Showing papers by "University of North Carolina at Charlotte published in 2013"

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

Abstract: Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconduc tor.org/packages/release/bioc/html/pathview.html and at http://

Controlled scalable synthesis of uniform, high-quality monolayer and few-layer MoS2 films

Abstract: Two dimensional (2D) materials with a monolayer of atoms represent an ultimate control of material dimension in the vertical direction. Molybdenum sulfide (MoS2) monolayers, with a direct bandgap of 1.8 eV, offer an unprecedented prospect of miniaturizing semiconductor science and technology down to a truly atomic scale. Recent studies have indeed demonstrated the promise of 2D MoS2 in fields including field effect transistors, low power switches, optoelectronics, and spintronics. However, device development with 2D MoS2 has been delayed by the lack of capabilities to produce large-area, uniform, and high-quality MoS2 monolayers. Here we present a self-limiting approach that can grow high quality monolayer and few-layer MoS2 films over an area of centimeters with unprecedented uniformity and controllability. This approach is compatible with the standard fabrication process in semiconductor industry. It paves the way for the development of practical devices with 2D MoS2 and opens up new avenues for fundamental research.

Energy-Limited Tolerance to Stress as a Conceptual Framework to Integrate the Effects of Multiple Stressors

Abstract: Integrating the effects of multiple stressors and predicting their consequences for the species' survival and distribution is an important problem in ecological physiology. This review applies the concept of energy-limited tolerance to stress to develop bioenergetic markers that can assist in integrating the effects of multiple stressors and distinguishing between the moderate stress compatible with long-term survival of populations and bioenergetically unsustainable extreme stress. These markers reflect the progressive decline of the aerobic scope of an organism (defined as the fraction of the energy flux and metabolic power supporting this flux available after the basal maintenance costs of an organism are met) with increasing levels of the environmental stress. During the exposure to moderate stress (i.e., in the pejus range of the environmental conditions), the aerobic scope is positive but reduced compared with the optimum conditions. The reduction of the metabolic scope can be due to the (1) elevated costs of basal metabolism, (2) activation of the mechanisms for protection and damage repair, (3) reduced assimilation of food, and/or (4) stress-induced impacts on the aerobic pathways producing ATP. This leads to suboptimal growth and reproductive rates in the pejus range of environmental conditions and is commonly observed in food-limited and energy-limited wild populations. The tolerance windows of the organisms are delimited by the pessimum range(s) of environmental conditions in which the aerobic scope of the organism disappears (so that all available energy and metabolic capacity are used in support of basal metabolism), energy resources are depleted, and partial anaerobiosis and/or metabolic rate depression set in. The habitats where environmental conditions remain in the pessimum zone long enough to prevent consistent growth and reproduction often coincide with the species' distributional limits. Thus, focus on the bioenergetic effects of environmental stressors and their immediate consequences for fitness provides a suitable framework for integrating physiology and functional ecology and can assist in understanding the driving forces and limitations of environmental adaptation and improving assessment of ecological risk as well as environmental management in field populations facing multiple stressors.

Spatial memory and animal movement

Abstract: Memory is critical to understanding animal movement but has proven challenging to study. Advances in animal tracking technology, theoretical movement models and cognitive sciences have facilitated research in each of these fields, but also created a need for synthetic examination of the linkages between memory and animal movement. Here, we draw together research from several disciplines to understand the relationship between animal memory and movement processes. First, we frame the problem in terms of the characteristics, costs and benefits of memory as outlined in psychology and neuroscience. Next, we provide an overview of the theories and conceptual frameworks that have emerged from behavioural ecology and animal cognition. Third, we turn to movement ecology and summarise recent, rapid developments in the types and quantities of available movement data, and in the statistical measures applicable to such data. Fourth, we discuss the advantages and interrelationships of diverse modelling approaches that have been used to explore the memory–movement interface. Finally, we outline key research challenges for the memory and movement communities, focusing on data needs and mathematical and computational challenges. We conclude with a roadmap for future work in this area, outlining axes along which focused research should yield rapid progress.

The impacts of information quality and system quality on users' continuance intention in information-exchange virtual communities

Abstract: An information-exchange virtual community (VC) is an IT-supported virtual space that is composed of a group of people for accessing, sharing and disseminating topic-related experiences and knowledge through communication and social interaction 36,43]. With the increasing number of VCs and low switching cost, it is challenging to retain existing users and encourage their continued participation. By integrating the IS post-adoption research and IS Success model, we propose a research framework to investigate VC users' continuance intention from a quality perspective. Based on a field survey, we find that information and system quality directly affect perceived individual benefits and user satisfaction, which ultimately determine user continuance intention to consume and to provide information. Furthermore, by modeling information quality and system quality as multifaceted constructs, our results reveal key quality concerns in information-exchange VCs. Implications for VC design and management are also discussed.

