Showing papers by "University of Delaware published in 2009"

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Aldehyde dehydrogenase 1 is a marker for normal and malignant human colonic stem cells (SC) and tracks SC overpopulation during colon tumorigenesis.

Abstract: Although the concept that cancers originate from stem cells (SC) is becoming scientifically accepted, mechanisms by which SC contribute to tumor initiation and progression are largely unknown. For colorectal cancer (CRC), investigation of this problem has been hindered by a paucity of specific markers for identification and isolation of SC from normal and malignant colon. Accordingly, aldehyde dehydrogenase 1 (ALDH1) was investigated as a possible marker for identifying colonic SC and for tracking them during cancer progression. Immunostaining showed that ALDH1 + cells are sparse and limited to the normal crypt bottom, where SCs reside. During progression from normal epithelium to mutant ( APC ) epithelium to adenoma, ALDH1 + cells increased in number and became distributed farther up the crypt. CD133 + and CD44 + cells, which are more numerous and broadly distributed in normal crypts, showed similar changes during tumorigenesis. Flow cytometric isolation of cancer cells based on enzymatic activity of ALDH (Aldefluor assay) and implantation of these cells in nonobese diabetic–severe combined immunodeficient mice ( a ) generated xenograft tumors (Aldefluor − cells did not), ( b ) generated them after implanting as few as 25 cells, and ( c ) generated them dose dependently. Further isolation of cancer cells using a second marker (CD44 + or CD133 + serially) only modestly increased enrichment based on tumor-initiating ability. Thus, ALDH1 seems to be a specific marker for identifying, isolating, and tracking human colonic SC during CRC development. These findings also support our original hypothesis, derived previously from mathematical modeling of crypt dynamics, that progressive colonic SC overpopulation occurs during colon tumorigenesis and drives CRC development. [Cancer Res 2009;69(8):3382–9]

Early math matters: kindergarten number competence and later mathematics outcomes.

Abstract: Children's number competencies over 6 time points, from the beginning of kindergarten to the middle of 1st grade, were examined in relation to their mathematics achievement over 5 later time points, from the end of 1st grade to the end of 3rd grade. The relation between early number competence and mathematics achievement was strong and significant throughout the study period. A sequential process growth curve model showed that kindergarten number competence predicted rate of growth in mathematics achievement between 1st and 3rd grades as well as achievement level through 3rd grade. Further, rate of growth in early number competence predicted mathematics performance level in 3rd grade. Although low-income children performed more poorly than their middle-income counterparts in mathematics achievement and progressed at a slower rate, their performance and growth were mediated through relatively weak kindergarten number competence. Similarly, the better performance and faster growth of children who entered kindergarten at an older age were explained by kindergarten number competence. The findings show the importance of early number competence for setting children's learning trajectories in elementary school mathematics.

Emotion Theory and Research: Highlights, Unanswered Questions, and Emerging Issues

Abstract: Emotion feeling is a phase of neurobiological activity, the key component of emotions and emotion-cognition interactions. Emotion schemas, the most frequently occurring emotion experiences, are dynamic emotion-cognition interactions that may consist of momentary/situational responding or enduring traits of personality that emerge over developmental time. Emotions play a critical role in the evolution of consciousness and the operations of all mental processes. Types of emotion relate differentially to types or levels of consciousness. Unbridled imagination and the ability for sympathetic regulation of empathy may represent both potential gains and losses from the evolution and ontogeny of emotion processes and consciousness. Unresolved issues include psychology's neglect of levels of consciousness that are distinct from access or reflective consciousness and use of the term “unconscious mind” as a dumpster for all mental processes that are considered unreportable. The relation of memes and the mirror neur...

Testing a Social-Cognitive Model of Moral Behavior: The Interactive Influence of Situations and Moral Identity Centrality

Abstract: This article proposes and tests a social-cognitive framework for examining the joint influence of situational factors and the centrality of moral identity on moral intentions and behaviors. The authors hypothesized that if a situational factor increases the current accessibility of moral identity within the working self-concept, then it strengthens the motivation to act morally. In contrast, if a situational factor decreases the current accessibility of moral identity, then it weakens the motivation to act morally. The authors also expected the influence of situational factors to vary depending on the extent to which moral identity was central to a person's overall self-conception. Hypotheses derived from the framework were tested in 4 studies. The studies used recalling and reading a list of the Ten Commandments (Study 1), writing a story using morally laden terms (Study 4), and the presence of performance-based financial incentives (Studies 2 and 3) as situational factors. Participants' willingness to initiate a cause-related marketing program (Study 1), lie to a job candidate during a salary negotiation (Studies 2 and 3), and contribute to a public good (Study 4) were examined. Results provide strong support for the proposed framework.

