Showing papers by "University of Massachusetts Amherst published in 2010"

MAUI: making smartphones last longer with code offload

Abstract: This paper presents MAUI, a system that enables fine-grained energy-aware offload of mobile code to the infrastructure. Previous approaches to these problems either relied heavily on programmer support to partition an application, or they were coarse-grained requiring full process (or full VM) migration. MAUI uses the benefits of a managed code environment to offer the best of both worlds: it supports fine-grained code offload to maximize energy savings with minimal burden on the programmer. MAUI decides at run-time which methods should be remotely executed, driven by an optimization engine that achieves the best energy savings possible under the mobile device's current connectivity constrains. In our evaluation, we show that MAUI enables: 1) a resource-intensive face recognition application that consumes an order of magnitude less energy, 2) a latency-sensitive arcade game application that doubles its refresh rate, and 3) a voice-based language translation application that bypasses the limitations of the smartphone environment by executing unsupported components remotely.

HITEMP, the high-temperature molecular spectroscopic database

Abstract: A new molecular spectroscopic database for high-temperature modeling of the spectra of molecules in the gas phase is described. This database, called HITEMP, is analogous to the HITRAN database but encompasses many more bands and transitions than HITRAN for the absorbers H2O, CO2, CO, NO, and OH. HITEMP provides users with a powerful tool for a great many applications: astrophysics, planetary and stellar atmospheres, industrial processes, surveillance, non-local thermodynamic equilibrium problems, and investigating molecular interactions, to name a few. The sources and implementation of the spectroscopic parameters incorporated into HITEMP are discussed.

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Abstract: It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.

Exercise and type 2 diabetes: the American College of Sports Medicine and the American Diabetes Association: joint position statement.

Abstract: Although physical activity (PA) is a key element in the prevention and management of type 2 diabetes, many with this chronic disease do not become or remain regularly active. High-quality studies establishing the importance of exercise and fitness in diabetes were lacking until recently, but it is now well established that participation in regular PA improves blood glucose control and can prevent or delay type 2 diabetes, along with positively affecting lipids, blood pressure, cardiovascular events, mortality, and quality of life. Structured interventions combining PA and modest weight loss have been shown to lower type 2 diabetes risk by up to 58% in high-risk populations. Most benefits of PA on diabetes management are realized through acute and chronic improvements in insulin action, accomplished with both aerobic and resistance training. The benefits of physical training are discussed, along with recommendations for varying activities, PA-associated blood glucose management, diabetes prevention, gestational diabetes mellitus, and safe and effective practices for PA with diabetes-related complications.

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.

The ATLAS Simulation Infrastructure

Abstract: The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.

Modeling relations and their mentions without labeled text

Abstract: Several recent works on relation extraction have been applying the distant supervision paradigm: instead of relying on annotated text to learn how to predict relations, they employ existing knowledge bases (KBs) as source of supervision. Crucially, these approaches are trained based on the assumption that each sentence which mentions the two related entities is an expression of the given relation. Here we argue that this leads to noisy patterns that hurt precision, in particular if the knowledge base is not directly related to the text we are working with. We present a novel approach to distant supervision that can alleviate this problem based on the following two ideas: First, we use a factor graph to explicitly model the decision whether two entities are related, and the decision whether this relation is mentioned in a given sentence; second, we apply constraint-driven semi-supervision to train this model without any knowledge about which sentences express the relations in our training KB. We apply our approach to extract relations from the New York Times corpus and use Freebase as knowledge base. When compared to a state-of-the-art approach for relation extraction under distant supervision, we achieve 31% error reduction.

