bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing serum responses to acute feedings of an extensively hydrolyzed whey protein concentrate versus a native whey protein concentrate in rats: a metabolomics approach
Authors: Roberts Michael D. , Cruthirds Clayton L. , Lockwood Christopher M. , Pappan Kirk , Childs Thomas E. , Company Joseph M. , Brown Jacob D. , Toedebusch Ryan G. , Booth Frank W.
Published: July 2013

We examined how gavage feeding extensively hydrolyzed whey protein (WPH) versus a native whey protein concentrate (WPC) transiently affected serum biochemical profiles in rodents. Male Wistar rats (250–300 g) were 8 h fasted and subsequently fed isonitrogenous amounts of WPH or WPC, or remained unfed (control). Animals were sacrificed 15 min, 30 min, and 60 min post-gavage for serum extraction, and serum was analyzed using untargeted global metabolic profiling via gas chromatography/mass spectrometry (MS) and liquid chromatography/MS/MS platforms. We detected 333 serum metabolites amongst the experimental and control groups. Both WPH and WPC generally increased amino acids (1.2–2.8-fold), branched-chain amino acids (1.2–1.7-fold), and serum di- and oligo-peptides (1.1–2.7-fold) over the 60 min time course compared with control (q < 0.05). However, WPH increased lysine (false discovery rate using a q-value <0.05) and tended to increase isoleucine and valine 15 min post-feeding (q < 0.10) as well as aspartylleucine 30 min post-feeding compared with WPC (q < 0.05). While both protein sources led to a dramatic increase in free fatty acids compared with control (up to 6-fold increases, q < 0.05), WPH also uniquely resulted in a 30 min post-feeding elevation in free fatty acids compared with WPC (q < 0.05), an effect which may be due to the robust 30 min postprandial increase in epinephrine in the WPH cohort. These data provide a unique postprandial time-course perspective on how WPH versus WPC feedings affect circulating biochemicals and will guide future research comparing these 2 protein sources.
U–Pb zircon ages and field relationships of Archean basement and Proterozoic intrusions, south-central Wopmay Orogen, NWT: implications for tectonic assignments
Authors: Jackson V.A. , van Breemen O. , Ootes L. , Bleeker W. , Bennett V. , Davis W.J. , Ketchum J.W.F. , Smar L.
Published: July 2013

New field and U–Pb zircon data from the south-central Wopmay Orogen (south of 65°N) establish crystallization ages of basement and plutonic phases and bring to the forefront questions on the architecture of the orogen. The complex and extensive >3300–2575 Ma basement domain was derived from the adjacent Slave craton. Paleoproterozoic supracrustal rocks, dominated by an extensive pelitic–psammitic sequence with basal arenite, conglomerate, and carbonate, unconformably overlie this basement. Pre- to post-kinematic Paleoproterozoic plutons intrude both basement and overlying strata and crystallized at 1877, 1867–1862, and 1858–1850 Ma. The first pulse of plutonism constrains an early generation of metamorphism and deformation to younger than 1877 Ma and is corroborated by metamorphic zircon in Archean basement. The interval from 1867 to 1862 Ma brackets ductile deformation in granite and granodiorite intrusions; although corresponding structure in the metasedimentary strata is equivocal. Post-kinematic ca. 1858–1850 Ma plutons were coeval with localized high-grade metamorphism and concomitant recrystallization of Archean basement. The absence of older (>1880 Ma) phases of the Hepburn intrusive suite in south-central Wopmay Orogen demonstrates a previously unrecognized north–south plutonic dichotomy and that the historical assignment of Calderian metamorphism to ca. 1885 Ma may be too old. The designation of part of the area to a klippe of Hottah terrane is not compatible with field and zircon age data which shows that basement and the overlying strata can be tied directly to the Slave craton. The study raises questions regarding the tectonic relationship between the Hottah terrane and Slave craton.
Factors influencing ultraviolet radiation dose to developing frogs in northern vernal pools
Authors: Olker Jennifer H. , Johnson Lucinda B. , Axler Richard P. , Johnson Catherine M.
Published: August 2013

Ultraviolet-B (UV-B) radiation exposure is one hypothesized mechanism explaining amphibian population declines and malformations, but it is rarely quantified in amphibian habitats. We measured spatial and temporal variations in northern vernal pools with UV-B attenuation through the water column, incident UV-B across pool surfaces and seasons, and cumulative UV-B dose. Atmospheric, local, and landscape effects were compared with variances across spatial and temporal scales, plus influence on exposure risk. Risk was evaluated using published reports on detrimental levels for amphibian survival and health, with life history and behavior of vernal pool breeding Rana sylvatica L. (wood frog). Pools were exposed to sufficiently high UV-B at or near the surface for developing amphibians to be at risk of reduced survival, altered growth, and malformation. Atmospheric conditions, vegetative cover, and water column properties significantly influenced UV-B levels, with oviposition and larval behavior controlling actual embryonic and larval exposure. UV-B risk to vernal pool species is greater than predicted in previous studies. Given changes in light regimes, climate change, and forest harvesting, amphibian UV-B exposure could reach levels of great concern.
Genetic relationships of North American bears (Ursus) inferred from amplified fragment length polymorphisms and mitochondrial DNA sequences
Authors: Cronin M.A. , McDonough M.M. , Huynh H.M. , Baker R.J.
Published: July 2013

