Showing papers by "University of Texas at Arlington published in 2010"

Efficient and Robust Feature Selection via Joint ℓ2,1-Norms Minimization

Abstract: Feature selection is an important component of many machine learning applications. Especially in many bioinformatics tasks, efficient and robust feature selection methods are desired to extract meaningful features and eliminate noisy ones. In this paper, we propose a new robust feature selection method with emphasizing joint l2,1-norm minimization on both loss function and regularization. The l2,1-norm based loss function is robust to outliers in data points and the l2,1-norm regularization selects features across all data points with joint sparsity. An efficient algorithm is introduced with proved convergence. Our regression based objective makes the feature selection process more efficient. Our method has been applied into both genomic and proteomic biomarkers discovery. Extensive empirical studies are performed on six data sets to demonstrate the performance of our feature selection method.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

Convex and Semi-Nonnegative Matrix Factorizations

Abstract: We present several new variations on the theme of nonnegative matrix factorization (NMF). Considering factorizations of the form X = FGT, we focus on algorithms in which G is restricted to containing nonnegative entries, but allowing the data matrix X to have mixed signs, thus extending the applicable range of NMF methods. We also consider algorithms in which the basis vectors of F are constrained to be convex combinations of the data points. This is used for a kernel extension of NMF. We provide algorithms for computing these new factorizations and we provide supporting theoretical analysis. We also analyze the relationships between our algorithms and clustering algorithms, and consider the implications for sparseness of solutions. Finally, we present experimental results that explore the properties of these new methods.

Observation of a centrality-dependent dijet asymmetry in lead-lead collisions at √sNN=2.76 Tev with the ATLAS detector at the LHC

Abstract: By using the ATLAS detector, observations have been made of a centrality-dependent dijet asymmetry in the collisions of lead ions at the Large Hadron Collider. In a sample of lead-lead events with a per-nucleon center of mass energy of 2.76 TeV, selected with a minimum bias trigger, jets are reconstructed in fine-grained, longitudinally segmented electromagnetic and hadronic calorimeters. The transverse energies of dijets in opposite hemispheres are observed to become systematically more unbalanced with increasing event centrality leading to a large number of events which contain highly asymmetric dijets. This is the first observation of an enhancement of events with such large dijet asymmetries, not observed in proton-proton collisions, which may point to an interpretation in terms of strong jet energy loss in a hot, dense medium.

Nanomaterial cytotoxicity is composition, size, and cell type dependent

Abstract: Despite intensive research efforts, reports of cellular responses to nanomaterials are often inconsistent and even contradictory. Additionally, relationships between the responding cell type and nanomaterial properties are not well understood. Using three model cell lines representing different physiological compartments and nanomaterials of different compositions and sizes, we have systematically investigated the influence of nanomaterial properties on the degrees and pathways of cytotoxicity. In this study, we selected nanomaterials of different compositions (TiO2 and SiO2 nanoparticles, and multi-wall carbon nanotubes [MWCNTs]) with differing size (MWCNTs of different diameters 50 nm; but same length 0.5-2 μm) to analyze the effects of composition and size on toxicity to 3T3 fibroblasts, RAW 264.7 macrophages, and telomerase-immortalized (hT) bronchiolar epithelial cells. Following characterization of nanomaterial properties in PBS and serum containing solutions, cells were exposed to nanomaterials of differing compositions and sizes, with cytotoxicity monitored through reduction in mitochondrial activity. In addition to cytotoxicity, the cellular response to nanomaterials was characterized by quantifying generation of reactive oxygen species, lysosomal membrane destabilization and mitochondrial permeability. The effect of these responses on cellular fate - apoptosis or necrosis - was then analyzed. Nanomaterial toxicity was variable based on exposed cell type and dependent on nanomaterial composition and size. In addition, nanomaterial exposure led to cell type dependent intracellular responses resulting in unique breakdown of cellular functions for each nanomaterial: cell combination. Nanomaterials induce cell specific responses resulting in variable toxicity and subsequent cell fate based on the type of exposed cell. Our results indicate that the composition and size of nanomaterials as well as the target cell type are critical determinants of intracellular responses, degree of cytotoxicity and potential mechanisms of toxicity.