Solar influences on climate

Abstract: The development of this review article has evolved from work carried out by an international team of the International Space Science Institute (ISSI), Bern, Switzerland, and from work carried out under the auspices of Scientific Committee on Solar Terrestrial Physics (SCOSTEP) Climate and Weather of the Sun‐Earth System (CAWSES‐1). The support of ISSI in providing workshop and meeting facilities is acknowledged, especially support from Y. Calisesi and V. Manno. SCOSTEP is acknowledged for kindly providing financial assistance to allow the paper to be published under an open access policy. L.J.G. was supported by the UK Natural Environment Research Council (NERC) through their National Centre for Atmospheric Research (NCAS) Climate program. K.M. was supported by a Marie Curie International Outgoing Fellowship within the 6th European Community Framework Programme. J.L. acknowledges support by the EU/FP7 program Assessing Climate Impacts on the Quantity and Quality of Water (ACQWA, 212250) and from the DFG Project Precipitation in the Past Millennium in Europe (PRIME) within the Priority Program INTERDYNAMIK. L.H. acknowledges support from the U.S. NASA Living With a Star program. G.M. acknowledges support from the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement DE‐FC02‐97ER62402, and the National Science Foundation. We also wish to thank Karin Labitzke and Markus Kunze for supplying an updated Figure 13, Andrew Heaps for technical support, and Paul Dickinson for editorial support. Part of the research was carried out under the SPP CAWSES funded by GFG. J.B. was financially supported by NCCR Climate–Swiss Climate Research.

Predictions for the rates of compact binary coalescences observable by ground-based gravitational-wave detectors

Abstract: We present an up-to-date, comprehensive summary of the rates for all types of compact binary coalescence sources detectable by the initial and advanced versions of the ground-based gravitational-wave detectors LIGO and Virgo. Astrophysical estimates for compact-binary coalescence rates depend on a number of assumptions and unknown model parameters and are still uncertain. The most confident among these estimates are the rate predictions for coalescing binary neutron stars which are based on extrapolations from observed binary pulsars in our galaxy. These yield a likely coalescence rate of 100 Myr−1 per Milky Way Equivalent Galaxy (MWEG), although the rate could plausibly range from 1 Myr−1 MWEG−1 to 1000 Myr−1 MWEG−1 (Kalogera et al 2004 Astrophys. J. 601 L179; Kalogera et al 2004 Astrophys. J. 614 L137 (erratum)). We convert coalescence rates into detection rates based on data from the LIGO S5 and Virgo VSR2 science runs and projected sensitivities for our advanced detectors. Using the detector sensitivities derived from these data, we find a likely detection rate of 0.02 per year for Initial LIGO–Virgo interferometers, with a plausible range between 2 × 10−4 and 0.2 per year. The likely binary neutron–star detection rate for the Advanced LIGO–Virgo network increases to 40 events per year, with a range between 0.4 and 400 per year.

Renewable Chemical Commodity Feedstocks from Integrated Catalytic Processing of Pyrolysis Oils

Abstract: Fast pyrolysis of lignocellulosic biomass produces a renewable liquid fuel called pyrolysis oil that is the cheapest liquid fuel produced from biomass today Here we show that pyrolysis oils can be converted into industrial commodity chemical feedstocks using an integrated catalytic approach that combines hydroprocessing with zeolite catalysis The hydroprocessing increases the intrinsic hydrogen content of the pyrolysis oil, producing polyols and alcohols The zeolite catalyst then converts these hydrogenated products into light olefins and aromatic hydrocarbons in a yield as much as three times higher than that produced with the pure pyrolysis oil The yield of aromatic hydrocarbons and light olefins from the biomass conversion over zeolite is proportional to the intrinsic amount of hydrogen added to the biomass feedstock during hydroprocessing The total product yield can be adjusted depending on market values of the chemical feedstocks and the relative prices of the hydrogen and biomass

FDDB: A benchmark for face detection in unconstrained settings

Abstract: Despite the maturity of face detection research, it remains difficult to compare different algorithms for face detection. This is partly due to the lack of common evaluation schemes. Also, existing data sets for evaluating face detection algorithms do not capture some aspects of face appearances that are manifested in real-world scenarios. In this work, we address both of these issues. We present a new data set of face images with more faces and more accurate annotations for face regions than in previous data sets. We also propose two rigorous and precise methods for evaluating the performance of face detection algorithms. We report results of several standard algorithms on the new benchmark.

Microbial Electrosynthesis: Feeding Microbes Electricity To Convert Carbon Dioxide and Water to Multicarbon Extracellular Organic Compounds

Abstract: The possibility of providing the acetogenic microorganism Sporomusa ovata with electrons delivered directly to the cells with a graphite electrode for the reduction of carbon dioxide to organic compounds was investigated. Biofilms of S. ovata growing on graphite cathode surfaces consumed electrons with the reduction of carbon dioxide to acetate and small amounts of 2-oxobutyrate. Electrons appearing in these products accounted for over 85% of the electrons consumed. These results demonstrate that microbial production of multicarbon organic compounds from carbon dioxide and water with electricity as the energy source is feasible.