The three species of bears in North America, polar bears (Ursus maritimus Phipps, 1774), brown bears (Ursus arctos L., 1758), and black bears (Ursus americanus Pallas, 1780), have differentiated morphologies and nuclear and mitochondrial genomes. An exception is a paraphyletic mitochondrial DNA relationship and some nuclear gene lineages common to polar bears and a population of brown bears from islands in southeast Alaska. In this study, we quantified the genetic relationships of extant brown bears and black bears from Alaska and Montana, and polar bears from Alaska, with amplified fragment length polymorphisms (AFLP) and mtDNA cytochrome-b sequences. Bayesian cluster analyses of the AFLP data show each species is distinct. All brown bears, including those from the islands in southeast Alaska, cluster separately from polar bears, and black bears cluster separately from brown bears and polar bears. The mtDNA of polar bears and southeast Alaska island brown bears is paraphyletic as reported previously, but the species have different haplotypes. These data indicate that extant populations of brown bears and polar bears have separate nuclear and mitochondrial gene pools and are supported as species under the genetic species concept.
Comparing growth and maturity of sympatric Atlantic (Gadus morhua) and Greenland (Gadus ogac) cod in coastal Newfoundland
Authors: Knickle D.C. , Rose G.A.
Published: July 2013

Growth and maturity of two sympatric gadids were examined from 48 Atlantic (Gadus morhua L., 1758) and 42 Greenland (Gadus ogac Richardson, 1836) cod ranging from 17 to 74 cm in length collected from an inshore area of Trinity Bay, Newfoundland, Canada, during 2009 and 2010. Ages estimated from otolith readings ranged from 2 to 7 for both species. Age and size at 50% maturity differed between species, being 2.3 years and 28.2 cm for G. ogac and 4.6 years and 48.8 cm for G. morhua. von Bertalanffy growth models did not differ between species with parameters L∞ = 91 cm, k = 0.16 year−1, t0 = –0.02 years for G. ogac and L∞ = 112 cm, k = 0.13 year−1, t0 = 0.18 years for G. morhua. Length (L) – mass (W) relationships differed; W = 0.000005 kg·cm−b × L3.17 for G. ogac and W = 0.000011 kg·cm−b × L2.91 for G. morhua suggested slightly positive and negative allometric growth, respectively. For G. morhua, growth curves, length–mass relationships, and maturity rates did not differ between fish collected during this and earlier studies. Differences in maturity schedules and growth may decrease resource competition and help facilitate coexistence of these species.
RESOLUTIONS AND COHOMOLOGIES OF TORIC SHEAVES: THE AFFINE CASE
Authors: PERLING MARKUS
Published: August 2013

We study equivariant resolutions and local cohomologies of toric sheaves for affine toric varieties, where our focus is on the construction of new examples of indecomposable maximal Cohen–Macaulay modules of higher rank. A result of Klyachko states that the category of reflexive toric sheaves is equivalent to the category of vector spaces together with a certain family of filtrations. Within this setting, we develop machinery which facilitates the construction of minimal free resolutions for the smooth case as well as resolutions which are acyclic with respect to local cohomology functors for the general case. We give two main applications. First, over the polynomial ring, we determine in explicit combinatorial terms the ℤn-graded Betti numbers and local cohomology of reflexive modules whose associated filtrations form a hyperplane arrangement. Second, for the nonsmooth, simplicial case in dimension d ≥ 3, we construct new examples of indecomposable maximal Cohen–Macaulay modules of rank d – 1.
ONE-DIMENSIONAL QUANTUM LATTICE BOLTZMANN SCHEME FOR THE NONLINEAR DIRAC EQUATION
Authors: PALPACELLI SILVIA , ROMATSCHKE PAUL , SUCCI SAURO
Published: July 2013

We develop a quantum lattice Boltzmann (QLB) scheme for the Dirac equation with a nonlinear fermion interaction provided by the Nambu–Jona-Lasinio (NJL) model. Numerical simulations in 1 + 1 space-time dimensions, provide evidence of dynamic mass generation, through spontaneous breaking of chiral symmetry.
NUMERICAL SIMULATION ON FLOW IN COLUMN CHROMATOGRAPHY
Authors: YAMAMOTO KAZUHIRO , KOMIYAMA RYO , UMEMURA TOMONARI
Published: July 2013

Monolithic columns have attracted much attention as a novel platform for high throughput analysis, but there is little information about the fluid profile in the flow channels. In this paper, we presented our approach for the fluid simulation in column chromatography by the lattice Boltzmann method (LBM). To simulate the monolithic column system, the calculation domain was modeled by the 3D channel flow through sphere obstacles. Several types of porous structure were used, with uniform and nonuniform pores. Based on the simulations results, we discussed fluid flow and pressure variation for the optimization of the suitable structure for HPLC system.
LATTICE BOLTZMANN SIMULATION OF STEADY AND OSCILLATORY FLOWS IN LID-DRIVEN CUBIC CAVITY
Authors: MYNAM MAHESH , PATHAK AMAR DEEP
Published: July 2013

Flow in a three-dimensional lid-driven cavity (LDC) is studied using the lattice Boltzmann method (LBM) for various values of Reynolds number (Re). The 1000 Re flow is simulated on two grid sizes: viz. 2253and 3013. We further compute the Richardson extrapolated flow profiles. Our results agree quantitatively with the spectral simulation results. We observe a steady to oscillatory transition of the flow in the range of Re [1900, 2000].
MODELING THE IMPEDANCE OF NANOSTRUCTURED PV IN SIMULINK/MATLAB
Authors: HOUSHMAND MOHAMMAD , ZANDI MOHAMMAD. H. , GORJI NIMA E.
Published: August 2013

