signals, including ADP, thrombin, and collagen. Anticoagulants disrupt elements of both the intrinsic and extrinsic pathways. Vasodilators include nitrophorins (nitric oxide storage and transport heme proteins), a variety of peptides that mimic endogenous vasodilatory neuropeptides, and proteins that catabolize or sequester endogenous vasoconstrictors. Multiple salivary proteins may be directed against each component of hemostasis, resulting in both redundancy and in some cases cooperative interactions between antihemostatic proteins. The complexity and redundancy of saliva ensures an efficient blood meal for the arthropod, but it also provides a diverse array of novel antihemostatic molecules for the pharmacologist.

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey

Physiological functions of human genes may be studied by gene-knockout experiments in model organisms such as the mouse. This strategy relies on the existence of one-to-one gene orthology between the human and mouse. When lineage-specific gene duplication occurs and paralogous genes share a certain degree of functional redundancy, knockout mice may not provide accurate functional information on human genes. Angiogenin is a small protein that stimulates blood-vessel growth and promotes tumor development. Humans and related primates only have one angiogenin gene, while mice have three paralogous genes. This makes it difficult to generate angiogenin-knockout mice and even more difficult to interpret the genotype-phenotype relation from such animals should they be generated. We here show that in the douc langur (Pygathrix nemaeus), an Asian leaf-eating colobine monkey, the single-copy angiogenin gene has a one-nucleotide deletion in the sixth codon of the mature peptide, generating a premature stop codon. This nucleotide deletion is found in five unrelated individuals sequenced, and therefore is likely to have been fixed in the species. Five colobine species that are closely related to the douc langur have intact angiogenin genes, suggesting that the pseudogenization event was recent and unique to the douc langur lineage. This natural knockout experiment suggests that primate angiogenin is dispensable even in the wild. Further physiological studies of douc largurs may offer additional information on the role of this cancer-related gene in normal physiology of primates, including humans. Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions. (C) 2003 Elsevier Science B.V. All rights reserved.

Accurate real-time feedback of surface EMG during fMRI.

Real-time acquisition of EMG during functional MRI (fMRI) provides a novel method of controlling motor experiments in the scanner using feedback of EMG. Because of the redundancy in the human muscle system, this is not possible from recordings of joint torque and kinematics alone, because these provide no information about individual muscle activation. This is particularly critical during brain imaging because brain activations are not only related to joint torques and kinematics but are also related to individual muscle activation. However, EMG collected during imaging is corrupted by large artifacts induced by the varying magnetic fields and radio frequency (RF) pulses in the scanner. Methods proposed in literature for artifact removal are complex, computationally expensive, and difficult to implement for real-time noise removal. We describe an acquisition system and algorithm that enables real-time acquisition for the first time. The algorithm removes particular frequencies from the EMG spectrum in which the noise is concentrated. Although this decreases the power content of the EMG, this method provides excellent estimates of EMG with good resolution. Comparisons show that the cleaned EMG obtained with the algorithm is, like actual EMG, very well correlated with joint torque and can thus be used for real-time visual feedback during functional studies.

Computational mechanisms of sensorimotor control.

In order to generate skilled and efficient actions, the motor system must find solutions to several problems inherent in sensorimotor control, including nonlinearity, nonstationarity, delays, redundancy, uncertainty, and noise. We review these problems and five computational mechanisms that the brain may use to limit their deleterious effects: optimal feedback control, impedance control, predictive control, Bayesian decision theory, and sensorimotor learning. Together, these computational mechanisms allow skilled and fluent sensorimotor behavior.

Complex wavelets and shift invariance

Recently we have developed a new form of discrete wavelet transform, which generates complex coefficients by using a dual tree of wavelet filters to obtain their real and imaginary parts. This introduces limited redundancy (2 m:1 for m-dimensional signals) and allows the transform to provide approximate shift invariance and directionally selective filters (properties lacking in the traditional wavelet transform) while preserving the usual properties of perfect reconstruction and computational efficiency with good well-balanced frequency responses. In this paper we analyse why the new transform can be designed to be shift invariant, and describe how to estimate the accuracy of this approximation and design suitable filters to achieve this.

Biologically-inspired object recognition system with features from complex wavelets

In this paper, a novel cortex-inspired feed-forward hierarchical object recognition system based on complex wavelets is proposed and tested. Complex wavelets contain three key properties for object representation: shift invariance, which enables the extraction of stable local features; good directional selectivity, which simplifies the determination of image orientations; and limited redundancy, which allows for efficient signal analysis using the multi-resolution decomposition offered by complex wavelets. In this paper, we propose a complete cortex-inspired object recognition system based on complex wavelets. We find that the implementation of the HMAX model for object recognition in [1, 2] is rather over-complete and includes too much redundant information and processing. We have optimized the structure of the model to make it more efficient. Specifically, we have used the Caltech 5 standard dataset to compare with Serre's model in [2] (which employs Gabor filter bands). Results demonstrate that the complex wavelet model achieves a speed improvement of about 4 times over the Serre model and gives comparable recognition performance. © 2011 IEEE.

Robust F0 estimation based on a multi-microphone periodicity function for distant-talking speech

This work addresses the problem of deriving F0 from distanttalking speech signals acquired by a microphone network. The method here proposed exploits the redundancy across the channels by jointly processing the different signals. To this purpose, a multi-microphone periodicity function is derived from the magnitude spectrum of all the channels. This function allows to estimate F0 reliably, even under reverberant conditions, without the need of any post-processing or smoothing technique. Experiments, conducted on real data, showed that the proposed frequency-domain algorithm is more suitable than other time-domain based ones.

Sparsity-Inducing Optimization Algorithm for the Extraction of Planar Structures in Noisy Point-Cloud Data

Most of the manual labor needed to create the geometric building information model (BIM) of an existing facility is spent converting raw point cloud data (PCD) to a BIM description. Automating this process would drastically reduce the modeling cost. Surface extraction from PCD is a fundamental step in this process. Compact modeling of redundant points in PCD as a set of planes leads to smaller file size and fast interactive visualization on cheap hardware. Traditional approaches for smooth surface reconstruction do not explicitly model the sparse scene structure or significantly exploit the redundancy. This paper proposes a method based on sparsity-inducing optimization to address the planar surface extraction problem. Through sparse optimization, points in PCD are segmented according to their embedded linear subspaces. Within each segmented part, plane models can be estimated. Experimental results on a typical noisy PCD demonstrate the effectiveness of the algorithm.