Tree-based iterated local search for Markov random fields with applications in image analysis

The maximum a posteriori assignment for general structure Markov random fields is computationally intractable. In this paper, we exploit tree-based methods to efficiently address this problem. Our novel method, named Tree-based Iterated Local Search (T-ILS), takes advantage of the tractability of tree-structures embedded within MRFs to derive strong local search in an ILS framework. The method efficiently explores exponentially large neighborhoods using a limited memory without any requirement on the cost functions. We evaluate the T-ILS on a simulated Ising model and two real-world vision problems: stereo matching and image denoising. Experimental results demonstrate that our methods are competitive against state-of-the-art rivals with significant computational gain.

Clustering and visualization of failure modes using an evolving tree

Despite the popularity of Failure Mode and Effect Analysis (FMEA) in a wide range of industries, two well-known shortcomings are the complexity of the FMEA worksheet and its intricacy of use. To the best of our knowledge, the use of computation techniques for solving the aforementioned shortcomings is limited. As such, the idea of clustering and visualization pertaining to the failure modes in FMEA is proposed in this paper. A neural network visualization model with an incremental learning feature, i.e., the evolving tree (ETree), is adopted to allow the failure modes in FMEA to be clustered and visualized as a tree structure. In addition, the ideas of risk interval and risk ordering for different groups of failure modes are proposed to allow the failure modes to be ordered, analyzed, and evaluated in groups. The main advantages of the proposed method lie in its ability to transform failure modes in a complex FMEA worksheet to a tree structure for better visualization, while maintaining the risk evaluation and ordering features. It can be applied to the conventional FMEA methodology without requiring additional information or data. A real world case study in the edible bird nest industry in Sarawak (Borneo Island) is used to evaluate the usefulness of the proposed method. The experiments show that the failure modes in FMEA can be effectively visualized through the tree structure. A discussion with FMEA users engaged in the case study indicates that such visualization is helpful in comprehending and analyzing the respective failure modes, as compared with those in an FMEA table. The resulting tree structure, together with risk interval and risk ordering, provides a quick and easily understandable framework to elucidate important information from complex FMEA forms; therefore facilitating the decision-making tasks by FMEA users. The significance of this study is twofold, viz., the use of a computational visualization approach to tackling two well-known shortcomings of FMEA; and the use of ETree as an effective neural network learning paradigm to facilitate FMEA implementations. These findings aim to spearhead the potential adoption of FMEA as a useful and usable risk evaluation and management tool by the wider community.

Searching Baxter's URDF robot joint and link tree for active serial chains

Teleoperation is integral to society's uptake of modern robotic systems. Given the wide array of readily available robots, ranging from simple mobile platforms and UAVs to advanced humanoid robots such as ASIMO and PR2, teleoperation is required in many different forms. The recent advances in virtual reality systems, interactive input controls and even haptic devices facilitate a wide range of new approaches to teleoperation control. This paper considers a dynamic user interface for improving the operator's ability to teleoperate heterogeneous robotic systems in dynamic and challenging environments. In order to achieve the proposed dynamic user interface the robot(s) comprising the heterogeneous robotic system and their active components need to be categorized. The recent uptake of ROS means that many robots are now represented within the standardized Unified Robot Descriptive Format (URDF), and this paper proposes a method for searching the URDF for active serial chains in individual robot systems. Results demonstrate the ability of the approach to determine active serial chains and associated kinematic information for the Baxter torso robot.