Impedance measurement is a common method to study the electrical properties of thin film photovoltaics. For the first time, we use the MATLAB/Simulink environment to extract the complex impedance of the nanostructured heterojunction solar cells. The impedance magnitude, phase and Nyquist plot of the PV are simulated in LTI Viewer and Impedance versus Frequency analysis tools of SimPower GUI block of Simulink. We examined a variety of the equivalent circuits consisting of capacitance, series and shunt resistances representing the solar cell structure. The model uses the parameters with values reported in the literature at room temperature and zero bias. The effect of the additional capacitance and resistances in the equivalent circuits on the impedance components of the cells is considered by Simulink environment.
ANALYSIS OF THE MELTING PROCESS OF THE 14-PARTICLE MORSE CLUSTER THROUGH THE ATOMIC EQUIVALENCE INDEXES
Authors: REN SHI-WEI , HAO YAN-ZHONG
Published: August 2013

In this paper, by using the standard microcanonical molecular-dynamics simulations, the melting processes of the 14-particle Morse clusters are investigated. The three steps melting process found in 2004 by one of the authors of this paper are analyzed further by the atomic equivalence indexes. The properties of the structure of the cluster in different melting processes are explored by the atomic equivalence indexes. It is found that in the melting process for most of the time the cluster keeps the basic structure frame similar to that in the solid-like state while there are very short time periods when the particles of the cluster exchange their locations.
THE ELECTRONIC TRANSPORT PROPERTIES IN NAPHTHOPYRAN-BASED OPTICAL MOLECULAR SWITCH WITH CARBON NANOTUBE ELECTRODES
Authors: XIA CAI-JUAN , ZHANG DE-HUA , ZHANG YING-TANG
Published: August 2013

By applying nonequilibrium Green's function (NEGF) formalism combined first-principles density functional theory (DFT), we investigate the electronic transport properties of optical molecular switch based on the naphthopyran molecule with two different single-walled carbon nanotube (SWCNT) electrodes. The molecule that comprises the switch can convert between the closed and open forms upon photoexcitation. Theoretical results show that these two forms exhibit very different conductance properties both in armchair and zigzag junction, which can realize the on and off states of the molecular switch. Meantime, the chirality of the SWCNT electrodes strongly affects the switching characteristics of the molecular junctions. The maximum value of on–off ratio can reach 292 at 1.6 V for the switch with zigzag SWCNT electrodes.
MODELING THE CONCENTRATIONS AND EFFICIENCIES FOR THE INTERACTING SPECIES OF PYROPHEOPHORBIDE METHYL ESTER-COPPER ASSOCIATION
Authors: AL-OMARI S.
Published: July 2013

The interaction between pyropheophorbide methyl ester (PPME) and Cu 2+ was investigated using UV-vis and fluorescence spectrscopy. Study of the binding interaction between PPME and Cu 2+ could contribute to understanding of its pharmacokinetics and pharmacodynamics. Parameters of the static and dynamic fluorescence quenching of PPME- Cu 2+ association were calculated at different temperatures. For binding site of 1:1 at 299 K, the static binding constant (kS), the static isosbestic concentration ([Formula: see text]), the dynamic binding constant (kD), and the dynamic isosbestic concentration ([Formula: see text]) are, respectively, 61 M-1, 0.0164 M, 75 M-1, and 0.0133 M. The concentrations and efficiencies of the intermediates species were modeled. Satisfactory correspondence between the experimental and calculated results was found.
CONSTRUCTION OF A HIGH TEMPERATURE TEG MEASUREMENT SYSTEM FOR THE EVALUATION OF THERMOELECTRIC OXIDE MODULES
Authors: POPULOH S. , TROTTMANN M. , BRUNKO O. C. , THIEL P. , WEIDENKAFF A.
Published: July 2013

A dedicated test stand was developed and built to characterize the efficiency, power output and open circuit voltage of various thermoelectric generators (TEGs) based on tellurides, heusler compounds and thermoelectric oxides. The test stand allows measurements of TEGs of sizes up to 4 cm × 4 cm at hot side temperatures up to 1150 K in different atmospheres. Special care was taken about the heat flux measurement by precise measurement of the temperature distribution within the reference block. In order to demonstrate the functionality of the test stand thermoelectric oxide modules (TOM) were built from n-type perovskite-type manganates and p-type cuprates. The modules were tested regarding their stability, maximum power output and efficiency at temperatures up to 1100 K. The TOMs withstand large temperature gradients and operated in ambient air yielding high power densities.
NANOPARTICLES FOR SKIN WOUND HEALING
Authors: PRZYBOROWSKI MELISSA , BERTHIAUME FRANCOIS
Published: July 2013

