Shared and Unique Gene Expression in Systemic Lupus Erythematosus Depending on Disease Activity

Patients presenting with active Systemic lupus erythematosus (SLE) manifestations may exhibit distinct pathogenetic features in relation to inactive SLE. Also, cDNA microarrays may potentially discriminate the gene expression profile of a disease or disease variant. Therefore, we evaluated the expression profile of 4500 genes in peripheral blood lymphocytes (PBL) of SLE patients. We studied 11 patients with SLE (seven with active SLE and four with inactive SLE) and eight healthy controls. Total RNA was isolated from PBL, reverse transcribed into cDNA, and postlabeled with Cy3 fluorochrome. These probes were then hybridized to a glass slide cDNA microarray containing 4500 human IMAGE cDNA target sequences. An equimolar amount of total RNA from human cell lines served as reference. The microarray images were quantified, normalized, and analyzed using the R environment (ANOVA, significant analysis of microarrays, and cluster-tree view algorithms). Disease activity was assessed by the SLE disease activity index. Compared to the healthy controls, 104 genes in active SLE patients (80 repressed and 24 induced) and 52 genes in nonactive SLE patients (31 induced and 21 repressed) were differentially expressed. The modulation of 12 genes, either induced or repressed, was found in both disease variants; however, each disease variant had differential expression of different genes. Taken together, these results indicate that the two lupus variants studied have common and unique differentially expressed genes. Although the biological significance of the differentially expressed genes discussed above has not been completely understood, they may serve as a platform to further explore the molecular basis of immune deregulation in SLE.

Affected and non-affected skin fibroblasts from systemic sclerosis patients share a gene expression profile deviated from the one observed in healthy individuals

Objectives To evaluate the gene expression profile of fibroblasts from affected and non-affected skin of systemic sclerosis (SSc) patients and from controls. Materials and methods Labeled cDNA from fibroblast cultures from forearm (affected) and axillary (non-affected) skin from six diffuse SSc patients, from three normal controls, and from MOLT-4/HEp-2/normal fibroblasts (reference pool) was probed in microarrays generated with 4193 human cDNAs from the IMAGE Consortium. Microarray images were converted into numerical data and gene expression was calculated as the ratio between fibroblast cDNA (Cy5) and reference pool cDNA (Cy3) data and analyzed by R environment/Aroma, Cluster, Tree View, and SAM softwares. Differential expression was confirmed by real time PCR for a set of selected genes. Results Eighty-eight genes were up- and 241 genes down-regulated in SSc fibroblasts. Gene expression correlation was strong between affected and non-affected fibroblast samples from the same patient (r>0.8), moderate among fibroblasts from all patients (r=0.72) and among fibroblasts from all controls (r=0.70), and modest among fibroblasts from patients and controls (r=0.55). The differential expression was confirmed by real time PCR for all selected genes. Conclusions Fibroblasts from affected and non-affected skin of SSc patients shared a similar abnormal gene expression profile, suggesting that the widespread molecular disturbance in SSc fibroblasts is more sensitive than histological and clinical alterations. Novel molecular elements potentially involved in SSc pathogenesis were identified.

Mutual Information and Perplexity based Clustering of Dialogue Information for Dynamic Adaptation of Language Models

We present two approaches to cluster dialogue-based information obtained by the speech understanding module and the dialogue manager of a spoken dialogue system. The purpose is to estimate a language model related to each cluster, and use them to dynamically modify the model of the speech recognizer at each dialogue turn. In the first approach we build the cluster tree using local decisions based on a Maximum Normalized Mutual Information criterion. In the second one we take global decisions, based on the optimization of the global perplexity of the combination of the cluster-related LMs. Our experiments show a relative reduction of the word error rate of 15.17%, which helps to improve the performance of the understanding and the dialogue manager modules.

Mutual Information and Perplexity based Clustering of Dialogue Information for Dynamic Adaptation of Language Models

We present two approaches to cluster dialogue-based information obtained by the speech understanding module and the dialogue manager of a spoken dialogue system. The purpose is to estimate a language model related to each cluster, and use them to dynamically modify the model of the speech recognizer at each dialogue turn. In the first approach we build the cluster tree using local decisions based on a Maximum Normalized Mutual Information criterion. In the second one we take global decisions, based on the optimization of the global perplexity of the combination of the cluster-related LMs. Our experiments show a relative reduction of the word error rate of 15.17%, which helps to improve the performance of the understanding and the dialogue manager modules.