Perceived organizational support and embeddedness as key mechanisms connecting socialization tactics to commitment and turnover among new employees

Abstract: Summary Retention of new hires is a critical issue for organizations. We propose that relationships are important mechanisms through which socialization tactics influence commitment and turnover. The key theoretical mechanisms connecting socialization tactics to turnover in our model are the extent to which newcomers perceive their relationship with the organization as supportive, caring, and entailing positive social exchanges and the extent to which newcomers become embedded within the organization. We collected longitudinal data from over 500 employees over the first year of employment. Consistent with our hypotheses, socialization tactics influence perceived organizational support (POS) and job embeddedness, and POS and embeddedness both relate to organizational commitment and voluntary turnover. Results support POS and embeddedness as relational mechanisms that bind employees to the organization as a result of socialization tactics. Copyright © 2012 John Wiley & Sons, Ltd.

A Survey of Social-Based Routing in Delay Tolerant Networks: Positive and Negative Social Effects

Abstract: Delay tolerant networks (DTNs) may lack continuous network connectivity. Routing in DTNs is thus challenging since it must handle network partitioning, long delays, and dynamic topology in such networks. In recent years, social-based approaches, which attempt to exploit social behaviors of DTN nodes to make better routing decision, have drawn tremendous interests in DTN routing design. In this article, we summarize the social properties in DTNs, and provide a survey of recent social-based DTN routing approaches. To improve routing performance, these methods either take advantages of positive social characteristics such as community and friendship to assist packet forwarding or consider negative social characteristics such as selfishness. We conclude by discussing some open issues and challenges in social-based approaches regarding the design of DTN routing protocols.

Pose-Free Facial Landmark Fitting via Optimized Part Mixtures and Cascaded Deformable Shape Model

Abstract: This paper addresses the problem of facial landmark localization and tracking from a single camera. We present a two-stage cascaded deformable shape model to effectively and efficiently localize facial landmarks with large head pose variations. For face detection, we propose a group sparse learning method to automatically select the most salient facial landmarks. By introducing 3D face shape model, we use procrustes analysis to achieve pose-free facial landmark initialization. For deformation, the first step uses mean-shift local search with constrained local model to rapidly approach the global optimum. The second step uses component-wise active contours to discriminatively refine the subtle shape variation. Our framework can simultaneously handle face detection, pose-free landmark localization and tracking in real time. Extensive experiments are conducted on both laboratory environmental face databases and face-in-the-wild databases. All results demonstrate that our approach has certain advantages over state-of-the-art methods in handling pose variations.

The fate of duplicated genes in a polyploid plant genome.

Abstract: SUMMARYPolyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result inextensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally andevolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 millionyears ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutesa good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, wetested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested,approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only asmall proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition,duplicated genes were often found in collinear blocks, and several blocks of duplicated genes wereco-regulated, suggesting some type of epigenetic or positional regulation. We also found thattranscription factors and ribosomal protein genes were differentially expressed in many tissues, suggest-ing that the main consequence of polyploidy in soybean may be at the regulatory level.Keywords: polyploidy, duplicated gene expression, sub-functionalization, Glycine max, RNA-seq, genomeevolution.INTRODUCTIONAngiosperms represent the largest group of plants, with350 000 known taxa (Van de Peer et al., 2009). They under-went diversification in the mid-Cretaceous period (i.e. 100million years ago, MYA), and, in contrast to pteridophytesand gymnosperms, maintained a high radiation rate over along period of time (Lidgard and Crane, 1988; Crane andLidgard, 1989; Crepet and Niklas, 2009). Defined by Darwinas an ‘abominable mystery’, this prominence of floweringplants on earth has been extensively studied. Recent theo-ries suggest that carpel evolution, double fertilization andflower development, as well as additional innovations suchas reduced cost of seed production and short generationtime, contributed to the explosive success of angiosperms(Stuessy, 2004; Lord and Westoby, 2011). Because manygenes involved in reproduction and flower developmentwere duplicated before the monocot/dicot radiation (Jiaoet al., 2011), whole-genome duplications (WGDs) arebelieved to be at the origin of angiosperm radiation(De Bodt et al., 2005). Polyploidy, or WGD, is a process thatrecurrently shaped eukaryotic genomes. Although, in ani-mals, this process is mainly restricted to amphibians andfish (Otto and Whitton, 2000), polyploidy has played amajor evolutionary role in plants. Complete genomeanalyses strongly support the conclusion that, in additionto lineage-specific WGDs, a triplication (c) and two WGD(q and r), respectively, occurred in eudicots and monocots(Vision, 2000; Jaillon et al., 2007; Lyons et al., 2008; Tanget al., 2010). Recent work also demonstrated that two