Decision Tree Classification Model In Water Supply Network

With the service life of water supply network (WSN) growth, the growing phenomenon of aging pipe network has become exceedingly serious. As urban water supply network is hidden underground asset, it is difficult for monitoring staff to make a direct classification towards the faults of pipe network by means of the modern detecting technology. In this paper, based on the basic property data (e.g. diameter, material, pressure, distance to pump, distance to tank, load, etc.) of water supply network, decision tree algorithm (C4.5) has been carried out to classify the specific situation of water supply pipeline. Part of the historical data was used to establish a decision tree classification model, and the remaining historical data was used to validate this established model. Adopting statistical methods were used to access the decision tree model including basic statistical method, Receiver Operating Characteristic (ROC) and Recall-Precision Curves (RPC). These methods has been successfully used to assess the accuracy of this established classification model of water pipe network. The purpose of classification model was to classify the specific condition of water pipe network. It is important to maintain the pipeline according to the classification results including asset unserviceable (AU), near perfect condition (NPC) and serious deterioration (SD). Finally, this research focused on pipe classification which plays a significant role in maintaining water supply networks in the future.

Vegetative propagation of bauhinia x blakeana, an ornamental sterile tree

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Is The amphibian tree of life really fatally flawed?

Wiens (2007, Q. Rev. Biol. 82, 55-56) recently published a severe critique of Frost et al.'s (2006, Bull. Am. Mus. Nat. Hist. 297, 1-370) monographic study of amphibian systematics, concluding that it is a disaster and recommending that readers simply ignore this study. Beyond the hyperbole, Wiens raised four general objections that he regarded as fatal flaws: (1) the sampling design was insufficient for the generic changes made and taxonomic changes were made without including all type species; (2) the nuclear gene most commonly used in amphibian phylogenetics, RAG-1, was not included, nor were the morphological characters that had justified the older taxonomy; (3) the analytical method employed is questionable because equally weighted parsimony assumes that all characters are evolving at equal rates; and (4) the results were at times clearly erroneous, as evidenced by the inferred non-monophyly of marsupial frogs. In this paper we respond to these criticisms. In brief: (1) the study of Frost et al. did not exist in a vacuum and we discussed our evidence and evidence previously obtained by others that documented the non-monophyletic taxa that we corrected. Beyond that, we agree that all type species should ideally be included, but inclusion of all potentially relevant type species is not feasible in a study of the magnitude of Frost et al. and we contend that this should not prevent progress in the formulation of phylogenetic hypotheses or their application outside of systematics. (2) Rhodopsin, a gene included by Frost et al. is the nuclear gene that is most commonly used in amphibian systematics, not RAG-1. Regardless, ignoring a study because of the absence of a single locus strikes us as unsound practice. With respect to previously hypothesized morphological synapomorphies, Frost et al. provided a lengthy review of the published evidence for all groups, and this was used to inform taxonomic decisions. We noted that confirming and reconciling all morphological transformation series published among previous studies needed to be done, and we included evidence from the only published data set at that time to explicitly code morphological characters (including a number of traditionally applied synapomorphies from adult morphology) across the bulk of the diversity of amphibians (Haas, 2003, Cladistics 19, 23-90). Moreover, the phylogenetic results of the Frost et al. study were largely consistent with previous morphological and molecular studies and where they differed, this was discussed with reference to the weight of evidence. (3) The claim that equally weighted parsimony assumes that all characters are evolving at equal rates has been shown to be false in both analytical and simulation studies. (4) The claimed strong support for marsupial frog monophyly is questionable. Several studies have also found marsupial frogs to be non-monophyletic. Wiens et al. (2005, Syst. Biol. 54, 719-748) recovered marsupial frogs as monophyletic, but that result was strongly supported only by Bayesian clade confidence values (which are known to overestimate support) and bootstrap support in his parsimony analysis was < 50%. Further, in a more recent parsimony analysis of an expanded data set that included RAG-1 and the three traditional morphological synapomorphies of marsupial frogs, Wiens et al. (2006, Am. Nat. 168, 579-596) also found them to be non-monophyletic.Although we attempted to apply the rule of monophyly to the naming of taxonomic groups, our phylogenetic results are largely consistent with conventional views even if not wth the taxonomy current at the time of our writing. Most of our taxonomic changes addressed examples of non-monophyly that had previously been known or suspected (e.g., the non-monophyly of traditional Hyperoliidae, Microhylidae, Hemiphractinae, Leptodactylidae, Phrynobatrachus, Ranidae, Rana, Bufo; and the placement of Brachycephalus within Eleutherodactylus, and Lineatriton within Pseudoeurycea), and it is troubling that Wiens and others, as evidenced by recent publications, continue to perpetuate recognition of non-monophyletic taxonomic groups that so profoundly misrepresent what is known about amphibian phylogeny. (C) The Willi Hennig Society 2007.