Mixed rain forest in southeastern Brazil: tree species regeneration and floristic relationships in a remaining stretch of forest near the city of Itaberá, Brazil

The aim of this work was to evaluate the floristic composition, richness, and diversity of the upper and lower strata of a stretch of mixed rain forest near the city of Itaberá, in southeastern Brazil. We also investigated the differences between this conservation area and other stretches of mixed rain forest in southern and southeastern Brazil, as well as other nearby forest formations, in terms of their floristic relationships. For our survey of the upper stratum (diameter at breast height [DBH] > 15 cm), we established 50 permanent plots of 10 × 20 m. Within each of those plots, we designated five, randomly located, 1 × 1 m subplots, in order to survey the lower stratum (total height > 30 cm and DBH < 15 cm). In the upper stratum, we sampled 1429 trees and shrubs, belonging to 134 species, 93 genera, and 47 families. In the lower stratum, we sampled 758 trees and shrubs, belonging to 93 species, 66 genera, and 39 families. In our floristic and phytosociological surveys, we recorded 177 species, belonging to 106 genera and 52 families. The Shannon Diversity Index was 4.12 and 3.5 for the upper and lower strata, respectively. Cluster analysis indicated that nearby forest formations had the strongest floristic influence on the study area, which was therefore distinct from other mixed rain forests in southern Brazil and in the Serra da Mantiqueira mountain range.

Tree performance and fruit yield and quality of `Okitsu` Satsuma mandarin grafted on 12 rootstocks

The citriculture in Brazil, as well as in other important regions in the world, is based on very few mandarin cultivars. This fact leads to a short harvest period and higher prices for off-season fruit. The `Okitsu` Satsuma (Citrus unshiu Marc.) is among the earliest ripening mandarin cultivars and it is considered to be tolerant to, citrus canker (Xanthomonas citri subsp. citri Schaad et al.) and to citrus variegated chlorosis (Xylella fastidiosa Wells et al.). Despite having regular fruit quality under hot climate conditions, the early fruit maturation and absence of seeds of `Okitsu` fruits are well suited for the local market in the summer(December through March), when the availability of citrus fruits for fresh consumption is limited. Yet, only a few studies have been conducted in Brazil on rootstocks for `Okitsu`. Consequently, a field trial was carried out in Bebeclouro, Sao Paulo State, to evaluate the horticultural performance of `Okitsu` Satsuma mandarin budded onto 12 rootstocks: the citrandarin `Changsha` mandarin (Citrus reticulata Blanco) x Poncirus trifoliata `English Small`: the hybrid Rangpur lime (Citrus limonia Osbeck) x `Swingle` citrumelo (P. trifoliata (L.) Raf. x Citrus paradisi Macfad.); the trifoliates (P. trifoliata (L) Raf)`Rubidoux`,`FCAV` and `Flying Dragon`(P. trifoliata var. monstrosa); the mandarins `Sun Chu Sha Kat`(C. reticulata Blanco) and `Sunki`(Citrus sunki (Hayata) Hort. ex. Tanaka); the Rangpur limes (C. limonia Osbeck) `Cravo Limeira` and `Cravo FCAV`;`Carrizo` citrange (Citrus sinensis x P. trifoliata), `Swingle` citrumelo (P. trifoliata x C. paradisi), and `Orlando` tangelo (C. paradisi x Citrus tangerina cv. `Dancy`). The experimental grove was planted in 2001, using a 6 m x 3 m spacing, in a randomized block design. No supplementary irrigation was applied. Fruit yield, canopy volume, and fruit quality were assessed for each rootstock. A cluster multivariate analysis identified three different rootstock pairs with similar effects on plant growth, yield and fruit quality of `Okitsu` mandarin. The `Flying Dragon `trifoliate had a unique effect over the `Okitsu` trees performance, inducing lower canopy volume and higher yield efficiency and fruit quality, and might be suitable for high-density plantings. The `Cravo Limeira` and `Cravo FCAV` Rangpur limes induced early-ripening of fruits, with low fruit quality. `Sun Chu Sha Kat` and `Sunki` mandarins and the `Orlando` tangelo conferred lower yield efficiency and less content of soluble solids for the latter rootstock. (C) 2009 Elsevier B.V. All rights reserved.