Does Size Matter? Scaling of CO2 Emissions and U.S. Urban Areas

Abstract: Urban areas consume more than 66% of the world’s energy and generate more than 70% of global greenhouse gas emissions. With the world’s population expected to reach 10 billion by 2100, nearly 90% of whom will live in urban areas, a critical question for planetary sustainability is how the size of cities affects energy use and carbon dioxide (CO2) emissions. Are larger cities more energy and emissions efficient than smaller ones? Do larger cities exhibit gains from economies of scale with regard to emissions? Here we examine the relationship between city size and CO2 emissions for U.S. metropolitan areas using a production accounting allocation of emissions. We find that for the time period of 1999–2008, CO2 emissions scale proportionally with urban population size. Contrary to theoretical expectations, larger cities are not more emissions efficient than smaller ones.

SilentSense: silent user identification via touch and movement behavioral biometrics

Abstract: In this work, we present SilentSense, a framework to authenticate users silently and transparently by exploiting the user touch behavior biometrics and leveraging the integrated sensors to capture the micro-movement of the device caused by user's screen-touch actions. By tracking the fine-detailed touch actions of the user, we build a "touch-based biometrics" model of the owner by extracting some principle features, and then verify whether the current user is the owner or guest/attacker. When using the smartphone, the unique operating pattern of the user is detected and learnt by collecting the sensor data and touch events silently. When users are mobile, the micro-movement of mobile devices caused by touch is suppressed by that due to the large scale user-movement which will render the touch-based biometrics ineffective. To address this, we integrate a movement-based biometrics for each user with previous touch-based biometrics. We conduct extensive evaluations of our approaches on the Android smartphone, we show that the user identification accuracy is over 99%.

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

Abstract: Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray experiments combined with empirically defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which has previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an overrepresentation of type-B Arabidopsis response regulator binding elements, consistent with the role of type-B Arabidopsis response regulators as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using quantitative reverse transcription-polymerase chain reaction and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin-responsive genes that are useful in the analysis of cytokinin function in plants.

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing

Abstract: Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve our understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein-coding genes expressed in pollen, including 289 assayed only by nonspecific probe sets. Additional exons and previously unannotated 5′ and 3′ untranslated regions for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 were confirmed by polymerase chain reaction. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of ongoing annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

Abstract: Maternal transmission and cage effects are powerful confounding factors in microbiome studies. To assess the consequences of cage microenvironment on the mouse gut microbiome, two groups of germ-free (GF) wild-type (WT) mice, one gavaged with a microbiota harvested from adult WT mice and another allowed to acquire the microbiome from the cage microenvironment, were monitored using Illumina 16S rRNA sequencing over a period of 8 weeks. Our results revealed that cage effects in WT mice moved from GF to specific pathogen free (SPF) conditions take several weeks to develop and are not eliminated by the initial gavage treatment. Initial gavage influenced, but did not eliminate a successional pattern in which Proteobacteria became less abundant over time. An analysis in which 16S rRNA sequences are mapped to the closest sequenced whole genome suggests that the functional potential of microbial genomes changes significantly over time shifting from an emphasis on pathogenesis and motility early in community assembly to metabolic processes at later time points. Functionally, mice allowed to naturally acquire a microbial community from their cage, but not mice gavaged with a common biome, exhibit a cage effect in Dextran Sulfate Sodium-induced inflammation. Our results argue that while there are long-term effects of the founding community, these effects are mitigated by cage microenvironment and successional community assembly over time, which must both be explicitly considered in the interpretation of microbiome mouse experiments.

Predictors of posttraumatic growth in women with breast cancer

Abstract: Objective Posttraumatic growth (PTG) is defined as ‘positive psychological change experienced as a result of a struggle with highly challenging life circumstances’. The current study examined change in PTG over 2 years following breast cancer diagnosis and variables associated with PTG over time.