The absolute configuration of 1-(3 ',4 '-dihydroxycinnamoyl)cyclopentane-2,3-diol from the Amazonian tree Chimarrhis turbinata

An antioxidant, 1-(3',4'-dihydroxycinnamoyl) cyclopentane-2,3-diol [ or ( E)-2,3-dihydroxycyclopentyl-3-(3',4'-dihydroxyphenyl) acrylate ( 1)], and two known trans- and cis-chlorogenic acid methyl esters were isolated from the ethanolic extract of the leaves of Chimarrhis turbinata. The relative configuration of 1 was determined by NMR and by comparison of the circular dichroic spectrum ( CD) with those of the enantiomers of synthetic 3', 4'-dimethoxycinnamoyl analogues. The absolute configuration of one of the synthetic enantiomers was determined using the CD exciton chirality method. This established the structure of naturally occurring 1 as (E)- 2,3-dihydroxycyclopentyl- 3-(3', 4'-dihydroxyphenyl) acrylate.

Phytosociological study on the tree stratum of a semideciduous mesophytic forest in the municipality of Jau, SP, Brazil

Through the point-centered quarter method, a phytosociological study was carried out in an area of semideciduous mesophytic forest with 190 ha, in the municipality of Jahu,SP. Due to the fact of the forest be crossed by three small rivers, for the sampling process, the Total Area was divided in two sampling areas: the Area I (under the influence of the rivers) and the Area II (without this influence). Some differences between the two regions were observed.

Phytosociological study of the tree stratum of a semideciduous mesophytic forest in the municipality of Botucatu, SP, Brazil

The phytosociological structure was studied in an area of semideciduous mesophytic forest lied on the ascent of the Cuesta of Botucatu. Once the relief of the area was very heterogeneous, the forest, for the sampling process, was divided in three sampling regions: the upper one (on the plateau), the middle one (on the ascent properly said) and the lower one (on the plain). Through the point-centered method, 1224 (408 in each region) trees were sampled. For this work, only the trees with shaft equal or higher than 1.30m high were considered. The three sampling regions showed some interesting differences in regard to the phytosociologic structure. Once there are differences among the soil of the three regions, the variations in the structure must be connected to the differences in the soil.

Estimation of variance components and prediction of breeding values in rubber tree breeding using the REML/BLUP procedure

The present paper deals with estimation of variance components, prediction of breeding values and selection in a population of rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Müell.-Arg.] from Rio Branco, State of Acre, Brazil. The REML/BLUP (restricted maximum likelihood/best linear unbiased prediction) procedure was applied. For this purpose, 37 rubber tree families were obtained and assessed in a randomized complete block design, with three unbalanced replications. The field trial was carried out at the Experimental Station of UNESP, located in Selvíria, State of Mato Grosso do Sul, Brazil. The quantitative traits evaluated were: girth (G), bark thickness (BT), number of latex vessel rings (NR), and plant height (PH). Given the unbalanced condition of the progeny test, the REML/BLUP procedure was used for estimation. The narrow-sense individual heritability estimates were 0.43 for G, 0.18 for BT, 0.01 for NR, and 0.51 for PH. Two selection strategies were adopted: one short-term (ST - selection intensity of 8.85%) and the other long-term (LT - selection intensity of 26.56%). For G, the estimated genetic gains in relation to the population average were 26.80% and 17.94%, respectively, according to the ST and LT strategies. The effective population sizes were 22.35 and 46.03, respectively. The LT and ST strategies maintained 45.80% and 28.24%, respectively, of the original genetic diversity represented in the progeny test. So, it can be inferred that this population has potential for both breeding and ex situ genetic conservation as a supplier of genetic material for advanced rubber tree breeding programs. Copyright by the Brazilian Society of Genetics.

