bluuebunny/crossref_metadata_2025 huggingface dataset:
Engineering Efficient Paging Algorithms
Authors: Moruz Gabriel , Negoescu Andrei , Neumann Christian , Weichert Volker
Published: January 2015

In the field of online algorithms, paging is a well-studied problem. LRU is a simple paging algorithm that incurs few cache misses and supports efficient implementations. Algorithms outperforming LRU in terms of cache misses exist but are in general more complex and thus not automatically better, since their increased runtime might annihilate the gains in cache misses. In this article, we focus on efficient implementations for the O
n
OPT class described in Moruz and Negoescu [2012], particularly on an algorithm in this class, denoted
RDM
, that was shown to typically incur fewer misses than LRU. We provide experimental evidence on a wide range of cache traces showing that our implementation of RDM is competitive to LRU with respect to runtime. In a scenario incurring realistic time penalties for cache misses, we show that our implementation consistently outperforms LRU, even if the runtime of LRU is set to zero.
Candidate Sets for Alternative Routes in Road Networks
Authors: Luxen Dennis , Schieferdecker Dennis
Published: January 2015

We study the computation of good alternatives to the shortest path in road networks. Our approach is based on single via-node routing on top of contraction hierarchies and achieves superior quality and efficiency compared to previous methods. We present a fast preprocessing method for computing multiple good alternatives and apply this result in an online setting. This setting makes our result applicable in legacy systems with negligible memory overhead. An extensive experimental analysis on a continental-sized real- world road network proves the performance of our algorithm and supports the general systematic algorithm engineering approach. We also show how to combine our results with the competing concept of alternative graphs that encode many alternative paths at once.
Efficient Data Encoding for Convolutional Neural Network application
Authors: Trinh Hong-Phuc , Duranton Marc , Paindavoine Michel
Published: January 2015

This article presents an approximate data encoding scheme called
Significant Position Encoding (SPE)
. The encoding allows efficient implementation of the recall phase (forward propagation pass) of Convolutional Neural Networks (CNN)—a typical Feed-Forward Neural Network. This implementation uses only 7 bits data representation and achieves almost the same classification performance compared with the initial network: on MNIST handwriting recognition task, using this data encoding scheme losses only 0.03% in terms of recognition rate (99.27% vs. 99.3%). In terms of storage, we achieve a 12.5% gain compared with an 8 bits fixed-point implementation of the same CNN. Moreover, this data encoding allows efficient implementation of processing unit thanks to the simplicity of scalar product operation—the principal operation in a Feed-Forward Neural Network.
Low-Power High-Efficiency Video Decoding using General-Purpose Processors
Authors: Chi Chi Ching , Alvarez-Mesa Mauricio , Juurlink Ben
Published: January 2015

In this article, we investigate how code optimization techniques and low-power states of general-purpose processors improve the power efficiency of HEVC decoding. The power and performance efficiency of the use of SIMD instructions, multicore architectures, and low-power active and idle states are analyzed in detail for offline video decoding. In addition, the power efficiency of techniques such as “race to idle” and “exploiting slack” with DVFS are evaluated for real-time video decoding. Results show that “exploiting slack” is more power efficient than “race to idle” for all evaluated platforms representing smartphone, tablet, laptop, and desktop computing systems.
Optimizing Memory Translation Emulation in Full System Emulators
Authors: Tong Xin , Koju Toshihiko , Kawahito Motohiro , Moshovos Andreas
Published: January 2015

The emulation speed of a full system emulator (FSE) determines its usefulness. This work quantitatively measures where time is spent in QEMU [Bellard 2005], an industrial-strength FSE. The analysis finds that memory emulation is one of the most heavily exercised emulator components. For workloads studied, 38.1% of the emulation time is spent in memory emulation on average, even though QEMU implements a software translation lookaside buffer (STLB) to accelerate dynamic address translation. Despite the amount of time spent in memory emulation, there has been no study on how to further improve its speed. This work analyzes where time is spent in memory emulation and studies the performance impact of a number of STLB optimizations. Although there are several performance optimization techniques for hardware TLBs, this work finds that the trade-offs with an STLB are quite different compared to those with hardware TLBs. As a result, not all hardware TLB performance optimization techniques are applicable to STLBs and vice versa. The evaluated STLB optimizations target STLB lookups, as well as refills, and result in an average emulator performance improvement of 24.4% over the baseline.
The Effects of Parameter Tuning in Software Thread-Level Speculation in JavaScript Engines
Authors: Martinsen Jan Kasper , Grahn Håkan , Isberg Anders
Published: January 2015