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

Abstract: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution.

Abstract: Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation.

Undone Science: Charting Social Movement and Civil Society Challenges to Research Agenda Setting.

Abstract: "Undone science" refers to areas of research that are left unfunded, incomplete, or generally ignored but that social movements or civil society organizations often identify as worthy of more research. This study mobilizes four recent studies to further elaborate the concept of undone science as it relates to the political construction of research agendas. Using these cases, we develop the argument that undone science is part of a broader politics of knowledge, wherein multiple and competing groups struggle over the construction and implementation of alternative research agendas. Overall, the study demonstrates the analytic potential of the concept of undone science to deepen understanding of the systematic nonproduction of knowledge in the institutional matrix of state, industry, and social movements that is characteristic of recent calls for a "new political sociology of science."

A survey on sensor localization

Abstract: Localization is one of the fundamental problems in wireless sensor networks (WSNs), since locations of the sensor nodes are critical to both network operations and most application level tasks. Although the GPS based localization schemes can be used to determine node locations within a few meters, the cost of GPS devices and non-availability of GPS signals in confined environments prevent their use in large scale sensor networks. There exists an extensive body of research that aims at obtaining locations as well as spatial relations of nodes in WSNs without requiring specialized hardware and/or employing only a limited number of anchors that are aware of their own locations. In this paper, we present a comprehensive survey on sensor localization in WSNs covering motivations, problem formulations, solution approaches and performance summary. Future research issues will also be discussed.

Opportunities in Opportunistic Computing

Abstract: When two devices come into contact, albeit opportunistically, it provides a great opportunity to match services to resources, exchange information, cyberforage, execute tasks remotely, and forward messages.

Microfinance: Creating Opportunities for the Poor?

Abstract: Executive Overview Microfinance is an emerging phenomenon that opens access to capital for individuals previously shut out from financial services. In its direct engagement with the poor, microfinance represents a new way for financial capital to potentially stimulate economic growth in developing countries. However, microfinance is poorly understood, and it remains unclear whether it delivers on its promises. The goal of this paper is to introduce the topic of microfinancing to a wider audience of management researchers and to identify opportunities for future research in this new and growing area.

Collaborative filtering: Weighted nonnegative matrix factorization incorporating user and item graphs

Abstract: Collaborative filtering is an important topic in data mining and has been widely used in recommendation system. In this paper, we proposed a unified model for collaborative filtering based on graph regularized weighted nonnegative matrix factorization. In our model, two graphs are constructed on users and items, which exploit the internal information (e.g. neighborhood information in the user-item rating matrix) and external information (e.g. content information such as user’s occupation and item’s genre, or other kind of knowledge such as social trust network). The proposed method not only inherits the advantages of model-based method, but also owns the merits of memory-based method which considers the neighborhood information. Moreover, it has the ability to make use of content information and any additional information regarding user-user such as social trust network. Due to the use of these internal and external information, the proposed method is able to find more interpretable lowdimensional representations for users and items, which is helpful for improving the recommendation accuracy. Experimental results on benchmark collaborative filtering data sets demonstrate that the proposed methods outperform the state of the art collaborative filtering methods a lot.