Stretchable supercapacitors based on buckled single-walled carbon-nanotube macrofilms.

Abstract: Adv. Mater. 2009, 21, 4793–4797 2009 WILEY-VCH Verlag G N Stretchable electronic devices, such as p–n diodes, photovoltaic devices, transistors, and functional electronic eyes, have been fabricated using buckled single-crystal (e.g., Si, GaAs) thin films supported by elastomeric substrates. Recently, carbon nanotube (CNT)-based highly conducting elastic composites and stretchable graphene films have been reported, which are suitable as interconnects in stretchable electronic devices. As an indispensable component of stretchable electronics, a stretchable power-source device should be able to accommodate large strains while retaining intact function. Of various power-source devices, supercapacitors have attracted great interest in recent years due to their high power and energy densities compared with lithium-ion batteries and conventional dielectric capacitors, respectively. The most active research in supercapacitors is the development of new electrode materials. Recently, CNTs have been studied as good candidates for electrode materials because of several advantages, including a high surface area, nanoscale dimensions, and excellent electrical conductivity. Here, we report stretchable supercapacitors based on periodically sinusoidal single-walled carbon nanotube (SWNT) macrofilms (a 2D network of randomly oriented SWNTs). The stretchable supercapacitors comprise two sinusoidal SWNT macrofilms as stretchable electrodes, an organic electrolyte, and a polymeric separator. Electrochemical tests were performed and the fabricated stretchable supercapacitors are found to possess energy and power densities comparable with those of supercapacitors using pristine SWNT macrofilms as electrodes. Remarkably, the electrochemical performance of the stretchable supercapacitors remains unchanged even under 30% applied tensile strain. The preparation of the periodically sinusoidal SWNT macrofilms is of primary importance for stretchable supercapacitors. The synthesis of high-quality, purified, and functionalized SWNT macrofilms is, thus, an important preprocess, which has been presented elsewhere. The purified SWNT macrofilm was then shaped to a sinusoidal form by following the steps shown in Figure 1a. The procedure introduced here (step i in Fig. 1a) involves the uniaxial prestretching (epre) of an elastomeric substrate of a poly(dimethylsiloxane) (PDMS) slab (epre1⁄4DL/L for length changed from L to LþDL), followed by a chemical surface treatment to form a hydrophilic surface (see Experimental Section). The exposure of UV light introduces atomic oxygen, an activated species that reacts with PDMS and, thus, changes the

Ternary Pt/Rh/SnO2 electrocatalysts for oxidizing ethanol to CO2.

Abstract: The development of a direct ethanol fuel cell has been hampered by ethanol’s inefficient and slow oxidation. A ternary electrocatalyst consisting of platinum and rhodium deposited on carbon-supported tin dioxide nanoparticles is now shown to oxidize ethanol to carbon dioxide with high efficiency by splitting C–C bonds at room temperature. Ethanol, with its high energy density, likely production from renewable sources and ease of storage and transportation, is almost the ideal combustible for fuel cells wherein its chemical energy can be converted directly into electrical energy. However, commercialization of direct ethanol fuel cells has been impeded by ethanol’s slow, inefficient oxidation even at the best electrocatalysts1,2. We synthesized a ternary PtRhSnO2/C electrocatalyst by depositing platinum and rhodium atoms on carbon-supported tin dioxide nanoparticles that is capable of oxidizing ethanol with high efficiency and holds great promise for resolving the impediments to developing practical direct ethanol fuel cells. This electrocatalyst effectively splits the C–C bond in ethanol at room temperature in acid solutions, facilitating its oxidation at low potentials to CO2, which has not been achieved with existing catalysts. Our experiments and density functional theory calculations indicate that the electrocatalyst’s activity is due to the specific property of each of its constituents, induced by their interactions. These findings help explain the high activity of Pt–Ru for methanol oxidation and the lack of it for ethanol oxidation, and point to the way to accomplishing the C–C bond splitting in other catalytic processes.

Robot Assisted Gait Training With Active Leg Exoskeleton (ALEX)

Abstract: Gait training of stroke survivors is crucial to facilitate neuromuscular plasticity needed for improvements in functional walking ability. Robot assisted gait training (RAGT) was developed for stroke survivors using active leg exoskeleton (ALEX) and a force-field controller, which uses assist-as-needed paradigm for rehabilitation. In this paradigm undesirable gait motion is resisted and assistance is provided towards desired motion. The force-field controller achieves this paradigm by effectively applying forces at the ankle of the subject through actuators on the hip and knee joints. Two stroke survivors participated in a 15-session gait training study each with ALEX. The results show that by the end of the training the gait pattern of the patients improved and became closer to a healthy subject's gait pattern. Improvement is seen as an increase in the size of the patients' gait pattern, increased knee and ankle joint excursions and increase in their walking speeds on the treadmill.