Over the past two decades, there has been a surge in the development of nanoparticle technologies for therapeutic applications. In the area of skin wound healing, silver nanoparticles have been long used as topical antibacterials, but new types of multifunctional nanosystems that can provide more comprehensive therapeutic effects on wounds are being rolled out. The ability to provide a reservoir of bioactive molecules that can be released over time is a feature of many of these systems, which is critically important for nonhealing wounds, where there often is a persistent bacterial load and a chronic lack of growth factors necessary for healing. A great advantage of nanosystems is that by virtue of their extremely small size, they can be easily incorporated into a wide variety of topical treatments that are currently available for use in the clinic. For example, nanoparticles can be easily introduced into decellularized skin products as well as other bioengineered skin substitutes. The design options available for the nanocarriers are very diverse, including encapsulating the drug in the particle's core or presenting it on the outside of the particle, which can also be decorated with a targeting agent, and the ability to change conformation in response to environmental cues (e.g., pH). These various design elements have been optimized differently to treat different types of wounds.
The application of outcrop-based research boreholes for reservoir modelling: potential, challenges and pitfalls
Authors: Luthi S. M. , Flint S. S.
Published: July 2013

Research boreholes drilled in outcrop studies of reservoir analogues can have two distinctly different objectives. One is to assess how the sequences observed on outcrops are represented in cores and wireline logs, an exercise that can form an important link between data retrieved from actual reservoirs and observations made on outcrops. The second objective is to obtain information on the lateral and vertical extensions of the exposed rock types and possible changes in lithofacies beyond the limits of exposure. This can provide improved insights into the three-dimensional (3D) architecture of the system and the 3D distribution of reservoir rock types. Additional information gained from research boreholes concerns lithofacies types prone to weathering such as shales; cores are generally less weathered than outcrops and therefore provide a fresher and often more representative appearance. Electrical borehole images are found to be particularly useful as they have a large dynamic range that makes subtle sedimentary structures more visible, and their 3D nature allows accurate determination of directional structures such as cross-bedding. The costs and logistics of drilling research boreholes are important issues to consider before embarking on such projects.
Proof-Directed Parallelization Synthesis by Separation Logic
Authors: Botinčan Matko , Dodds Mike , Jagannathan Suresh
Published: July 2013

We present an analysis which takes as its input a sequential program, augmented with annotations indicating potential parallelization opportunities, and a sequential proof, written in separation logic, and produces a correctly synchronized parallelized program and proof of that program. Unlike previous work, ours is not a simple independence analysis that admits parallelization only when threads do not interfere; rather, we insert synchronization to preserve dependencies in the sequential program that might be violated by a naïve translation. Separation logic allows us to parallelize fine-grained patterns of resource usage, moving beyond straightforward points-to analysis. The sequential proof need only represent shape properties, meaning we can handle complex algorithms without verifying every aspect of their behavior.

Our analysis works by using the sequential proof to discover dependencies between different parts of the program. It leverages these discovered dependencies to guide the insertion of synchronization primitives into the parallelized program, and to ensure that the resulting parallelized program satisfies the same specification as the original sequential program, and exhibits the same sequential behavior. Our analysis is built using frame inference and abduction, two techniques supported by an increasing number of separation logic tools.
Introduction to the special issue on interaction with smart objects
Authors: Schreiber Daniel , Luyten Kris , Mühlhäuser Max , Brdiczka Oliver , Hartman Melanie
Published: August 2013

Smart objects can be smart because of the information and communication technology that is added to human-made artifacts. It is not, however, the technology itself that makes them smart but rather the way in which the technology is integrated, and their smartness surfaces through how people are able to interact with these objects. Hence, the key challenge for making smart objects successful is to design usable and useful interactions with them. We list five features that can contribute to the smartness of an object, and we discuss how smart objects can help resolve the
simplicity-featurism paradox.
We conclude by introducing the three articles in this special issue, which dive into various aspects of smart object interaction: augmenting objects with projection, service-oriented interaction with smart objects via a mobile portal, and an analysis of input-output relations in interaction with tangible smart objects.
The 24th ACM Conference on Hypertext and Social Media (HT2013)
Authors: Trattner Christoph
Published: August 2013

This article provides a review of this year's ACM Hypertext and Social Media Conference (Hypertext). Hypertext 2013 was part of the First ACM European Computing Research Congress (ECRC 2013), which was co-located with the ACM SIGCHI Conference on Human Factors in Computing Systems (CHI 2013) and the ACM Web Science Conference 2013 (WebSci 2013) at the Palais des Congrès in Paris. The entire event attracted certainly around 4,000 participants from all over the world. As in 2012, this year the focus was on exploring, studying and shaping relationships between three major dimensions of links in hypertextual systems: people, data and documents. This year, Hypertext was organized by Gerd Stumme and Andreas Hotho and featured 16 full and 20 short papers oral presentations, three exciting workshops, two vibrant keynotes delivered by one of \the fathers of the Internet" Vinton Cerf (Google, USA) and by Denny Vrandečić (Wikimedia, Germany), and two social events with delicious French food and wine. This article reflects the authors personal view of Hypertext 2013 and may not represent the opinions of other individuals who attended the conference.
Interview with Jessica Rubart
Authors: Atzenbeck Claus
Published: August 2013

Dr. Jessica Rubart (http://www.jessicarubart.de) is professor for business information systems at the University of Applied Sciences Ostwestfalen-Lippe, Germany, and SIGWEB's current Newsletter Editor. She has a strong industry background as software architect, project manager, system analyst, and software developer. Her main research areas are flexible information systems, hypertext, groupware and knowledge management as well as software engineering.
Flicker
Authors: Petrica Paula , Izraelevitz Adam M. , Albonesi David H. , Shoemaker Christine A.
Published: July 2013

Future microprocessors may become so power constrained that not all transistors will be able to be powered on at once. These systems will be required to nimbly adapt to changes in the chip power that is allocated to general-purpose cores and to specialized accelerators.