JavaScript is a sequential programming language that has a large potential for parallel execution in Web applications. Thread-level speculation can take advantage of this, but it has a large memory overhead. In this article, we evaluate the effects of adjusting various parameters for thread-level speculation. Our results clearly show that thread-level speculation is a useful technique for taking advantage of multicore architectures for JavaScript in Web applications, that nested speculation is required in thread-level speculation, and that the execution characteristics of Web applications significantly reduce the needed memory, the number of threads, and the depth of our speculation.
Optimal Parallelogram Selection for Hierarchical Tiling
Authors: Zhou Xing , Garzarán María J. , Padua David A.
Published: January 2015

Loop tiling is an effective optimization to improve performance of multiply nested loops, which are the most time-consuming parts in many programs. Most massively parallel systems today are organized hierarchically, and different levels of the hierarchy differ in the organization of parallelism and the memory models they adopt. To make better use of these machines, it is clear that loop nests should be tiled hierarchically to fit the hierarchical organization of the machine; however, it is not so clear what should be the exact form of these hierarchical tiles. In particular, tile shape selection is of critical importance to expose parallelism of the tiled loop nests. Although loop tiling is a well-known optimization, not much is known about tile shape selection.

In this article, we study tile shape selection when the shapes are any type of parallelograms and introduce a model to relate the tile shape of the hierarchy to the execution time. Using this model, we implement a system that automatically finds the tile shapes that minimize the execution time in a hierarchical system. Our experimental results show that in several cases, the tiles automatically selected by our system outperform the most intuitive tiling schemes usually adopted by programmers because of their simplicity.
Making the Most of SMT in HPC
Authors: Porter Leo , Laurenzano Michael A. , Tiwari Ananta , Jundt Adam , Ward, Jr. William A. , Campbell Roy , Carrington Laura
Published: January 2015

This work presents an end-to-end methodology for quantifying the performance and power benefits of simultaneous multithreading (SMT) for HPC centers and applies this methodology to a production system and workload. Ultimately, SMT’s value system-wide depends on whether users effectively employ SMT at the application level. However, predicting SMT’s benefit for HPC applications is challenging; by doubling the number of threads, the application’s characteristics may change. This work proposes statistical modeling techniques to predict the speedup SMT confers to HPC applications. This approach, accurate to within 8%, uses only lightweight, transparent performance monitors collected during a single run of the application.
Following or leading?
Authors: Schmidt Albrecht
Published: January 2015

Envisioning, designing, and implementing the user interface require a comprehensive understanding of interaction technologies. In this forum we scout trends and discuss new technologies with the potential to influence interaction design.
--- Albrecht Schmidt, Editor
On Using the Roofline Model with Lower Bounds on Data Movement
Authors: Elango Venmugil , Sedaghati Naser , Rastello Fabrice , Pouchet Louis-Noël , Ramanujam J. , Teodorescu Radu , Sadayappan P.
Published: January 2015

The roofline model is a popular approach for “bound and bottleneck” performance analysis. It focuses on the limits to the performance of processors because of limited bandwidth to off-chip memory. It models upper bounds on performance as a function of operational intensity, the ratio of computational operations per byte of data moved from/to memory. While operational intensity can be directly measured for a specific implementation of an algorithm on a particular target platform, it is of interest to obtain broader insights on bottlenecks, where various semantically equivalent implementations of an algorithm are considered, along with analysis for variations in architectural parameters. This is currently very cumbersome and requires performance modeling and analysis of many variants.

In this article, we address this problem by using the roofline model in conjunction with upper bounds on the operational intensity of computations as a function of cache capacity, derived from lower bounds on data movement. This enables bottleneck analysis that holds across all dependence-preserving semantically equivalent implementations of an algorithm. We demonstrate the utility of the approach in assessing fundamental limits to performance and energy efficiency for several benchmark algorithms across a design space of architectural variations.
LG's G3 GUI
Authors: Lee Chul Bae , Lee Kunho
Published: January 2015

A slick smartphone GUI rides the new wave of digital modernism.
An Evaluation of Tail Loss Recovery Mechanisms for TCP
Authors: Rajiullah Mohammad , Hurtig Per , Brunstrom Anna , Petlund Andreas , Welzl Michael
Published: January 2015