Mental- and Physical-Health Effects of Acute Exposure to Media Images of the September 11, 2001, Attacks and the Iraq War

Abstract: Millions of people witnessed early, repeated television coverage of the September 11 (9/11), 2001, terrorist attacks and were subsequently exposed to graphic media images of the Iraq War. In the present study, we examined psychological- and physical-health impacts of exposure to these collective traumas. A U.S. national sample (N = 2,189) completed Web-based surveys 1 to 3 weeks after 9/11; a subsample (n = 1,322) also completed surveys at the initiation of the Iraq War. These surveys measured media exposure and acute stress responses. Posttraumatic stress symptoms related to 9/11 and physician-diagnosed health ailments were assessed annually for 3 years. Early 9/11- and Iraq War-related television exposure and frequency of exposure to war images predicted increased posttraumatic stress symptoms 2 to 3 years after 9/11. Exposure to 4 or more hr daily of early 9/11-related television and cumulative acute stress predicted increased incidence of health ailments 2 to 3 years later. These findings suggest that exposure to graphic media images may result in physical and psychological effects previously assumed to require direct trauma exposure.

The relationship of core belief challenge, rumination, disclosure, and sociocultural elements to posttraumatic growth.

Abstract: The relationship of challenge to core beliefs, rumination, disclosure, and some sociocultural elements to posttraumatic growth (PTG) were explored. Participants were college students enrolled in psychology classes who reported having experienced a stressful event within the past 2 years and who completed measures in groups. Findings suggested that challenge to core beliefs was the main predictor of PTG, and that a very large proportion of the sample had encountered themes of PTG in their sociocultural contexts.

Interactive effects of elevated temperature and CO2 levels on metabolism and oxidative stress in two common marine bivalves (Crassostrea virginica and Mercenaria mercenaria)

Abstract: Marine bivalves such as the hard shell clams Mercenaria mercenaria and eastern oysters Crassostrea virginica are affected by multiple stressors, including fluctuations in temperature and CO 2 levels in estuaries, and these stresses are expected to be exacerbated by ongoing global climate change. Hypercapnia (elevated CO 2 levels) and temperature stress can affect survival, growth and development of marine bivalves, but the cellular mechanisms of these effects are not yet fully understood. In this study, we investigated whether oxidative stress is implicated in cellular responses to elevated temperature and CO 2 levels in marine bivalves. We measured the whole-organism standard metabolic rate (SMR), total antioxidant capacity (TAOC), and levels of oxidative stress biomarkers in the muscle tissues of clams and oysters exposed to different temperatures (22 and 27 °C) and CO 2 levels (the present day conditions of ~ 400 ppm CO 2 and 800 ppm CO 2 predicted by a consensus business-as-usual IPCC emission scenario for the year 2100). SMR was significantly higher and the antioxidant capacity was lower in oysters than in clams. Aerobic metabolism was largely temperature-independent in these two species in the studied temperature range (22–27 °C). However, the combined exposure to elevated temperature and hypercapnia led to elevated SMR in clams indicating elevated costs of basal maintenance. No persistent oxidative stress signal (measured by the levels of protein carbonyls, and protein conjugates with malondialdehyde and 4-hydroxynonenal) was observed during the long-term exposure to moderate warming (+ 5 °C) and hypercapnia (~ 800 ppm CO 2 ). This indicates that long-term exposure to moderately elevated CO 2 and temperature minimally affects the cellular redox status in these bivalve species and that the earlier observed negative physiological effects of elevated CO 2 and temperature must be explained by other cellular mechanisms.

Randomizing AMI configuration for proactive defense in smart grid

Abstract: Smart grids are capable of bi-directional communication between smart meters and headend systems. It is a core feature of smart grid provided by the underlying Advanced Metering Infrastructure (AMI). Due to the critical nature of AMI, threats have been targeted towards it and a need of tailored defense mechanism has been highlighted in the recent studies. Since limited number of protocols and applications are supported in the AMI, it exhibits a predictable and deterministic behavior. This predictability makes it easier for an attacker to learn the network behavior and launch an evasion attack by generating similar traffic. To combat this, we present a mutable AMI configuration technique for Proactive Defense. We randomize three different configuration parameters in order to make the AMI behavior unpredictable.While providing the randomization, the approach stays deterministic for the AMI devices like smart collector in order to detect any evasion attempts. We use real-world dataset comprising of approximately 2000 meters collected at an AMI of a leading utility provider for analysis. We also use smart grid testbed to show the effectiveness of our mutation technique.

Understanding and treating lateral ankle sprains and their consequences: a constraints-based approach.