Evaluation of ERIC-PCR as Genotyping Method for Corynebacterium pseudotuberculosis Isolates

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Automatic method to classify images based on multiscale fractal descriptors and paraconsistent logic

In this study is presented an automatic method to classify images from fractal descriptors as decision rules, such as multiscale fractal dimension and lacunarity. The proposed methodology was divided in three steps: quantification of the regions of interest with fractal dimension and lacunarity, techniques under a multiscale approach; definition of reference patterns, which are the limits of each studied group; and, classification of each group, considering the combination of the reference patterns with signals maximization (an approach commonly considered in paraconsistent logic). The proposed method was used to classify histological prostatic images, aiming the diagnostic of prostate cancer. The accuracy levels were important, overcoming those obtained with Support Vector Machine (SVM) and Bestfirst Decicion Tree (BFTree) classifiers. The proposed approach allows recognize and classify patterns, offering the advantage of giving comprehensive results to the specialists.

Chlorophyll fluorescence in guanandi tree (calophyllum brasiliense) after herbicide application

Chlorophyll fluorescence is currently used as a rapid diagnostic and nondestructive method to detect and quantify damage on the photosynthetic apparatus of leaves on weeds, crops and ornamental/coniferous trees in response to both environmental stress and herbicides. This study aimed to evaluate chlorophyll fluorescence in guanandi plants (Calophyllum brasiliense) after application of different postemergence herbicides. The experiment was performed in a completely randomized design, with six treatments (control, bentazon, sulfentrazone, isoxaflutole, atrazine and glyphosate) and five replications. The herbicide treatments were applied with a stationary sprayer, and electron transport rate (ETR) was subsequently analyzed with OS5p Multi-Mode Chlorophyll Fluorometer. In the monitored period, guanandi plants subjected to atrazine showed higher sensitivity to chlorophyll fluorescence than the other treatments. Although bentazon is a photosystem II inhibitor, it showed no major changes in electron transport for the studied species and in the monitored period. In summary, ETR is a good parameter to evaluate the effect of some herbicides on Calophyllum brasiliense plants.

EXPERIMENTAL TREE TRIMMING TO CONTROL AN URBAN WINTER BLACKBIRD ROOST

Every fall millions of blackbirds come down the Mississippi Flyway to return to their winter roosts in Arkansas, Louisiana, and East Texas. When these roosts are located in urban areas, public pressure makes the more common chemical means of control impractical. A less destructive and more permanent method of control was sought. At Rice University, in Houston, Texas, there has been a blackbird roost of various sizes and durations since 1956. For the past two years we have had the opportunity both to study roosting blackbird biology and experiment with habitat alteration as a control method. This particular report concentrates on the results and interpretation of the tree- trimming program initiated in August 1974. The birds involved are primarily Brown-headed Cowbirds (Molothrus ater), along with Starlings (sturnus vulgaris), Common and Great-tailed Grackles (Quiscalus quiscula and Cassidix mexicanus), Red-winged Blackbirds (Agelaius phoenicus) and Robins (Turdus migratorius). The campus comprises 121 ha and was planted with live oaks (Quercus virginiana) in 1912. These trees retain their foliage throughout the winter and now form a closed canopy over some 5-6 ha. In the 60s and early 70s most of the birds that came to Houston for the winter roosted in a 64-ha woodlot 10 km north of campus. In January 1970, the U.S. Fish and Wildlife Roosting Survey reported one million birds at this site we call the North Loop. Fifteen- thousand birds were estimated at Rice.