Interactive applications do not require more bandwidth to go faster. Instead, they require less latency. Unfortunately, the current design of transport protocols such as TCP limits possible latency reductions. In this paper we evaluate and compare different loss recovery enhancements to fight tail loss latency. The two recently proposed mechanisms "RTO Restart" (RTOR) and "Tail Loss Probe" (TLP) as well as a new mechanism that applies the logic of RTOR to the TLP timer management (TLPR) are considered. The results show that the relative performance of RTOR and TLP when tail loss occurs is scenario dependent, but with TLP having potentially larger gains. The TLPR mechanism reaps the benefits of both approaches and in most scenarios it shows the best performance.
Life in the Fast Lane
Authors: Varghese George
Published: January 2015

The most striking ideas in systems are abstractions such as virtual memory, sockets, or packet scheduling. Algorithmics is the servant of abstraction, allowing the performance of the system to approach that of the underlying hardware. I survey the trajectory of network algorithmics, starting with a focus on speed and scale in the 1990s to measurement and security in the 2000s, using what I call the
confluence lens
.

Confluence sees interdisciplinary work as a merger of two or more disciplines made compelling by an inflection point in the real world, while also producing genuinely transformed ideas. I attempt to show that Network Algorithmics represented a confluence in the 1990s between computer systems, algorithms, and networking. I suggest confluence diagrams as a means to identify future interdisciplinary opportunities, and describe the emerging field of network verification as a new confluence between networking and programming languages.
Responses of Temperate Forest Productivity to Insect and Pathogen Disturbances
Authors: Flower Charles E. , Gonzalez-Meler Miquel A.
Published: January 2015

Pest and pathogen disturbances are ubiquitous across forest ecosystems, impacting their species composition, structure, and function. Whereas severe abiotic disturbances (e.g., clear-cutting and fire) largely reset successional trajectories, pest and pathogen disturbances cause diffuse mortality, driving forests into nonanalogous system states. Biotic perturbations that disrupt forest carbon dynamics either reduce or enhance net primary production (NPP) and carbon storage, depending on pathogen type. Relative to defoliators, wood borers and invasive pests have the largest negative impact on NPP and the longest recovery time. Forest diversity is an important contributing factor to productivity: NPP is neutral, marginally enhanced, or reduced in high-diversity stands in which a small portion of the canopy is affected (temperate deciduous or mixed forests) but very negative in low-diversity stands in which a large portion of the canopy is affected (western US forests). Pests and pathogens reduce forest structural and functional redundancy, affecting their resilience to future climate change or new outbreaks. Therefore, pests and pathogens can be considered biotic forcing agents capable of causing consequences of similar magnitude to climate forcing factors.
Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes
Authors: van Wijk Klaas J.
Published: January 2015

Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events.
Clinical Dysfunction and Psychosocial Interventions: The Interplay of Research, Methods, and Conceptualization of Challenges
Authors: Kazdin Alan E.
Published: January 2015

I describe the development and course of my research in studying clinical dysfunction among children, adolescents, and adults. This is an autobiographical account that highlights programs of research, career moves, and experiences along the way that were particularly influential. Research on specific topics and the methods to study them were inherently fascinating but invariably led me to broader issues well beyond what I was studying. The research alerted me to how and why current methods, assumptions, and research practices might be constraining and perhaps slightly misguided. My research and specific findings in a given area were not necessarily part of any particular breakthrough but rather helped me see how more, different, and better work was needed. Collaborations with a diverse set of colleagues and models from other disciplines than psychology helped me conceptualize the goals of research on a given topic (e.g., developing evidence-based treatments, reducing the burden of mental illness, promoting a sustainable environment to mitigate climate change) and propose a shift from current practices as a means to obtain them.
Self-Reported Experiences of Discrimination and Health: Scientific Advances, Ongoing Controversies, and Emerging Issues
Authors: Lewis Tené T. , Cogburn Courtney D. , Williams David R.
Published: January 2015