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Abstract: Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA Gln is dependent on Dicer in vivo and

The effectiveness and costs of speed reductions on emissions from international shipping

Abstract: Greenhouse gas emissions from international shipping are an increasing concern. The paper evaluates whether vessel speed reduction can be a potentially cost-effective CO2 mitigation option for ships calling on US ports. By applying a profit-maximizing equation to estimate route-specific, economically-efficient speeds, we explore policy impacts of a fuel tax and a speed reduction mandate on CO2 emissions. The profit-maximizing function incorporates opportunity costs associated with speed reduction that go unobserved in more traditional marginal abatement cost analyses. We find that a fuel tax of about $150/ton fuel will lead to average speed-related CO2 reductions of about 20–30%. Moreover, a speed reduction mandate targeted to achieve 20% CO2 reduction in the container fleet costs between $30 and $200 per ton CO2 abated, depending on how the fleet responds to a speed reduction mandate.

Commonality and the Complexity of “We”: Social Attitudes and Social Change:

Abstract: The present article explores the complex role of collective identities in the development of intergroup biases and disparities, in interventions to improve orientations toward members of other groups, and in inhibiting or facilitating social action. The article revolves around the common ingroup identity model, examining general empirical support but also acknowledging potential limitations and emphasizing new insights and extensions. It proposes that the motivations of majority group members to preserve a system that advantages them and the motivations of minority group members to enhance their status have direct implications for preferred group representations and consequent intergroup relations. In particular, the effects of majority group members' preferences for a common, one-group identity and minority group members' preference for a dual identity (in which differences are acknowledged within the context of a superordinate identity) are considered in terms of intergroup attitudes, recognition of unfair disparities, and support for social action.

Cosmic ray interaction event generator SIBYLL 2.1

Abstract: The cosmic ray interaction event generator Sibyll is widely used in extensive air shower simulations. We describe in detail the properties of Sibyll 2.1 and the differences with the original version 1.7. The major structural improvements are the possibility to have multiple soft interactions, introduction of new parton density functions, and an improved treatment of diffraction. Sibyll 2.1 gives better agreement with fixed target and collider data, especially for the inelastic cross sections and multiplicities of secondary particles. Shortcomings and suggestions for future improvements are also discussed.

Effect of temperature on the capacitance of carbon nanotube supercapacitors.

Abstract: The effect of temperature on the kinetics and the diffusion mechanism of the ions in a supercapacitor assembled with single-walled carbon nanotube (SWNT) film electrodes and an organic electrolyte were thoroughly investigated. An improved room temperature performance of the supercapacitor was observed due to the combined effects of an increase in the conductivity of the SWNT films and surface modifications on the SWNT films by repeatedly heating and cooling the supercapacitor between the temperatures of 25 and 100 °C. Modified Randles equivalent circuit was employed to carry out an extensive analysis of the Nyquist spectra measured at different temperatures between 25 and 100 °C in order to understand the fundamentals of the capacitive and resistive variations in the supercapacitor. The experimental results and their thorough analysis will have significant impact not only on the fundamental understanding of the temperature-dependent electrode/electrolyte interfacial properties but also on supercapacitor d...

Short Sellers and Financial Misconduct

Abstract: We examine whether short sellers detect firms that misrepresent their financial statements, and whether their trading conveys external costs or benefits to other investors. Abnormal short interest increases steadily in the 19 months before the misrepresentation is publicly revealed, particularly when the misconduct is severe. Short selling is associated with a faster time-to-discovery, and it dampens the share price inflation that occurs when firms misstate their earnings. These results indicate that short sellers anticipate the eventual discovery and severity of financial misconduct. They also convey external benefits, helping to uncover misconduct and keeping prices closer to fundamental values when firms provide incorrect financial information.