Novel benzofuroxan derivatives against multidrug-resistant Staphylococcus aureus strains: Design using Topliss` decision tree, synthesis and biological assay

The aim of this study was the design of a set of benzofuroxan derivatives as antimicrobial agents exploring the physicochemical properties of the related substituents. Topliss` decision tree approach was applied to select the substituent groups. Hierarchical cluster analysis was also performed to emphasize natural clusters and patterns. The compounds were obtained using two synthetic approaches for reducing the synthetic steps as well as improving the yield. The minimal inhibitory concentration method was employed to evaluate the activity against multidrug-resistant Staphylococcus aureus strains. The most active compound was 4-nitro-3-(trifluoromethyl)[N`-(benzofuroxan-5-yl) methylene] benzhydrazide (MIC range 12.7-11.4 mu g/mL), pointing out that the antimicrobial activity was indeed influenced by the hydrophobic and electron-withdrawing property of the substituent groups 3-CF(3) and 4-NO(2), respectively. (C) 2011 Elsevier Ltd. All rights reserved.

LNT: a logical neighbor tree secure group communication scheme for wireless sensor networks

Secure group communication is a paradigm that primarily designates one-to-many communication security. The proposed works relevant to secure group communication have predominantly considered the whole network as being a single group managed by a central powerful node capable of supporting heavy communication, computation and storage cost. However, a typical Wireless Sensor Network (WSN) may contain several groups, and each one is maintained by a sensor node (the group controller) with constrained resources. Moreover, the previously proposed schemes require a multicast routing support to deliver the rekeying messages. Nevertheless, multicast routing can incur heavy storage and communication overheads in the case of a wireless sensor network. Due to these two major limitations, we have reckoned it necessary to propose a new secure group communication with a lightweight rekeying process. Our proposal overcomes the two limitations mentioned above, and can be applied to a homogeneous WSN with resource-constrained nodes with no need for a multicast routing support. Actually, the analysis and simulation results have clearly demonstrated that our scheme outperforms the previous well-known solutions.

Ever-young sex chromosomes in European tree frogs.

Non-recombining sex chromosomes are expected to undergo evolutionary decay, ending up genetically degenerated, as has happened in birds and mammals. Why are then sex chromosomes so often homomorphic in cold-blooded vertebrates? One possible explanation is a high rate of turnover events, replacing master sex-determining genes by new ones on other chromosomes. An alternative is that X-Y similarity is maintained by occasional recombination events, occurring in sex-reversed XY females. Based on mitochondrial and nuclear gene sequences, we estimated the divergence times between European tree frogs (Hyla arborea, H. intermedia, and H. molleri) to the upper Miocene, about 5.4-7.1 million years ago. Sibship analyses of microsatellite polymorphisms revealed that all three species have the same pair of sex chromosomes, with complete absence of X-Y recombination in males. Despite this, sequences of sex-linked loci show no divergence between the X and Y chromosomes. In the phylogeny, the X and Y alleles cluster according to species, not in groups of gametologs. We conclude that sex-chromosome homomorphy in these tree frogs does not result from a recent turnover but is maintained over evolutionary timescales by occasional X-Y recombination. Seemingly young sex chromosomes may thus carry old-established sex-determining genes, a result at odds with the view that sex chromosomes necessarily decay until they are replaced. This raises intriguing perspectives regarding the evolutionary dynamics of sexually antagonistic genes and the mechanisms that control X-Y recombination.

Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil

The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS) and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as Pestalotiopsis clavispora and three as P. cocculi. The other isolates remained as an undefined species. The morphological characters were efficient for an initial separation of the isolates, which were grouped according to differences at species level, mainly colony diameter, which was identified as an important morphological describer. Beta-tubulin gene sequencing was less informative than the ITS region sequencing for species identification.

Cluster-based active learning for compact image classification

In this paper, we consider active sampling to label pixels grouped with hierarchical clustering. The objective of the method is to match the data relationships discovered by the clustering algorithm with the user's desired class semantics. The first is represented as a complete tree to be pruned and the second is iteratively provided by the user. The active learning algorithm proposed searches the pruning of the tree that best matches the labels of the sampled points. By choosing the part of the tree to sample from according to current pruning's uncertainty, sampling is focused on most uncertain clusters. This way, large clusters for which the class membership is already fixed are no longer queried and sampling is focused on division of clusters showing mixed labels. The model is tested on a VHR image in a multiclass classification setting. The method clearly outperforms random sampling in a transductive setting, but cannot generalize to unseen data, since it aims at optimizing the classification of a given cluster structure.