Over the past two decades, research examining the impact of self-reported experiences of discrimination on mental and physical health has increased dramatically. Studies have found consistent associations between exposure to discrimination and a wide range of Diagnostic and Statistical Manual of Mental Disorders (DSM)-diagnosed mental disorders as well as objective physical health outcomes. Associations are seen in cross-sectional as well as longitudinal studies and persist even after adjustment for confounding variables, including personality characteristics and other threats to validity. However, controversies remain, particularly around the best approach to measuring experiences of discrimination, the significance of racial/ethnic discrimination versus overall mistreatment, the need to account for “intersectionalities,” and the importance of comprehensive assessments. These issues are discussed in detail, along with emerging areas of emphasis including cyber discrimination, anticipatory stress or vigilance around discrimination, and interventions with potential to reduce the negative effects of discrimination on health. We also discuss priorities for future research and implications for interventions and policy.
Recent Advances in Autism Research as Reflected in DSM-5 Criteria for Autism Spectrum Disorder
Authors: Lord Catherine , Bishop Somer L.
Published: January 2015

This article provides a selective review of advances in scientific knowledge about autism spectrum disorder (ASD), using DSM-5 (Diagnostic and Statistical Manual of Mental Disorders, fifth edition) diagnostic criteria as a framework for the discussion. We review literature that prompted changes to the organization of ASD symptoms and diagnostic subtypes in DSM-IV, and we examine the rationale for new DSM-5 specifiers, modifiers, and severity ratings as well as the introduction of the diagnosis of social (pragmatic) communication disorder. Our goal is to summarize and critically consider the contribution of clinical psychology research, along with that of other disciplines, to the current conceptualization of ASD.
fMRI Functional Connectivity Applied to Adolescent Neurodevelopment
Authors: Ernst Monique , Torrisi Salvatore , Balderston Nicholas , Grillon Christian , Hale Elizabeth A.
Published: January 2015

The exponential rise in the number of functional brain connectivity studies, particularly those examining intrinsic functional connectivity (iFC) at rest, and the promises of this work for unraveling the ontogeny of functional neural systems motivate this review. Shortly before this explosion in functional connectivity research, developmental neuroscientists had proposed theories based on neural systems models to explain behavioral changes, particularly in adolescence. The current review presents recent advances in imaging in brain connectivity research, which provides a unique tool for the study of neural systems. Understanding the potential of neuroimaging for refining neurodevelopmental models of brain function requires a description of various functional connectivity approaches. In this review, we describe task-based and resting-state functional magnetic resonance imaging (fMRI) analytic strategies, but we focus on iFC findings from resting-state data to describe general developmental trajectories of brain network organization. Finally, we use the example of drug addiction to frame a discussion of psychopathology that emerges in adolescence.
Clinical Features, Cognitive Biases, and Treatment of Body Dysmorphic Disorder
Authors: Fang Angela , Wilhelm Sabine
Published: January 2015

In the past two decades, research advances have enhanced our understanding of the clinical features, cognitive biases, and treatment of body dysmorphic disorder (BDD). In this review, we critically examine the current state of the evidence on the proposed cognitive and emotional processing mechanisms of BDD. We describe how major findings in these areas made unique contributions to the development of an empirically informed cognitive-behavioral model of BDD, which in turn facilitated the translation of research to treatment strategies. Finally, we outline important areas of future research.
Etiologic, Phenomenologic, and Endophenotypic Overlap of Schizophrenia and Bipolar Disorder
Authors: Pearlson Godfrey D.
Published: January 2015

This review examines the history of psychiatric nosology, with particular reference to the nineteenth-century origins of the concepts of manic-depressive illness and schizophrenia as distinct clinical syndromes and their evolution and diagnostic refinement over time. I document how the terminology applied to these entities has generated controversy, and discuss the ways in which the resulting diagnostic entities as defined by pure phenomenological symptom descriptors fail to capture discrete diagnostic distinctions, leading some researchers to posit an illness continuum rather than separate disorders. Furthermore, the two syndromes overlap substantially on multiple biologic measures, and clarity is lacking as to the underlying etiology and pathology necessary to move from descriptions of clinical syndromes to diseases. I next examine how biologically based classifications agnostic to conventional diagnostic schemes may be useful and how these are being implemented in practice, and conclude by summarizing where such approaches are likely to lead.
Plutonium-Based Heavy-Fermion Systems
Authors: Bauer E.D. , Thompson J.D.
Published: January 2015