Winter Northern Hemisphere weather patterns remember summer Arctic sea‐ice extent

Abstract: [1] The dramatic decline in Arctic summer sea-ice cover is a compelling indicator of change in the global climate system and has been attributed to a combination of natural and anthropogenic effects Through its role in regulating the exchange of energy between the ocean and atmosphere, ice loss is anticipated to influence atmospheric circulation and weather patterns By combining satellite measurements of sea-ice extent and conventional atmospheric observations, we find that varying summer ice conditions are associated with large-scale atmospheric features during the following autumn and winter well beyond the Arctic's boundary Mechanisms by which the atmosphere “remembers” a reduction in summer ice cover include warming and destabilization of the lower troposphere, increased cloudiness, and slackening of the poleward thickness gradient that weakens the polar jet stream This ice-atmosphere relationship suggests a potential long-range outlook for weather patterns in the northern hemisphere

TeV Gamma Rays from Geminga and the Origin of the GeV Positron Excess

Abstract: The Geminga pulsar has long been one of the most intriguing MeV-GeV gamma-ray point sources. We examine the implications of the recent Milagro gamma-ray Observatory detection of extended, multi-TeV gamma-ray emission from Geminga, finding that this reveals the existence of an ancient, powerful cosmic-ray accelerator that can plausibly account for the multi-GeV positron excess that has evaded explanation. We explore a number of testable predictions for gamma-ray and electron or positron experiments (up to approximately 100 TeV) that can confirm the first "direct" detection of a cosmic-ray source.

Looking for Gender: Gender Roles and Behaviors Among Online Gamers

Abstract: Several hypotheses regarding the importance of gender and relationships were tested by combining a large survey dataset with unobtrusive behavioral data from 1 year of play. Consistentwithexpectations,malesplayedforachievement-orientedreasonsandweremore aggressive, especially within romantic relationships where both partners played. Female players in such relationships had higher general happiness than their male counterparts. Contrary to stereotypes and current hypotheses, it was the female players who played the most. Female players were also healthier than male players or females in the general population. The findings have implications for gender theory and communication-oriented methods in games and online research—most notably for the use of self-reported time spent, which was systematically incorrect and different by gender. doi:10.1111/j.1460-2466.2009.01453.x Female video game players now comprise 40% of all players, and women over 18 make up more of the game-playing population than do males under 17 (Top 10 IndustryFacts, 2008). Yet, studies of men and women report both genders believe that computer games are a ‘‘particularly masculine pursuit’’ (Selwyn, 2007, p. 533). Are more women ignoring social sanctions for engaging in a supposedly masculine activity? Are men avoiding feminine actions while playing? To determine the answers, we must investigate how video game players are positioning their activity in relation to their gender, and better understand their reasons for playing games at all. Past media research on gaming has found that men and women perform in, and perceive, games differently (Blumberg & Sokol, 2004), but this research has not been updated since the mass adoption of large-scale online games. Likewise, social scientific research in the area of gender roles has not examined online game play, and how it may be changing gendered definitions of game play. At the same time, research covering a wide variety of social Internet activities has found women’s uses and considerations to be different

The IceCube data acquisition system: Signal capture, digitization, and timestamping

Abstract: IceCube is a km-scale neutrino observatory under construction at the South Pole with sensors both in the deep ice (InIce) and on the surface (IceTop). The sensors, called Digital Optical Modules (DOMs). detect, digitize and timestamp the signals from optical Cherenkov-radiation photons. The DOM Main Board (MB) data acquisition subsystem is connected to the central DAQ in the IceCube Laboratory (ICL) by a single twisted copper wire-pair and transmits packetized data on demand. Time calibration is maintained throughout the array by regular transmission to the DOMs of precisely timed analog signals, synchronized to a central GPS-disciplined clock. The design goals and consequent features, functional capabilities, and initial performance of the DOM MB, and the operation of a combined array of DOMs as a system, are described here. Experience with the first InIce strings and the IceTop stations indicates that the system design and performance goals have been achieved. (c) 2009 Elsevier B.V. All rights reserved.

Biomechanical and anatomic factors associated with a history of plantar fasciitis in female runners.

Abstract: Objective:To compare selected structural and biomechanical factors between female runners with a history of plantar fasciitis and healthy control subjects.Design:Cross-sectional.Setting:University of Delaware Motion Analysis Laboratory, Newark, Delaware; and University of Massachusetts Biomechanics

Impact of Native Plants on Bird and Butterfly Biodiversity in Suburban Landscapes

Abstract: Managed landscapes in which non-native ornamental plants are favored over native vegetation now dominate the United States, particularly east of the Mississippi River. We measured how landscaping with native plants affects the avian and lepidopteran communities on 6 pairs of suburban properties in southeastern Pennsylvania. One property in each pair was landscaped entirely with native plants and the other exhibited a more conventional suburban mixture of plants--a native canopy with non-native groundcover and shrubs. Vegetation sampling confirmed that total plant cover and plant diversity did not differ between treatments, but non-native plant cover was greater on the conventional sites and native plant cover was greater on the native sites. Several avian (abundance, species richness, biomass, and breeding-bird abundance) and larval lepidopteran (abundance and species richness) community parameters were measured from June 2006 to August 2006. Native properties supported significantly more caterpillars and caterpillar species and significantly greater bird abundance, diversity, species richness, biomass, and breeding pairs of native species. Of particular importance is that bird species of regional conservation concern were 8 times more abundant and significantly more diverse on native properties. In our study area, native landscaping positively influenced the avian and lepidopteran carrying capacity of suburbia and provided a mechanism for reducing biodiversity losses in human-dominated landscapes.