This paper presents
Flicker
, a general-purpose multicore architecture that dynamically adapts to varying and potentially stringent limits on allocated power. The Flicker core microarchitecture includes deconfigurable
lanes
--horizontal slices through the pipeline--that permit tailoring an individual core to the running application with lower overhead than microarchitecture-level adaptation, and greater flexibility than core-level power gating.

To exploit Flicker's flexible pipeline architecture, a new online multicore optimization algorithm combines reduced sampling techniques, application of response surface models to online optimization, and heuristic online search. The approach efficiently finds a near-global-optimum configuration of lanes without requiring offline training, microarchitecture state, or foreknowledge of the workload. At high power allocations, core-level gating is highly effective, and slightly outperforms Flicker overall. However, under stringent power constraints, Flicker significantly outperforms core-level gating, achieving an average 27% performance improvement.
Microarchitectural mechanisms to exploit value structure in SIMT architectures
Authors: Kim Ji , Torng Christopher , Srinath Shreesha , Lockhart Derek , Batten Christopher
Published: July 2013

SIMT architectures improve performance and efficiency by exploiting control and memory-access structure across data-parallel threads. Value structure occurs when multiple threads operate on values that can be compactly encoded, e.g., by using a simple function of the thread index. We characterize the availability of control, memory-access, and value structure in typical kernels and observe ample amounts of value structure that is largely ignored by current SIMT architectures. We propose three microarchitectural mechanisms to exploit value structure based on compact affine execution of arithmetic, branch, and memory instructions. We explore these mechanisms within the context of traditional SIMT microarchitectures (GP-SIMT), found in general-purpose graphics processing units, as well as fine-grain SIMT microarchitectures (FG-SIMT), a SIMT variant appropriate for compute-focused data-parallel accelerators. Cycle-level modeling of a modern GP-SIMT system and a VLSI implementation of an eight-lane FG-SIMT execution engine are used to evaluate a range of application kernels. When compared to a baseline without compact affine execution, our approach can improve GP-SIMT cycle-level performance by 4-17% and can improve FG-SIMT absolute performance by 20-65% and energy efficiency up to 30% for a majority of the kernels.
DNA-based molecular architecture with spatially localized components
Authors: Muscat Richard A. , Strauss Karin , Ceze Luis , Seelig Georg
Published: July 2013

Performing computation inside living cells offers life-changing applications, from improved medical diagnostics to better cancer therapy to intelligent drugs. Due to its bio-compatibility and ease of engineering, one promising approach for performing in-vivo computation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement "circuits", discusses associated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing components. This paper proposes practical
spatial
isolation of components, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9]. We believe that it is time for the computer architecture community to take notice and contribute.
Navigating big data with high-throughput, energy-efficient data partitioning
Authors: Wu Lisa , Barker Raymond J. , Kim Martha A. , Ross Kenneth A.
Published: July 2013

The global pool of data is growing at 2.5 quintillion bytes per day, with 90% of it produced in the last two years alone [24]. There is no doubt the era of big data has arrived. This paper explores targeted deployment of hardware accelerators to improve the throughput and energy efficiency of large-scale data processing. In particular, data partitioning is a critical operation for manipulating large data sets. It is often the limiting factor in database performance and represents a significant fraction of the overall runtime of large data queries.

To accelerate partitioning, this paper describes a hardware accelerator for range partitioning, or HARP, and a hardware-software data streaming framework. The streaming framework offers a seamless execution environment for streaming accelerators such as HARP. Together, HARP and the streaming framework provide an order of magnitude improvement in partitioning performance and energy. A detailed analysis of a 32
nm
physical design shows 7.8 times the throughput of a highly optimized and optimistic software implementation, while consuming just 6.9% of the area and 4.3% of the power of a single Xeon core in the same technology generation.
Zombie memory: Extending memory lifetime by reviving dead blocks
Authors: Azevedo Rodolfo , Davis John D. , Strauss Karin , Gopalan Parikshit , Manasse Mark , Yekhanin Sergey
Published: July 2013

Zombie is an endurance management framework that enables a variety of error correction mechanisms to extend the lifetimes of memories that suffer from bit failures caused by wearout, such as phase-change memory (PCM). Zombie supports both single-level cell (SLC) and multi-level cell (MLC) variants. It extends the lifetime of blocks in working memory pages (primary blocks) by pairing them with spare blocks, i.e., working blocks in pages that have been disabled due to exhaustion of a single block's error correction resources, which would be 'dead' otherwise. Spare blocks adaptively provide error correction resources to primary blocks as failures accumulate over time. This reduces the waste caused by early block failures, making working blocks in discarded pages a useful resource. Even though we use PCM as the target technology, Zombie applies to any memory technology that suffers stuck-at cell failures.