An effective mass of charge carriers that is significantly larger than the mass of a free electron develops at low temperatures in certain lanthanide- and actinide-based metals, including those formed with plutonium, owing to strong electron-electron interactions. This heavy-fermion mass is reflected in a substantially enhanced electronic coefficient of specific heat γ, which for elemental Pu is much larger than that of normal metals. By our definition, there are twelve Pu-based heavy-fermion compounds, most discovered recently, whose basic properties are known and discussed. Relative to other examples, these Pu-based heavy-fermion systems are particularly complex owing in part to the possible simultaneous presence of multiple, nearly degenerate 5fn configurations. This complexity poses significant opportunities as well as challenges, including understanding the origin of unconventional superconductivity in some of these materials.
Marginal Stability in Structural, Spin, and Electron Glasses
Authors: Müller Markus , Wyart Matthieu
Published: January 2015

We revisit the concept of marginal stability in glasses and determine its range of applicability in the context of an avalanche-type response to slow external driving. We argue that there is an intimate connection between a pseudogap in the distribution of local fields and crackling in systems with long-range interactions. We classify glassy systems according to the presence or absence of marginal stability, providing a unifying perspective on the phenomenology of systems as diverse as spin and electron glasses, hard spheres, pinned elastic interfaces, and soft amorphous solids undergoing plastic deformation.
Assembly of Biological Nanostructures: Isotropic and Liquid Crystalline Phases of Neurofilament Hydrogels
Authors: Safinya Cyrus R. , Deek Joanna , Beck Roy , Jones Jayna B. , Li Youli
Published: January 2015

Neurofilaments are the building blocks of the major cytoskeletal network found in the axons of vertebrate neurons. The filaments consist of three distinct molecular-weight subunits—neurofilament-low, neurofilament-medium, and neurofilament-high—which coassemble into 10-nm flexible rods with protruding intrinsically disordered C-terminal sidearms that mediate interfilament interactions and hydrogel formation. Molecular neuroscience research includes areas focused on elucidating the functions of each subunit in network formation, during which disruptions are a hallmark of motor-neuron diseases. Here, modern concepts and methods from soft condensed matter physics are combined to address the role of subunits as it relates to interfilament forces and phase behavior in neurofilament networks. Significantly, the phase behavior studies reveal that although neurofilament-medium subunits promote nematic liquid crystal hydrogel phase stability with parallel filament orientation, neurofilament-high subunits stabilize the hydrogel in the nematic phase close to the isotropic gel phase with random, crossed-filament orientation. This indicates a regulatory role for neurofilament-high subunits in filament orientational plasticity required for organelle (e.g., membrane-bound vesicle or mitochondrion) transport along microtubules embedded in neurofilament hydrogels. Future studies—for example, on neurofilament subunits mixed with tubulin and microtubule-associated proteins—should lead to a deeper understanding of forces and heterogeneous structures in neuronal cytoskeletons.
Motility-Induced Phase Separation
Authors: Cates Michael E. , Tailleur Julien
Published: January 2015

Self-propelled particles include both self-phoretic synthetic colloids and various microorganisms. By continually consuming energy, they bypass the laws of equilibrium thermodynamics. These laws enforce the Boltzmann distribution in thermal equilibrium: The steady state is then independent of kinetic parameters. In contrast, self-propelled particles tend to accumulate where they move more slowly. They may also slow down at high density for either biochemical or steric reasons. This creates positive feedback, which can lead to motility-induced phase separation (MIPS) between dense and dilute fluid phases. At leading order in gradients, a mapping relates variable-speed, self-propelled particles to passive particles with attractions. This deep link to equilibrium phase separation is confirmed by simulations but generally breaks down at higher order in gradients: New effects, with no equilibrium counterpart, then emerge. We give a selective overview of the fast-developing field of MIPS, focusing on theory and simulation but including a brief speculative survey of its experimental implications.
Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine
Authors: Caballero Silvia , Pamer Eric G.
Published: January 2015

The diverse microbial populations constituting the intestinal microbiota promote immune development and differentiation, but because of their complex metabolic requirements and the consequent difficulty culturing them, they remained, until recently, largely uncharacterized and mysterious. In the last decade, deep nucleic acid sequencing platforms, new computational and bioinformatics tools, and full-genome characterization of several hundred commensal bacterial species facilitated studies of the microbiota and revealed that differences in microbiota composition can be associated with inflammatory, metabolic, and infectious diseases, that each human is colonized by a distinct bacterial flora, and that the microbiota can be manipulated to reduce and even cure some diseases. Different bacterial species induce distinct immune cell populations that can play pro- and anti-inflammatory roles, and thus the composition of the microbiota determines, in part, the level of resistance to infection and susceptibility to inflammatory diseases. This review summarizes recent work characterizing commensal microbes that contribute to the antimicrobial defense/inflammation axis.
Ethical Leadership
Authors: Den Hartog Deanne N.
Published: January 2015