Causes and Consequences of Goodwill Impairment Losses

Abstract: The paper examines the reaction of market participants to the announcement of a goodwill impairment loss, the nature of the information conveyed by the loss, and whether a cause of goodwill impairment can be traced back to overpayment for targets at the time of prior acquisitions. We use a comprehensive sample of goodwill impairment announcements made under the regulatory regimes of SFAS 121 and SFAS 142 and explore how the information content changes over different reporting regimes. Our evidence suggests that investors as well as financial analysts revise their expectations downward on the announcement of a goodwill impairment loss and the downward revision is related to the magnitude of the loss. We find that the negative impact of the loss is significant under all three reporting regimes, i.e., pre-SFAS-142, transition period and post-SFAS-142, though it is lower in the post period. We further show that the impairment loss serves as a leading indicator of a decline in future profitability due to a slow-down in sales and/or higher operating costs. Our tests also reveal that proxies for overpayment for targets at the time of prior acquisitions can predict the subsequent goodwill impairment. From our analysis of firms with potentially impaired goodwill that do not report impairment, we find no evidence that market participants revise their expectations at the time of revelation of a zero impairment loss, especially in the post-SFAS-142 period. Indirect evidence suggests that some of these firms may have used their managerial discretion to avoid taking an impairment loss, consistent with the argument in Ramanna (2008) and Ramanna and Watts (2010) that the use of unverifiable fair values under SFAS 142 may lead to the opportunistic avoidance of impairment charges.

A Proposed Model of Online Consumer Behavior: Assessing the Role of Gender

Abstract: This research examined the influence of Internet experience and web atmospherics on consumer online behavior. It developed a model of web navigation behavior where these antecedent variables drove website exploratory behavior and website involvement, which in turn, drove site attitudes and pre-purchase evaluations. These relationships were tested and confirmed in the context of a pharmaceutical website. Further, men and women differed in web navigation behavior, with men engaging in less exploratory behavior and developing less website involvement than women. However, across the two sexes, entertainment, challenge, and effectiveness of information content were the key drivers of website attitudes. The findings provide several guidelines for online communication strategy.

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

Abstract: The horizontal transfer (HT) of genetic material between non-mating species, common in bacteria, is increasingly being recognized as a significant force in eukaryotic evolution. Most instances of HT described so far in metazoans involve mobile genetic elements — mainly transposons — but the mechanisms enabling this exchange between widely divergent species are unknown. Gilbert et al. now show that transposable elements spread between disparate species by hitch-hiking in the genomes of parasites shared by these species. Specifically, Rhodnius prolixus, an insect that feeds on the blood of tetrapods and which is the vector of Chagas disease in humans, carries four distinct transposon families in its genome that can invade the genomes of a range of tetrapods including the opossum and squirrel monkey. One of these transposon families is also present in the pond snail Lymnaea stagnalis, a vector of trematodes infecting many vertebrates. 'Horizontal gene transfer' refers to the passage of genetic material between non-mating species. Transposable elements (transposons) may be especially prone to horizontal gene transfer, but the mechanisms by which they can spread across diverged species have been elusive. Here it is shown that transposons can spread by hitchhiking in the genomes of parasites. The amount of DNA that can be transferred in this way underscores the impact of horizontal gene transfer on genome evolution. Horizontal transfer (HT), or the passage of genetic material between non-mating species, is increasingly recognized as an important force in the evolution of eukaryotic genomes1,2. Transposons, with their inherent ability to mobilize and amplify within genomes, may be especially prone to HT3,4,5,6,7. However, the means by which transposons can spread across widely diverged species remain elusive. Here we present evidence that host–parasite interactions have promoted the HT of four transposon families between invertebrates and vertebrates. We found that Rhodnius prolixus, a triatomine bug feeding on the blood of various tetrapods and vector of Chagas’ disease in humans, carries in its genome four distinct transposon families that also invaded the genomes of a diverse, but overlapping, set of tetrapods. The bug transposons are ∼98% identical and cluster phylogenetically with those of the opossum and squirrel monkey, two of its preferred mammalian hosts in South America. We also identified one of these transposon families in the pond snail Lymnaea stagnalis, a cosmopolitan vector of trematodes infecting diverse vertebrates, whose ancestral sequence is nearly identical and clusters with those found in Old World mammals. Together these data provide evidence for a previously hypothesized role of host–parasite interactions in facilitating HT among animals3,7. Furthermore, the large amount of DNA generated by the amplification of the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.