Abstract: Lateral ankle sprains are a common consequence of physical activity If not managed appropriately, a cascade of negative alterations to both the joint structure and a person's movement patterns continue to stress the injured ligaments These alterations result in an individual entering a continuum of disability as evidenced by the ~30 % of ankle sprains that develop into chronic ankle instability (CAI) and up to 78 % of CAI cases that develop into post-traumatic ankle osteoarthritis (OA) Despite this knowledge, no significant improvements in treatment efficacy have been made using traditional treatment paradigms Therefore, the purpose of this review is to (1) provide an overview of the consequences associated with acute lateral ankle sprains, CAI and post-traumatic ankle OA; (2) introduce the patient-, clinician-, laboratory (PCL)-oriented) model that addresses the lateral ankle sprains and their consequences from a constraints perspective; and (3) introduce the dynamic systems theory as the framework to illustrate how multiple post-injury adaptations create a singular pathology that predisposes individuals with lateral ankle sprains to fall into a continuum of disability The consequences associated with lateral ankle sprains, CAI and ankle OA are similar and encompass alterations to the structure of the ankle joint (eg ligament laxity, positional faults, etc) and the sensorimotor function responsible for proper ankle joint function (eg postural control, gait, etc) Further, the impairments have been quantified across a range of patient-oriented (eg self-report questionnaires), clinician-oriented (eg bedside measures of range of motion and postural control), and laboratory-oriented (eg arthrometry, gait analysis) outcome measures The interaction of PCL-oriented outcomes is critically important for understanding the phenomenon of CAI across the continuum of disability Through the integration of all three sources of evidence, we can clearly see that an ankle sprain is more than just a peripheral musculoskeletal pathology with only local consequences The dynamic systems theory illustrates that the organization of human movement/function is shaped by the interaction of (1) organismic constraints (health of the person); (2) task constraints; and (3) environmental constraints However, ankle sprains increase the organismic constraints (ie changes in joint structure and sensorimotor function) that significantly hinder an individual's function and may be the underlying cause for the continuum of disability associated with CAI To treat and/or prevent an individual from entering the continuum of disability, greater protection of the ankle ligaments is needed immediately after injury Subsequent rehabilitation should then focus on goal-oriented rehabilitation (ie quality of the movement pattern) rather that task-oriented rehabilitation (ie do these exercises) When evaluating patients with ankle inversion trauma and/or instability, it is imperative to remember that an ankle sprain is not simply a local joint injury; it can result in a constrained sensorimotor system that leads to a continuum of disability and life-long consequences such as high injury recurrence and decreased quality of life if not managed properly

Urban scaling and the production function for cities.

Abstract: The factors that account for the differences in the economic productivity of urban areas have remained difficult to measure and identify unambiguously. Here we show that a microscopic derivation of urban scaling relations for economic quantities vs. population, obtained from the consideration of social and infrastructural properties common to all cities, implies an effective model of economic output in the form of a Cobb-Douglas type production function. As a result we derive a new expression for the Total Factor Productivity (TFP) of urban areas, which is the standard measure of economic productivity per unit of aggregate production factors (labor and capital). Using these results we empirically demonstrate that there is a systematic dependence of urban productivity on city population size, resulting from the mismatch between the size dependence of wages and labor, so that in contemporary US cities productivity increases by about 11% with each doubling of their population. Moreover, deviations from the average scale dependence of economic output, capturing the effect of local factors, including history and other local contingencies, also manifest surprising regularities. Although, productivity is maximized by the combination of high wages and low labor input, high productivity cities show invariably high wages and high levels of employment relative to their size expectation. Conversely, low productivity cities show both low wages and employment. These results shed new light on the microscopic processes that underlie urban economic productivity, explain the emergence of effective aggregate urban economic output models in terms of labor and capital inputs and may inform the development of economic theory related to growth.

HierarchicalTopics: Visually Exploring Large Text Collections Using Topic Hierarchies

Abstract: Analyzing large textual collections has become increasingly challenging given the size of the data available and the rate that more data is being generated. Topic-based text summarization methods coupled with interactive visualizations have presented promising approaches to address the challenge of analyzing large text corpora. As the text corpora and vocabulary grow larger, more topics need to be generated in order to capture the meaningful latent themes and nuances in the corpora. However, it is difficult for most of current topic-based visualizations to represent large number of topics without being cluttered or illegible. To facilitate the representation and navigation of a large number of topics, we propose a visual analytics system - HierarchicalTopic (HT). HT integrates a computational algorithm, Topic Rose Tree, with an interactive visual interface. The Topic Rose Tree constructs a topic hierarchy based on a list of topics. The interactive visual interface is designed to present the topic content as well as temporal evolution of topics in a hierarchical fashion. User interactions are provided for users to make changes to the topic hierarchy based on their mental model of the topic space. To qualitatively evaluate HT, we present a case study that showcases how HierarchicalTopics aid expert users in making sense of a large number of topics and discovering interesting patterns of topic groups. We have also conducted a user study to quantitatively evaluate the effect of hierarchical topic structure. The study results reveal that the HT leads to faster identification of large number of relevant topics. We have also solicited user feedback during the experiments and incorporated some suggestions into the current version of HierarchicalTopics.