High-profile cases of leaders’ ethical failure in different settings and sectors have led to increased attention to ethical leadership in organizations. In this review, I discuss the rapidly developing field of ethical leadership from an organizational behavior/psychology perspective, taking a behavioral and perceptual angle. After addressing the background of ethical leadership in this field, I discuss how ethical leadership has been defined, which behaviors and characteristics contribute to a leader being seen as ethical by followers, and how ethical leadership relates to other leadership styles. I also contrast ethical with unethical leader behaviors. Next, I address what the research to date tells us about the effects of perceived ethical leader behavior, the mechanisms through which this form of leadership affects followers, and what the role of the context is. Finally, I summarize the challenges the field currently faces, outline several future research directions, and discuss some practical implications of the work to date.
Theoretical Description of Structural and Electronic Properties of Organic Photovoltaic Materials
Authors: Zhugayevych Andriy , Tretiak Sergei
Published: January 2015

We review recent progress in the modeling of organic solar cells and photovoltaic materials, as well as discuss the underlying theoretical methods with an emphasis on dynamical electronic processes occurring in organic semiconductors. The key feature of the latter is a strong electron-phonon interaction, making the evolution of electronic and structural degrees of freedom inseparable. We discuss commonly used approaches for first-principles modeling of this evolution, focusing on a multiscale framework based on the Holstein–Peierls Hamiltonian solved via polaron transformation. A challenge for both theoretical and experimental investigations of organic solar cells is the complex multiscale morphology of these devices. Nevertheless, predictive modeling of photovoltaic materials and devices is attainable and is rapidly developing, as reviewed here.
Advanced Physical Chemistry of Carbon Nanotubes
Authors: Li Jun , Pandey Gaind P.
Published: January 2015

The past decade has seen a surge of exciting research and applications of carbon nanotubes (CNTs) stimulated by deeper understanding of their fundamental properties and increasing production capability. The intrinsic properties of various CNTs were found to strongly depend on their internal microstructures. This review summarizes the fundamental structure-property relations of seamless tube-like single- and multiwalled CNTs and conically stacked carbon nanofibers, as well as the organized architectures of these CNTs (including randomly stacked thin films, parallel aligned thin films, and vertically aligned arrays). It highlights the recent development of CNTs as key components in selected applications, including nanoelectronics, filtration membranes, transparent conductive electrodes, fuel cells, electrical energy storage devices, and solar cells. Particular emphasis is placed on the link between the basic physical chemical properties of CNTs and the organized CNT architectures with their functions and performance in each application.
Molecular Force Spectroscopy on Cells
Authors: Liu Baoyu , Chen Wei , Zhu Cheng
Published: January 2015

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.
Site-Specific Infrared Probes of Proteins
Authors: Ma Jianqiang , Pazos Ileana M. , Zhang Wenkai , Culik Robert M. , Gai Feng
Published: January 2015

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
Biomolecular Damage Induced by Ionizing Radiation: The Direct and Indirect Effects of Low-Energy Electrons on DNA
Authors: Alizadeh Elahe , Orlando Thomas M. , Sanche Léon
Published: January 2015

Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.
The Impact of Toxins on the Developing Brain
Authors: Lanphear Bruce P.
Published: January 2015

The impact of toxins on the developing brain is usually subtle for an individual child, but the damage can be substantial at the population level. Numerous challenges must be addressed to definitively test the impact of toxins on brain development in children: We must quantify exposure using a biologic marker or pollutant; account for an ever-expanding set of potential confounders; identify critical windows of vulnerability; and repeatedly examine the association of biologic markers of toxins with intellectual abilities, behaviors, and brain function in distinct cohorts. Despite these challenges, numerous toxins have been implicated in the development of intellectual deficits and mental disorders in children. Yet, too little has been done to protect children from these ubiquitous but insidious toxins. The objective of this review is to provide an overview on the population impact of toxins on the developing brain and describe implications for public health.
Lessons from Complex Interventions to Improve Health
Authors: Hawe Penelope
Published: January 2015