Active Current Sharing and Source Management in Fuel Cell–Battery Hybrid Power System

Abstract: Fuel cells (FCs) are being considered as a potential alternative in long term to replace diesel/gasoline combustion engines in vehicles and emergency power sources. However, high cost and slow dynamic response of FC still persist as the main hurdles for wider applications. To remedy this problem, an energy storage system with adequate power capacity has to be incorporated. This paper presents a novel control design for FC-battery hybrid power system which enables both active current sharing and power source management control in such hybrid systems. Different hybrid power system structures are investigated and evaluated; dual-converter structure and four modes of operation are defined to provide efficient and sustainable solution to such a hybrid power system. A novel integrated control system with inherent current sharing and generation mode swapping capability is proposed; based on system component status, the control system is able to regulate the output power from each source under different scenarios. The dedicated control system is implemented in a TMS320F2812 DSP, and experimental results for an FC-battery-based uninterruptible power supply are provided to demonstrate the static and dynamic performance of the control system.

A practical wireless charging system based on ultra-wideband retro-reflective beamforming

Abstract: Numerous portable electronic devices (such as laptops, cell phones, digital cameras, and electric shavers) rely on rechargeable batteries and must be routinely charged by the line power. A wireless charging technique capable of delivering electromagnetic energy to these portable devices would make them tether free and “truly portable.” Wireless charging is especially valuable for devices with which wired connections are intractable, e.g., unattended radio frequency identification tags and implanted sensors. In recent years, enormous research efforts have been devoted to wireless charging. In 1990s, a case study is reported in [1] to construct a point-to-point wireless electricity transmission to a small isolated village called Grand-Bassin in France. In 2007, an inductive resonance coupling scheme, which makes use of near-field coupling between two magnetic resonators, was demonstrated able to power a 60-Watt light bulb over two meters by a team of Massachusetts Institute of Technology [2]. In addition, several companies (PowerCast, WildCharge, WiPower, etc.) have developed products targeting specific applications. Nevertheless, several technical challenges remain to be resolved in order to accomplish practical wireless charging. Specifically, (i) to achieve efficient charging over long distance, severe power loss due to electromagnetic wave propagation must be remedied; (ii) humans' exposure to electromagnetic radiation should always be kept below safety level while sufficient power is delivered to devices; and (iii) some existing systems are unsuitable for ubiquitous deployment due to high cost, large size, and/or heavy weight. In this paper, an innovative wireless charging system based on ultrawideband retro-reflective beamforming is proposed to address the above challenges. The proposed charger consists of multiple antenna elements distributed in space. According to pilot signals (which are short impulses) they receive from the target device, the antenna elements jointly construct a focused electromagnetic beam onto the device (i.e., beamforming). Beamforming enables spatially focused/dedicated power delivery to devices while keeping power level in all the other locations minimal. As a result, the proposed system attains high charging efficiency and leads to little hazard/interference to other objects. Performance of the proposed wireless charging system is demonstrated by some simulation results obtained by a full-wave Maxwell's equations solver.

Secondary transfer effects of intergroup contact: Alternative accounts and underlying processes.

Abstract: Although intergroup contact is one of the most prominent interventions to reduce prejudice, the generalization of contact effects is still a contentious issue. This research further examined the rarely studied secondary transfer effect (STE; Pettigrew, 2009), by which contact with a primary outgroup reduces prejudice toward secondary groups that are not directly involved in the contact. Across 3 cross-sectional studies conducted in Cyprus (N = 1,653), Northern Ireland (N = 1,973), and Texas (N = 275) and 1 longitudinal study conducted in Northern Ireland (N = 411), the present research sought to systematically rule out alternative accounts of the STE and to investigate 2 potential mediating mechanisms (ingroup reappraisal and attitude generalization). Results indicated that, consistent with the STE, contact with a primary outgroup predicts attitudes toward secondary outgroups, over and above contact with the secondary outgroup, socially desirable responding, and prior attitudes. Mediation analyses found strong evidence for attitude generalization but only limited evidence for ingroup reappraisal as an underlying process. Two out of 3 tests of a reverse model, where contact with the secondary outgroup predicts attitudes toward the primary outgroup, provide further evidence for an indirect effect through attitude generalization. Theoretical and practical implications of these results are discussed, and directions for future research are identified.