The Herschel-Heterodyne Instrument for the Far-Infrared (HIFI)

Abstract: Aims. This paper describes the Heterodyne Instrument for the Far-Infrared (HIFI) that was launched onboard ESA's Herschel Space Observatory in May 2009. Methods. The instrument is a set of 7 heterodyne receivers that are electronically tuneable, covering 480-1250 GHz with SIS mixers and the 1410-1910 GHz range with hot electron bolometer (HEB) mixers. The local oscillator (LO) subsystem comprises a Ka-band synthesizer followed by 14 chains of frequency multipliers and 2 chains for each frequency band. A pair of auto-correlators and a pair of acousto-optical spectrometers process the two IF signals from the dual-polarization, single-pixel front-ends to provide instantaneous frequency coverage of 2 × 4 GHz, with a set of resolutions (125 kHz to 1 MHz) that are better than 0.1 km s-1. Results. After a successful qualification and a pre-launch TB/TV test program, the flight instrument is now in-orbit and completed successfully the commissioning and performance verification phase. The in-orbit performance of the receivers matches the pre-launch sensitivities. We also report on the in-orbit performance of the receivers and some first results of HIFI's operations.

Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria.

Abstract: Microbial consortia that cooperatively exchange electrons play a key role in the anaerobic processing of organic matter. Interspecies hydrogen transfer is a well-documented strategy for electron exchange in dispersed laboratory cultures, but cooperative partners in natural environments often form multispecies aggregates. We found that laboratory evolution of a coculture of Geobacter metallireducens and Geobacter sulfurreducens metabolizing ethanol favored the formation of aggregates that were electrically conductive. Sequencing aggregate DNA revealed selection for a mutation that enhances the production of a c-type cytochrome involved in extracellular electron transfer and accelerates the formation of aggregates. Aggregate formation was also much faster in mutants that were deficient in interspecies hydrogen transfer, further suggesting direct interspecies electron transfer.

An Introduction to Conditional Random Fields

Abstract: Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.

Prolonged institutional rearing is associated with atypically large amygdala volume and difficulties in emotion regulation.

Abstract: Early adversity, for example poor caregiving, can have profound effects on emotional development. Orphanage rearing, even in the best circumstances, lies outside of the bounds of a species-typical caregiving environment. The long-term effects of this early adversity on the neurobiological development associated with socio-emotional behaviors are not well understood. Seventy-eight children, who include those who have experienced orphanage care and a comparison group, were assessed. Magnetic resonance imaging (MRI) was used to measure volumes of whole brain and limbic structures (e.g. amygdala, hippocampus). Emotion regulation was assessed with an emotional go-nogo paradigm, and anxiety and internalizing behaviors were assessed using the Screen for Child Anxiety Related Emotional Disorders, the Child Behavior Checklist, and a structured clinical interview. Late adoption was associated with larger corrected amygdala volumes, poorer emotion regulation, and increased anxiety. Although more than 50% of the children who experienced orphanage rearing met criteria for a psychiatric disorder, with a third having an anxiety disorder, the group differences observed in amygdala volume were not driven by the presence of an anxiety disorder. The findings are consistent with previous reports describing negative effects of prolonged orphanage care on emotional behavior and with animal models that show long-term changes in the amygdala and emotional behavior following early postnatal stress. These changes in limbic circuitry may underlie residual emotional and social problems experienced by children who have been internationally adopted.

The Akamai network: a platform for high-performance internet applications

Abstract: Comprising more than 61,000 servers located across nearly 1,000 networks in 70 countries worldwide, the Akamai platform delivers hundreds of billions of Internet interactions daily, helping thousands of enterprises boost the performance and reliability of their Internet applications. In this paper, we give an overview of the components and capabilities of this large-scale distributed computing platform, and offer some insight into its architecture, design principles, operation, and management.