Complexity—resulting from interactions among many component parts—is a property of both the intervention and the context (or system) into which it is placed. Complexity increases the unpredictability of effects. Complexity invites new approaches to logic modeling, definitions of integrity and means of standardization, and evaluation. New metaphors and terminology are needed to capture the recognition that knowledge generation comes from the hands of practitioners/implementers as much as it comes from those usually playing the role of intervention researcher. Failure to acknowledge this may blind us to the very mechanisms we seek to understand. Researchers in clinical settings are documenting health improvement gains made as a consequence of complex systems thinking. Improvement science in clinical settings has much to offer researchers in population health.
The Response of the US Centers for Disease Control and Prevention to the Obesity Epidemic
Authors: Dietz William H.
Published: January 2015

The recognition of the obesity epidemic as a national problem began in 1999 with the Centers for Disease Control and Prevention's (CDC's) publication of a series of annual state-based maps that demonstrated the rapid changes in the prevalence of obesity. Increasing rates of obesity had been noted in earlier CDC studies, but the maps provided evidence of a rapid, nationwide increase. The urgent need to respond to the epidemic led to the identification of state targets and the first generation of interventions for obesity prevention and control. The CDC's role was to provide setting- and intervention-specific guidance on implementing these strategies, and to assess changes in targeted policies and behaviors. The CDC's efforts were augmented by Congressional funding for community initiatives to improve nutrition and increase physical activity. Complementary investments by Kaiser Permanente, the Robert Wood Johnson Foundation, and the Institute of Medicine improved the evidence base and provided policy recommendations that reinforced the need for a multisectoral approach. Legislative, regulatory, and voluntary initiatives enacted by President Obama's administration translated many of the strategies into effective practice. Whether current efforts to address obesity can be sustained will depend on whether they can be translated into greater grass-roots engagement consistent with a social movement.
Cure Violence: A Public Health Model to Reduce Gun Violence
Authors: Butts Jeffrey A. , Roman Caterina Gouvis , Bostwick Lindsay , Porter Jeremy R.
Published: January 2015

Scholars and practitioners alike in recent years have suggested that real and lasting progress in the fight against gun violence requires changing the social norms and attitudes that perpetuate violence and the use of guns. The Cure Violence model is a public health approach to gun violence reduction that seeks to change individual and community attitudes and norms about gun violence. It considers gun violence to be analogous to a communicable disease that passes from person to person when left untreated. Cure Violence operates independently of, while hopefully not undermining, law enforcement. In this article, we describe the theoretical basis for the program, review existing program evaluations, identify several challenges facing evaluators, and offer directions for future research.
Effects of Policies Designed to Keep Firearms from High-Risk Individuals
Authors: Webster Daniel W. , Wintemute Garen J.
Published: January 2015

This article summarizes and critiques available evidence from studies published between 1999 and August 2014 on the effects of policies designed to keep firearms from high-risk individuals in the United States. Some prohibitions for high-risk individuals (e.g., those under domestic violence restraining orders, violent misdemeanants) and procedures for checking for more types of prohibiting conditions are associated with lower rates of violence. Certain laws intended to prevent prohibited persons from accessing firearms—rigorous permit-to-purchase, comprehensive background checks, strong regulation and oversight of gun dealers, and requiring gun owners to promptly report lost or stolen firearms—are negatively associated with the diversion of guns to criminals. Future research is needed to examine whether these laws curtail nonlethal gun violence and whether the effects of expanding prohibiting conditions for firearm possession are modified by the presence of policies to prevent diversion.
Uses of Electronic Health Records for Public Health Surveillance to Advance Public Health
Authors: Birkhead Guthrie S. , Klompas Michael , Shah Nirav R.
Published: January 2015

Public health surveillance conducted by health departments in the United States has improved in completeness and timeliness owing to electronic laboratory reporting. However, the collection of detailed clinical information about reported cases, which is necessary to confirm the diagnosis, to understand transmission, or to determine disease-related risk factors, is still heavily dependent on manual processes. The increasing prevalence and functionality of electronic health record (EHR) systems in the United States present important opportunities to advance public health surveillance. EHR data have the potential to further increase the breadth, detail, timeliness, and completeness of public health surveillance and thereby provide better data to guide public health interventions. EHRs also provide a unique opportunity to expand the role and vision of current surveillance efforts and to help bridge the gap between public health practice and clinical medicine.
What Is Health Resilience and How Can We Build It?
Authors: Wulff Katharine , Donato Darrin , Lurie Nicole
Published: January 2015