This paper describes the Zombie framework, a combination of two new error correction mechanisms (ZombieXOR for SLC and ZombieMLC for MLC) and the extension of two previously proposed SLC mechanisms (ZombieECP and ZombieERC). The result is a 58% to 92% improvement in endurance for Zombie SLC memory and an even more impressive 11x to 17x improvement for ZombieMLC, both with performance overheads of only 0.1% when memories using prior error correction mechanisms reach end of life.
Election manipulation
Authors: Mossel Elchanan , Rácz Miklós Z.
Published: August 2013

We review recent research on quantitative versions of the Gibbard-Satterthwaite theorem, which analyze the average-case manipulability of elections. The main message of these results is that computational hardness cannot hide manipulations completely. We conclude with open problems.
The dining bidder problem
Authors: Paes Leme Renato , Syrgkanis Vasilis , Tardos Éva
Published: August 2013

Item bidding auctions are a line of research which provides a simple and often efficient alternative to traditional combinatorial auction design - in particular, they were inspired by real world auction houses, like eBay and Sotheby's. We survey the literature from a culinary perspective, offering an intuitive illustration of the welfare in simultaneous and sequential auctions. Welfare in simultaneous first and second price auctions is high when bidders have complement-free valuations. In contrast, sequential second price auctions can lead to bad outcomes due to signaling problems and even in the case of first price, a good outcome is only guaranteed for unit demand bidders. We give an intuitive interpretation of an example with bad welfare in sequential first price auctions with submodular bidders from Paes Leme, Syrgkanis and Tardos (SODA'12).
Setting equilibrium prices, approximately
Authors: Lucier Brendan
Published: August 2013

We outline recent results, positive and negative, on pricing indivisible goods to approximately maximize social welfare. We describe a relaxation of standard pricing problems in which a seller can bundle goods together prior to sale.
Back to original frugality
Authors: Velez Rodrigo A.
Published: August 2013

We review recent research on frugality of mechanisms for the procurement of a spanning network. Frugality here is defined as the ratio of the maximum price that can be charged to the buyer in some equilibrium to the true minimal cost. Previous negative results are qualified under natural restrictions in costs.
Role of coagulation in the recruitment of colon adenocarcinoma cells to thrombus under shear
Authors: Baker-Groberg Sandra M. , Itakura Asako , Gruber András , McCarty Owen J. T.
Published: August 2013

Colorectal cancer metastases can appear on the peritoneum and in lymph nodes, liver, and lungs, suggesting both hematogenous and lymphatic spreading of the primary tumor. While antithrombotic agents have been shown to reduce both long-term incidence and metastasis, the role of coagulation in facilitating metastasis is ill defined. We investigated the kinetics and molecular mechanisms of metastatic colon adenocarcinoma cell recruitment to thrombi under shear flow, ex vivo. Platelet aggregates were formed by perfusing citrated anticoagulated whole blood over immobilized fibrinogen or fibrillar collagen. Thrombi were formed by perfusing recalcified whole blood over fibrinogen or fibrillar collagen in the presence of coagulation. Cultured colon adenocarcinoma cells (SW620) were perfused either during or following platelet aggregate or thrombus formation. The degree of transient tumor cell interactions (recruitment, rolling, and release) and the number of firmly adhered tumor cells were quantified using fluorescence microscopy. Platelet aggregates and thrombi formed on either fibrinogen- or fibrillar-collagen supported SW620 cell interactions and adhesion under shear. Thrombi or fibrin supported a greater degree of SW620 cell interactions and adhesion compared with platelet aggregates or fibrinogen, respectively, demonstrating that coagulation promoted SW620 cell recruitment under shear. Interestingly, in the absence of anticoagulation, we observed SW620 preferentially binding to thrombus-bound polymorphonuclear leukocytes (PMNs). The addition of purified PMNs to thrombi resulted in a doubling of the number of interacting and bound SW620 cells. Since thrombi often accumulate and activate leukocytes, our findings suggest that leukocytes may play a role in localizing metastases to sites of thrombogenesis.
Real-time endocytosis imaging as a rapid assay of ligand-GPCR binding in single cells
Authors: Zheng Liang-Hong , Wang Chang-He , Shang Shu-Jiang , Zhang Xiao-Yu , Wang Ye-Shi , Wu Qi-Hui , Hu Mei-Qin , Chai Zu-Yin , Wu Xi , Zheng Hui , Zhang Chen , Wang Lie-Cheng , Xiong Wei , Zhou Zhuan
Published: August 2013

Most G protein-coupled receptors (GPCRs) do not generate membrane currents in response to ligand-receptor binding (LRB). Here, we describe a novel technique using endocytosis as a bioassay that can detect activation of a GPCR in a way analogous to patch-clamp recording of an ion channel in a living cell. The confocal imaging technique, termed FM endocytosis imaging (FEI), can record ligand-GPCR binding with high temporal (second) and spatial (micrometer) resolution. LRB leads to internalization of an endocytic vesicle, which can be labeled by a styryl FM dye and visualized as a fluorescent spot. Distinct from the green fluorescence protein-labeling method, FEI can detect LRB endocytosis mediated by essentially any receptors (GPCRs or receptors of tyrosine kinase) in a native cell/cell line. Three modified versions of FEI permit promising applications in functional GPCR studies and drug screening in living cells: 1) LRB can be recorded in “real time” (time scale of seconds); 2) internalized vesicles mediated by different GPCRs can be discriminated by different colors; and 3) a high throughput method can screen ligands of a specific GPCR.
Sex differences in the physiology of eating
Authors: Asarian Lori , Geary Nori
Published: August 2013