Degradation of Antibiotic Activity during UV/H2O2 Advanced Oxidation and Photolysis in Wastewater Effluent

Abstract: Trace levels of antibiotics in treated wastewater effluents may present a human health risk due to the rise of antibacterial activity in the downstream environments. Advanced oxidation has a potential to become an effective treatment technology for transforming trace antibiotics in wastewater effluents, but residual or newly generated antibacterial properties of transformation products are a concern. This study demonstrates the effect of UV photolysis and UV/H2O2 advanced oxidation on transformation of 6 antibiotics, each a representative of a different structural class, in pure water and in two different effluents and reports new or confirmatory photolysis quantum yields and hydroxyl radical rate constants. The decay of the parent compound was monitored with HPLC/ITMS, and the corresponding changes in antibacterial activity were measured using bacterial inhibition assays. No antibacterially active products were observed following treatment for four of the six antibiotics (clindamycin, ciprofloxacin, peni...

Porphyrin and Heme Metabolism and the Porphyrias

Abstract: Porphyrins and metalloporphyrins are the key pigments of life on earth as we know it, because they include chlorophyll (a magnesium-containing metalloporphyrin) and heme (iron protoporphyrin). In eukaryotes, porphyrins and heme are synthesized by a multistep pathway that involves eight enzymes. The first and rate-controlling step is the formation of delta-aminolevulinic acid (ALA) from glycine plus succinyl CoA, catalyzed by ALA synthase. Intermediate steps occur in the cytoplasm, with formation of the monopyrrole porphobilinogen and the tetrapyrroles hydroxymethylbilane and a series of porphyrinogens, which are serially decarboxylated. Heme is utilized chiefly for the formation of hemoglobin in erythrocytes, myoglobin in muscle cells, cytochromes P-450 and mitochondrial cytochromes, and other hemoproteins in hepatocytes. The rate-controlling step of heme breakdown is catalyzed by heme oxygenase (HMOX), of which there are two isoforms, called HMOX1 and HMOX2. HMOX breaks down heme to form biliverdin, carbon monoxide, and iron. The porphyrias are a group of disorders, mainly inherited, in which there are defects in normal porphyrin and heme synthesis. The cardinal clinical features are cutaneous (due to the skin-damaging effects of excess deposited porphyrins) or neurovisceral attacks of pain, sometimes with weakness, delirium, seizures, and the like (probably due mainly to neurotoxic effects of ALA). The treatment of choice for the acute hepatic porphyrias is intravenous heme therapy, which repletes a critical regulatory heme pool in hepatocytes and leads to downregulation of hepatic ALA synthase, which is a biochemical hallmark of all forms of acute porphyria in relapse.

Nrf2 and Cardiovascular Defense

Abstract: The cardiovascular system is susceptible to a group of diseases that are responsible for a larger proportion of morbidity and mortality than any other disease. Many cardiovascular diseases are associated with a failure of defenses against oxidative stress-induced cellular damage and/or death, leading to organ dysfunction. The pleiotropic transcription factor, nuclear factor-erythroid (NF-E) 2-related factor 2 (Nrf2), regulates the expression of antioxidant enzymes and proteins through the antioxidant response element. Nrf2 is an important component in antioxidant defenses in cardiovascular diseases such as atherosclerosis, hypertension, and heart failure. Nrf2 is also involved in protection against oxidant stress during the processes of ischemia-reperfusion injury and aging. However, evidence suggests that Nrf2 activity does not always lead to a positive outcome and may accelerate the pathogenesis of some cardiovascular diseases (e.g., atherosclerosis). The precise conditions under which Nrf2 acts to attenuate or stimulate cardiovascular disease processes are unclear. Further studies on the cellular environments related to cardiovascular diseases that influence Nrf2 pathways are required before Nrf2 can be considered a therapeutic target for the treatment of cardiovascular diseases.