Whether a community is in the path of a natural disaster, the target of an act of terror, or simply striving to meet the demands of increasingly dense urban populations, a community resilience paradigm can help communities and individuals not just to mitigate damage and heal, but to thrive. This article discusses experiences from recent, large-scale disasters to explore how community resilience might serve as a sustainable paradigm for organizing public health and medical preparedness, response, and recovery. By strengthening health systems, meeting the needs of vulnerable populations, and promoting organizational competence, social connectedness, and psychological health, community resilience encourages actions that build preparedness, promote strong day-to-day systems, and address the underlying social determinants of health. Thus, community resilience resonates with a wide array of stakeholders, particularly those whose work routinely addresses health, wellness, or societal well-being.
Using New Technologies to Improve the Prevention and Management of Chronic Conditions in Populations
Authors: Oldenburg Brian , Taylor C. Barr , O'Neil Adrienne , Cocker Fiona , Cameron Linda D.
Published: January 2015

Lifestyle factors are important in the development of chronic diseases, such as heart disease, respiratory disease, and diabetes, and chronic disease risk can be reduced by changes in lifestyle behaviors linked to these conditions. The use of mass media and community-wide strategies targeting these behaviors has been extensively evaluated since the 1970s. This review summarizes some examples of interventions and their use of media conducted within the old communications landscape of the 1970s and 1980s and the key lessons learned from their design, implementation, and evaluation. We then consider the potential and evidence base for using contemporary technology applications and platforms—within the new communications landscape—to improve the prevention and management of lifestyle-related chronic diseases in the future. We discuss the implications and adaptation of lessons derived from the ways in which new technologies are being used in commercial and political contexts and their relevance for public health. Finally, we consider some recent examples of applying new technologies to public health issues and consider some of the challenges in this rapidly developing field.
Programming in Vienna Fortran
Authors: Chapman Barbara , Mehrotra Piyush , Zima Hans
Published: January 2015

Exploiting the full performance potential of distributed memory machines requires a careful distribution of data across the processors. Vienna Fortran is a language extension of Fortran which provides the user with a wide range of facilities for such mapping of data structures. In contrast to current programming practice, programs in Vienna Fortran are written using global data references. Thus, the user has the advantages of a shared memory programming paradigm while explicitly controlling the data distribution. In this paper, we present the language features of Vienna Fortran for FORTRAN 77, together with examples illustrating the use of these features.
C Versus Fortran‐77 for Scientific Programming
Authors: MacDonald Tom
Published: January 2015

The predominant programming language for numeric and scientific applications is Fortran‐77 and supercomputers are primarily used to run large‐scale numeric and scientific applications. Standard C* is not widely used for numerical and scientific programming, yet Standard C provides many desirable linguistic features not present in Fortran‐77. Furthermore, the existence of a standard library and preprocessor eliminates the worst portability problems. A comparison of Standard C and Fortran‐77 shows several key deficiencies in C that reduce its ability to adequately solve some numerical problems. Some of these problems have already been addressed by the C standard but others remain. Standard C with a few extensions and modifications could be suitable for all numerical applications and could become more popular in supercomputing environments.
Object‐Oriented Heterogeneous Database for Materials Science
Authors: Hansen David , Maier David , Stanley James , Walpole Jonathan
Published: January 2015

As a part of the scientific database research underway at the Oregon Graduate Institute, we are collaborating with materials scientists in the research and development of an extensible modeling and computation environment for materials science. Materials scientists are prolific users of computers for scientific research. Modeling techniques and algorithms are well known and refined, and computerized databases of chemical and physical property data abound. However, applications are typically developed in isolation, using information models specifically tailored for the needs of each application. Furthermore, available computerized databases in the form of CDs and on‐line information services are still accessed manually by the scientist in an off‐line fashion. Thus researchers are repeatedly constructing and populating new custom databases for each application. The goal of our research is to bridge this gulf between applications and sources of data. We believe that object‐oriented technology in general and data‐bases in particular, provide powerful tools for transparently bridging the gap between programs and data. An object‐oriented database that not only manages data generated by user applications, but also provides access to relevant external data sources can be used to bridge this gap. An object‐oriented database for materials science data is described that brings together data from heterogeneous non‐object‐oriented sources and formats, and presents the user with a single, uniform object‐oriented schema that transparently integrates these diverse databases. A unique multilevel architecture is presented that provides a mechanism for efficiently accessing both heterogeneous external data sources and new data stored within the database.