Microbial growth in the polar oceans — role of temperature and potential impact of climate change

Abstract: In this Analysis, Kirchman and colleagues compare microbial processes in the western Arctic Ocean and other polar waters with low-latitude oceans to attempt to understand the role of heterotrophic bacteria in oceanic biogeochemical cycles. This may further our understanding of the changes that could occur as these waters warm. Heterotrophic bacteria are the most abundant organisms on the planet and dominate oceanic biogeochemical cycles, including that of carbon. Their role in polar waters has been enigmatic, however, because of conflicting reports about how temperature and the supply of organic carbon control bacterial growth. In this Analysis article, we attempt to resolve this controversy by reviewing previous reports in light of new data on microbial processes in the western Arctic Ocean and by comparing polar waters with low-latitude oceans. Understanding the regulation of in situ microbial activity may help us understand the response of the Arctic Ocean and Antarctic coastal waters over the coming decades as they warm and ice coverage declines.

The star formation rate in the reionization era as indicated by gamma-ray bursts

Abstract: High-redshift gamma-ray bursts (GRBs) offer an extraordinary opportunity to study aspects of the early universe, including the cosmic star formation rate (SFR). Motivated by the two recent highest-z GRBs, GRB 080913 at z 6.7 and GRB 090423 at z 8.1, and more than four years of Swift observations, we first confirm that the GRB rate does not trace the SFR in an unbiased way. Correcting for this, we find that the implied SFR to beyond z = 8 is consistent with Lyman Break Galaxy-based measurements after accounting for unseen galaxies at the faint end of the UV luminosity function. We show that this provides support for the integrated star formation in the range 6 z 8 to have been alone sufficient to reionize the universe.

The Nature of Contemporary Prejudice: Insights from Aversive Racism

Abstract: Within the United States, declines in the overt expression of racial prejudice over several decades have given way to near universal endorsement of the principles of racial equality as a core cultural value. Yet, evidence of persistent and substantial disparities between Blacks and Whites remain. Here, we review research that demonstrates how the actions of even well-intentioned and ostensibly non-prejudiced individuals can inadvertently contribute to these disparities through subtle biases in decision making and social interactions. We argue that current racial attitudes of Whites toward Blacks in the United States are fundamentally ambivalent, characterized by a widespread contemporary form of racial prejudice, aversive racism, that is manifested in subtle and indirect ways, and illustrate its operation across a wide range of settings, from employment and legal decisions, to group problem-solving and everyday helping behavior. We conclude by describing research aimed at combating these biases and identify new avenues for future research.

Intercomparison of model simulations of mixed-phase clouds observed during the ARM Mixed-Phase Arctic Cloud Experiment. I: single-layer cloud

Abstract: Results are presented from an intercomparison of single-column and cloud-resolving model simulations of a cold-air outbreak mixed-phase stratocumulus cloud observed during the Atmospheric Radiation Measurement (ARM) programme's Mixed-Phase Arctic Cloud Experiment. The observed cloud occurred in a well-mixed boundary layer with a cloud-top temperature of −15 ◦ C. The average liquid water path of around 160 g m −2 was about two-thirds of the adiabatic value and far greater than the average mass of ice which when integrated from the surface to cloud top was around 15 gm −2 . Simulations of 17 single-column models (SCMs) and 9 cloud-resolving models (CRMs) are compared. While the simulated ice water path is generally consistent with observed values, the median SCM and CRM liquid water path is a factor-of-three smaller than observed. Results from a sensitivity study in which models removed ice microphysics suggest that in many models the interaction between liquid and ice-phase microphysics is responsible for the large model underestimate of liquid water path. Despite this underestimate, the simulated liquid and ice water paths of several models are consistent with observed values. Furthermore, models with more sophisticated microphysics simulate liquid and ice water paths that are in better agreement with the observed values, although considerable scatter exists. Although no single factor guarantees a good simulation, these results emphasize the need for improvement in the model representation of mixed-phase microphysics. Copyright c � 2009 Royal Meteorological Society