Hypothalamic-pituitary-gonadal (HPG) axis function fundamentally affects the physiology of eating. We review sex differences in the physiological and pathophysiological controls of amounts eaten in rats, mice, monkeys, and humans. These controls result from interactions among genetic effects, organizational effects of reproductive hormones (i.e., permanent early developmental effects), and activational effects of these hormones (i.e., effects dependent on hormone levels). Male-female sex differences in the physiology of eating involve both organizational and activational effects of androgens and estrogens. An activational effect of estrogens decreases eating 1) during the periovulatory period of the ovarian cycle in rats, mice, monkeys, and women and 2) tonically between puberty and reproductive senescence or ovariectomy in rats and monkeys, sometimes in mice, and possibly in women. Estrogens acting on estrogen receptor-α (ERα) in the caudal medial nucleus of the solitary tract appear to mediate these effects in rats. Androgens, prolactin, and other reproductive hormones also affect eating in rats. Sex differences in eating are mediated by alterations in orosensory capacity and hedonics, gastric mechanoreception, ghrelin, CCK, glucagon-like peptide-1 (GLP-1), glucagon, insulin, amylin, apolipoprotein A-IV, fatty-acid oxidation, and leptin. The control of eating by central neurochemical signaling via serotonin, MSH, neuropeptide Y, Agouti-related peptide (AgRP), melanin-concentrating hormone, and dopamine is modulated by HPG function. Finally, sex differences in the physiology of eating may contribute to human obesity, anorexia nervosa, and binge eating. The variety and physiological importance of what has been learned so far warrant intensifying basic, translational, and clinical research on sex differences in eating.
Temporal relationships of blood pressure, heart rate, baroreflex function, and body temperature change over a hibernation bout in Syrian hamsters
Authors: Horwitz Barbara A. , Chau Sat M. , Hamilton Jock S. , Song Christine , Gorgone Julia , Saenz Marissa , Horowitz John M. , Chen (陳昭吟) Chao-Yin
Published: August 2013

Hibernating mammals undergo torpor during which blood pressure (BP), heart rate (HR), metabolic rate, and core temperature (TC) dramatically decrease, conserving energy. While the cardiovascular system remains functional, temporal changes in BP, HR, and baroreceptor-HR reflex sensitivity (BRS) over complete hibernation bouts and their relation to TCare unknown. We implanted BP/temperature telemetry transmitters into Syrian hamsters to test three hypotheses: H-1) BP, HR, and BRS decrease concurrently during entry into hibernation and increase concurrently during arousal; H-2) these changes occur before changes in TC; and H-3) the pattern of changes is consistent over successive bouts. We found: 1) upon hibernation entry, BP and HR declined before TCand BRS, suggesting baroreflex control of HR continues to regulate BP as the BP set point decreases; 2) during the later phase of entry, BRS decreased rapidly whereas BP and TCfell gradually, suggesting the importance of TCin further BP declines; 3) during torpor, BP slowly increased (but remained relatively low) without changes in HR or BRS or increased TC, suggesting minimal baroreflex or temperature influence; 4) during arousal, increased TCand BRS significantly lagged increases in BP and HR, consistent with establishment of tissue perfusion before increased TC/metabolism; and 5) the temporal pattern of these changes was similar over successive bouts in all hamsters. These results negate H-1, support H-2 with respect to BP and HR, support H-3, and indicate that the baroreflex contributes to cardiovascular regulation over a hibernation bout, albeit operating in a fundamentally different manner during entry vs. arousal.
5-Aminolevulinic acid combined with ferrous iron induces carbon monoxide generation in mouse kidneys and protects from renal ischemia-reperfusion injury
Authors: Hou Jiangang , Cai Songjie , Kitajima Yuya , Fujino Masayuki , Ito Hidenori , Takahashi Kiwamu , Abe Fuminori , Tanaka Tohru , Ding Qiang , Li Xiao-Kang
Published: August 2013

Renal ischemia reperfusion injury (IRI) is a major factor responsible for acute renal failure. An intermediate in heme synthesis, 5-aminolevulinic acid (5-ALA) is fundamental in aerobic energy metabolism. Heme oxygenase (HO)-1 cleaves heme to form biliverdin, carbon monoxide (CO), and iron (Fe2+), which is used with 5-ALA. In the present study, we investigated the role of 5-ALA in the attenuation of acute renal IRI using a mouse model. Male Balb/c mice received 30 mg/kg 5-ALA with Fe2+48, 24, and 2 h before IRI and were subsequently subjected to bilateral renal pedicle occlusion for 45 min. The endogenous CO concentration of the kidneys from the mice administered 5-ALA/Fe2+increased significantly, and the peak concentrations of serum creatinine and blood urea nitrogen decreased. 5-ALA/Fe2+treatments significantly decreased the tubular damage and number of apoptotic cells. IRI-induced renal thiobarbituric acid-reactive substance levels were also significantly decreased in the 5-ALA/Fe2+group. Furthermore, mRNA expression of HO-1, TNF-α, and interferon-γ was significantly increased after IRI. Levels of HO-1 were increased and levels of TNF-α and interferon-γ were decreased in the 5-ALA/Fe2+-pretreated renal parenchyma after IRI. F4/80 staining showed reduced macrophage infiltration, and TUNEL staining revealed that there were fewer interstitial apoptotic cells. These findings suggest that 5-ALA/Fe2+can protect the kidneys against IRI by reducing macrophage infiltration and decreasing renal cell apoptosis via the generation of CO.
Redundancy gains in retinotopic cortex
Authors: Shim Won Mok , Jiang Yuhong V. , Kanwisher Nancy
Published: August 2013