The diversity and similarity of simulated cold dark matter haloes

Abstract: We study the structure ofCDM halos using a suite of N-body simulations of un- precedented numerical resolution. The Aquarius Project follows the formation of 6 different galaxy-sized halos simulated several times at varying numerical resolution, allowing numerical convergence to be assessed directly. The highest resolution sim- ulation represents a single dark matter halo using 4.4 billion particles, of which 1.1 billion end up within the virial radius. Our analysis confirms that the mass pro- file ofCDM halos deviates slightly but systematically from the form proposed by Navarro, Frenk & White. The spherically-averaged density profile becomes progres- sively shallower inwards and, at the innermost resolved radius, the logarithmic slope isdln�/dlnr < � 1, convincingly ruling out recent claims of a steep � / r 1.2 central cusp. The radial dependence of is well approximated by a power-law, / r � (the Einasto profile). The shape parameter, �, varies slightly but significantly from halo to halo, implying that the mass profiles ofCDM halos are not strictly universal: different halos cannot, in general, be rescaled to look exactly alike. Departures from similarity are also seen in velocity dispersion profiles and correlate with those in density profiles so as to preserve a power-law form for the spherically averaged pseudo-phase- space density, �/� 3 / r 1.875 . The index here is identical to that of Bertschinger's similarity solution for self-similar infall onto a point mass from an otherwise uniform Einstein-de Sitter Universe. The origin of this striking behaviour is unclear, but its robustness suggests that it reflects a fundamental structural property ofCDM halos. Our conclusions are reliable down to radii below 0.4% of the virial radius, providing well-defined predictions for halo structure when baryonic effects are neglected, and thus an instructive theoretical template against which the modifications induced by the baryonic components of real galaxies can be judged.

Adsorption of Organic Compounds by Carbon Nanomaterials in Aqueous Phase: Polanyi Theory and Its Application

Abstract: 11. Conclusions and Perspectives 6005 12. Acknowledgments 6006 13. References 6006

Augmenting mobile 3G using WiFi

Abstract: We investigate if WiFi access can be used to augment 3G capacity in mobile environments. We rst conduct a detailed study of 3G and WiFi access from moving vehicles, in three different cities. We find that the average 3G and WiFi availability across the cities is 87% and 11%, respectively. WiFi throughput is lower than 3G through-put, and WiFi loss rates are higher. We then design a system, called Wiffler, to augments mobile 3G capacity. It uses two key ideas leveraging delay tolerance and fast switching -- to overcome the poor availability and performance of WiFi. For delay tolerant applications, Wiffler uses a simple model of the environment to predict WiFi connectivity. It uses these predictions to delays transfers to offload more data on WiFi, but only if delaying reduces 3G usage and the transfers can be completed within the application's tolerance threshold. For applications that are extremely sensitive to delay or loss (e.g., VoIP), Wiffler quickly switches to 3G if WiFi is unable to successfully transmit the packet within a small time window. We implement and deploy Wiffler in our vehicular testbed. Our experiments show that Wiffler significantly reduces 3G usage. For a realistic workload, the reduction is 45% for a delay tolerance of 60 seconds.

Hydrogen Bond Networks in Graphene Oxide Composite Paper: Structure and Mechanical Properties

Abstract: A multilayered composite structure formed by a random stacking of graphene oxide (GO) platelets is an attractive candidate for novel applications in nanoelectromechanical systems and paper-like composites. We employ molecular dynamics simulations with reactive force fields to elucidate the structural and mechanical properties of GO paper-like materials. We find that the large-scale properties of these composites are controlled by hydrogen bond networks that involve functional groups on individual GO platelets and water molecules within the interlayer cavities. Water content controls both the extent and collective strength of these interlayer hydrogen bond networks, thereby affecting the interlayer spacing and elastic moduli of the composite. Additionally, the chemical composition of the individual GO platelets also plays a critical role in establishing the mechanical properties of the composite—a higher density of functional groups leads to increased hydrogen bonding and a corresponding increase in stiffn...

Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS

Abstract: Many mutations confer one or more toxic function(s) on copper/zinc superoxide dismutase 1 (SOD1) that impair motor neuron viability and cause familial amyotrophic lateral sclerosis (FALS). Using a conformation-specific antibody that detects misfolded SOD1 (C4F6), we found that oxidized wild-type SOD1 and mutant SOD1 share a conformational epitope that is not present in normal wild-type SOD1. In a subset of human sporadic ALS (SALS) cases, motor neurons in the lumbosacral spinal cord were markedly C4F6 immunoreactive, indicating that an aberrant wild-type SOD1 species was present. Recombinant, oxidized wild-type SOD1 and wild-type SOD1 immunopurified from SALS tissues inhibited kinesin-based fast axonal transport in a manner similar to that of FALS-linked mutant SOD1. Our findings suggest that wild-type SOD1 can be pathogenic in SALS and identify an SOD1-dependent pathogenic mechanism common to FALS and SALS.

Holey Silicon as an Efficient Thermoelectric Material

Abstract: This work investigated the thermoelectric properties of thin silicon membranes that have been decorated with high density of nanoscopic holes. These "holey silicon" (HS) structures were fabricated by either nanosphere or block-copolymer lithography, both of which are scalable for practical device application. By reducing the pitch of the hexagonal holey pattern down to 55 nm with 35% porosity, the thermal conductivity of HS is consistently reduced by 2 orders of magnitude and approaches the amorphous limit. With a ZT value of ∼0.4 at room temperature, the thermoelectric performance of HS is comparable with the best value recorded in silicon nanowire system.

Factors Influencing the Chemical Stability of Carotenoids in Foods

Abstract: In recent years, a number of studies have produced evidence to suggest that consuming carotenoids may provide a variety of health benefits including a reduced incidence of a number of cancers, reduced risk of cardiovascular disease, and improved eye health. Evolving evidence on the health benefits of several carotenoids has sparked interest in incorporating more carotenoids into functional food products. Unfortunately, the same structural attributes of carotenoids that are thought to impart health benefits also make these compounds highly susceptible to oxidation. Given the susceptibility of carotenoids to degradation, particularly once they have been extracted from biological tissues, it is important to understand the major mechanisms of oxidation in order to design delivery systems that protect these compounds when they are used as functional food ingredients. This article reviews current understanding of the oxidation mechanisms by which carotenoids are degraded, including pathways induced by heat, light, oxygen, acid, transition metal, or interactions with radical species. In addition, several carotenoid delivery systems are evaluated for their potential to decrease carotenoid degradation in functional food products.

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.

Optical spectroscopy and nebular oxygen abundances of the spitzer/sings galaxies

Abstract: We present intermediate-resolution optical spectrophotometry of 65 galaxies obtained in support of the Spitzer Infrared Nearby Galaxies Survey (SINGS). For each galaxy we obtain a nuclear, circumnuclear, and semi-integrated optical spectrum designed to coincide spatially with mid- and far-infrared spectroscopy from the Spitzer Space Telescope. We make the reduced, spectrophotometrically calibrated one-dimensional spectra, as well as measurements of the fluxes and equivalent widths of the strong nebular emission lines, publically available. We use optical emission-line ratios measured on all three spatial scales to classify the sample into star-forming, active galactic nuclei (AGNs), and galaxies with a mixture of star formation and nuclear activity. We find that the relative fraction of the sample classified as star forming versus AGN is a strong function of the integrated light enclosed by the spectroscopic aperture. We supplement our observations with a large database of nebular emission-line measurements of individual H II regions in the SINGS galaxies culled from the literature. We use these ancillary data to conduct a detailed analysis of the radial abundance gradients and average H II-region abundances of a large fraction of the sample. We combine these results with our new integrated spectra to estimate the central and characteristic (globally averaged) gas-phase oxygen abundances of all 75 SINGS galaxies. We conclude with an in-depth discussion of the absolute uncertainty in the nebular oxygen abundance scale.

Minimum Wage Effects Across State Borders: Estimates Using Contiguous Counties

Abstract: We use policy discontinuities at state borders to identify the effects of minimum wages on earnings and employment in restaurants and other low-wage sectors. Our approach generalizes the case study method by considering all local differences in minimum wage policies between 1990 and 2006. We compare all contiguous county pairs in the United States that straddle a state border and find no adverse employment effects. We show that traditional approaches that do not account for local economic conditions tend to produce spurious negative effects due to spatial heterogeneities in employment trends that are unrelated to minimum wage policies. Our findings are robust to allowing for long-term effects of minimum wage changes.