Peaches tree genetic divergence for brown rot reaction

It was evaluated the genetic divergence in peach genotypes for brown rot reaction. It was evaluated 26 and 29 peach genotypes in the 2009/2010 and 2010/2011 production cycle, respectively. The experiment was carried out at the Laboratório de Fitossanidade, da UTFPR - Campus Dois Vizinhos. The experimental design was entirely randomized, considering each peach genotype a treatment, and it was use three replication of nine fruits. The treatment control use three replication of three peach. The fruit epidermis were inoculated individually with 0.15 mL of M. fructicola conidial suspension (1.0 x 10(5) spores mL-1). In the control treatment was sprayed with 0.15 mL of distilled water. The fruits were examined 72 and 120 hours after inoculation, and the incidence and severity disease were evaluated. These results allowed realized study for genetic divergence, used as dissimilarity measure the Generalized Mahalanobis distance. Cluster analysis using Tocher´s optimization method and distances in the plan were applied. There was smallest genetic divergence among peach trees evaluated for brown rot, what can difficult to obtain resistance in the genotypes.

Energy-Efficient Cluster based Routing Schemes for Static and Mobile Sensor Networks

The theme of the thesis is centred around one important aspect of wireless sensor networks; the energy-efficiency.The limited energy source of the sensor nodes calls for design of energy-efficient routing protocols. The schemes for protocol design should try to minimize the number of communications among the nodes to save energy. Cluster based techniques were found energy-efficient. In this method clusters are formed and data from different nodes are collected under a cluster head belonging to each clusters and then forwarded it to the base station.Appropriate cluster head selection process and generation of desirable distribution of the clusters can reduce energy consumption of the network and prolong the network lifetime. In this work two such schemes were developed for static wireless sensor networks.In the first scheme, the energy wastage due to cluster rebuilding incorporating all the nodes were addressed. A tree based scheme is presented to alleviate this problem by rebuilding only sub clusters of the network. An analytical model of energy consumption of proposed scheme is developed and the scheme is compared with existing cluster based scheme. The simulation study proved the energy savings observed.The second scheme concentrated to build load-balanced energy efficient clusters to prolong the lifetime of the network. A voting based approach to utilise the neighbor node information in the cluster head selection process is proposed. The number of nodes joining a cluster is restricted to have equal sized optimum clusters. Multi-hop communication among the cluster heads is also introduced to reduce the energy consumption. The simulation study has shown that the scheme results in balanced clusters and the network achieves reduction in energy consumption.The main conclusion from the study was the routing scheme should pay attention on successful data delivery from node to base station in addition to the energy-efficiency. The cluster based protocols are extended from static scenario to mobile scenario by various authors. None of the proposals addresses cluster head election appropriately in view of mobility. An elegant scheme for electing cluster heads is presented to meet the challenge of handling cluster durability when all the nodes in the network are moving. The scheme has been simulated and compared with a similar approach.The proliferation of sensor networks enables users with large set of sensor information to utilise them in various applications. The sensor network programming is inherently difficult due to various reasons. There must be an elegant way to collect the data gathered by sensor networks with out worrying about the underlying structure of the network. The final work presented addresses a way to collect data from a sensor network and present it to the users in a flexible way.A service oriented architecture based application is built and data collection task is presented as a web service. This will enable composition of sensor data from different sensor networks to build interesting applications. The main objective of the thesis was to design energy-efficient routing schemes for both static as well as mobile sensor networks. A progressive approach was followed to achieve this goal.

Dynamic load balancing in parallel KD-tree k-means

One among the most influential and popular data mining methods is the k-Means algorithm for cluster analysis. Techniques for improving the efficiency of k-Means have been largely explored in two main directions. The amount of computation can be significantly reduced by adopting geometrical constraints and an efficient data structure, notably a multidimensional binary search tree (KD-Tree). These techniques allow to reduce the number of distance computations the algorithm performs at each iteration. A second direction is parallel processing, where data and computation loads are distributed over many processing nodes. However, little work has been done to provide a parallel formulation of the efficient sequential techniques based on KD-Trees. Such approaches are expected to have an irregular distribution of computation load and can suffer from load imbalance. This issue has so far limited the adoption of these efficient k-Means variants in parallel computing environments. In this work, we provide a parallel formulation of the KD-Tree based k-Means algorithm for distributed memory systems and address its load balancing issue. Three solutions have been developed and tested. Two approaches are based on a static partitioning of the data set and a third solution incorporates a dynamic load balancing policy.