It is widely claimed that interactions among simultaneously presented visual stimuli are suppressive and that these interactions primarily occur when stimuli fall within the same receptive field ( Desimone and Duncan 1995 ). Here, we show evidence for a novel form of interaction between simultaneously presented but distant stimuli that does not fit either pattern. To examine interactions between simultaneously presented stimuli, we measure the response to a single stimulus as a function of whether or not other stimuli are also presented simultaneously, and we further ask how the response to a given stimulus is affected by whether the simultaneously present stimuli are identical or different from each other. Our method reveals a new phenomenon of “redundancy gain:” the visual response to a stimulus is higher when accompanied by identical stimuli than when that stimulus is presented alone, even though the stimuli are displayed in separate visual quadrants. This pattern is observed throughout the visual hierarchy, including V1 and V2, and we show that it is distinct from the well-known simultaneous suppression effect (Kastner et al. 1998). We propose that the redundancy gain in early retinotopic cortex results from feedback from higher visual areas and may underlie perceptual averaging and other ensemble coding phenomena observed behaviorally.
Stimulus-specific adaptation in auditory thalamus of young and aged awake rats
Authors: Richardson Ben D. , Hancock Kenneth E. , Caspary Donald M.
Published: August 2013

Novel stimulus detection by single neurons in the auditory system, known as stimulus-specific adaptation (SSA), appears to function as a real-time filtering/gating mechanism in processing acoustic information. Particular stimulus paradigms allowing for quantification of a neuron's ability to detect novel or deviant stimuli have been used to examine SSA in the inferior colliculus, medial geniculate body (MGB), and auditory cortex of anesthetized rodents. However, the study of SSA in awake animals is limited to auditory cortex. The present study used individually advanceable tetrodes to record single-unit responses from auditory thalamus (MGB) of awake young adult and aged Fischer Brown Norway (FBN) rats to 1) examine the presence of SSA in the MGB of awake rats and 2) determine whether SSA is altered by aging in MGB. MGB single units in awake FBN rats displayed SSA in response to two stimulus paradigms: the oddball paradigm and a random blocked/interleaved presentation of a set of frequencies. SSA levels were modestly, but nonsignificantly, increased in the nonlemniscal regions of the MGB and at lower stimulus intensities, where 27 of 57 (47%) young adult MGB units displayed SSA. The present findings provide the initial description of SSA in the MGB of awake rats and support SSA as being qualitatively independent of arousal level or anesthetized state. Finally, contrary to previous studies in auditory cortex of anesthetized rats, MGB units in aged rats showed SSA levels indistinguishable from SSA levels in young adult rats, suggesting that SSA in MGB was not impacted by aging in an awake preparation.
Urine Biochemistry in the Early Postoperative Period after Cardiac Surgery: Role in Acute Kidney Injury Monitoring
Authors: Maciel Alexandre Toledo , Vitório Daniel
Published: July 2013

We have recently suggested that sequential urine electrolyte measurement in critically ill patients may be useful in monitoring kidney function. Cardiac surgery is one of the leading causes of acute kidney injury (AKI) in the intensive care unit (ICU). In this paper, we describe the sequential behavior of urine electrolytes in three patients in the early (first 60 hours) postoperative period after cardiac surgery according to AKI status: no AKI, transient AKI, and persistent AKI. We have found that the patient with no AKI had stable and high concentrations of sodium (NaU) and chloride (ClU) in sequential spot samples of urine. AKI development was characterized in the other two patients by decreases in NaU and ClU, which have started early after ICU admission. Transient AKI was marked by also transient and less severe decreases in NaU and ClU. Persistent AKI was marked by the less favorable clinical course with abrupt and prolonged declines in NaU and ClU values. These electrolytes in urine had a behavior like a “mirror image” in comparison with that of serum creatinine. We suggest that sequential urine electrolytes are useful in monitoring acute kidney injury development in the early postoperative period after cardiac surgery.
Microscopic Studies of Various Sizes of Gold Nanoparticles and Their Cellular Localizations
Authors: Boyoglu Cemil , He Qingwen , Willing Gerold , Boyoglu-Barnum Seyhan , Dennis Vida A. , Pillai Shreekumar , Singh Shree R.
Published: July 2013

Gold nanoparticles (GNPs) are widely used in biological and clinical applications due to their favorable chemical and optical properties. GNPs can be used for drug delivery to targeted cells. In addition, GNPs serve as ideal probes for biological and cell imaging applications. Recent studies indicate that the size diversity of GNPs plays an important role in targeting cellular components for biomedical applications. In this study, we conducted a series of studies using different sizes of gold nanoparticles, including 3, 10, 25, and 50 nm, to determine the effect of size variations on their intracellular localizations. Our cytotoxicity studies of GNPs into the HEp-2 cells using MTT assay indicated that 3 nm GNPs possess the highest toxicity. We exposed HEp-2 cells with various sizes of gold nanoparticles for different time intervals (1, 2, 4, 12, and 24 h) followed by imaging using scanning electron microscope (SEM) and atomic force microscope (AFM). Our SEM and AFM results showed that, after 1 hr incubation, 3 and 10 nm gold nanoparticles entered the nucleus, whereas 25 and 50 nm particles accumulated around the nucleus. As the time of exposure increased, GNPs entered the cells and accumulated in the cytosol and nucleus based solely on their sizes.