bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison Between Numerical and Experimental Dynamic Coefficients of a Hybrid Aerostatic Bearing
Authors: Amine Hassini Mohamed , Arghir Mihai , Frocot Manuel
Published: October 2012

Hybrid journal bearings have been considered for many years as a possible replacement for ball bearings in turbopumps used by the aerospace industry. Due to flow regimes dominated by inertia and due to the nature of the lubricant (cryogenic fluids), the prediction of the linearized dynamic coefficients in these bearings must be based on the compressible bulk-flow equations. Theoretical models based on these equations were validated for hybrid bearings working with water or for liquid or gas annular seals. Validations for hybrid compressible bearings are missing. Experimental data obtained for an air lubricated hybrid aerostatic bearing designed with shallow pockets were recently presented; the data consist of linearized dynamic coefficients obtained for rotation speeds up to 50 krpm and up to 7 bars feeding pressure. The present work introduces a consolidated numerical approach for predicting static and linearized dynamic characteristics. Theoretical predictions are based on bulk flow equations in conjunction with CFD analysis. It was found that, for a given feeding pressure, the value of the pressure downstream the orifice has a major influence on all results. Special care was then taken to describe the complex flow in the feeding system and the orifice. Three dimensional CFD was employed because the bulk-flow equations are inappropriate in this part of the bearing. The pressure downstream the orifice stemming from CFD results and the feeding pressure were next imposed in the bulk flow model and the equivalent area of the orifice was obtained from the numerical solution of the steady flow in the bearing. Since the pockets of the hybrid bearing are shallow, this equivalent area is considered as being the harmonic average of the orifice cross section area and of the cylindrical curtain area located between the orifice and the rotor. The comparisons between theoretical dynamic coefficients and experimental data validated this approach of the equivalent area of the orifice.
Implementation of an Automated Peripheral Resistance Device in a Mock Circulatory Loop With Characterization of Performance Values Using Simulink Simscape and Parameter Estimation
Authors: Taylor Charles E. , Miller Gerald E.
Published: October 2012

Accurate peripheral resistance simulation in a mock circulatory loop is critical to the evaluation of ventricular assist devices and heart valves. Implementation of an automated device that is capable of accurate resistance settings and precise reproduction of cardiovascular parameters allows for improved construction of experimental conditions within a mock circulatory loop. A mock circulatory loop resistor that employs a proportional valve design is proposed; a piston extending into the flow path to produce a resistance to flow. Real-time position feedback of the piston is used to determine orifice size, providing resolution in the change of resistance over time. Characterization of the physical system with The MathWorks SIMULINK™ SIMSCAPE™ block set allowed the determination of objective device parameters; the discharge coefficient and critical Reynolds number. The determination of these values was achieved utilizing the SIMULINK™ Parameter Estimation™ tool, experimental data, and a computational plant model of the experimental setup. With this information, an accurate computational model of the resistance device is presented for use in determining resistance settings in silico prior to implementation in the mock circulatory loop. Experimental in vitro trials verified the repeatability of the automated resistor performance by means of a staircase testing of piston position during several different continuous flow rates of a glycerin/water solution.
On the kinetics of spatial atomic layer deposition
Authors: Poodt Paul , van Lieshout Joep , Illiberi Andrea , Knaapen Raymond , Roozeboom Fred , van Asten Almie
Published: October 2012

Spatial atomic layer deposition (ALD) is a promising technology for high deposition rate and high-throughput ALD that can be used for roll-to-roll and large-area applications. In an ideal spatial ALD reactor, the design of the injector should be tuned to the deposition kinetics of the ALD reaction, requiring an in-depth knowledge of the dependencies of the growth per cycle (GPC) on the main kinetic parameters. The authors have investigated the deposition kinetics of spatial ALD of alumina from trimethylaluminum and H2O at atmospheric pressure. A kinetic model was developed, which describes the growth per cycle as a function of the main kinetic parameters. The observation of a √t time dependency in the GPC indicates that precursor diffusion to substrate is rate limiting. Next to a fundamental insight into the kinetics of atmospheric pressure spatial ALD, this model can be used for design optimization of new spatial ALD reactors. Furthermore, the model shows that the maximum alumina deposition rates obtainable with spatial ALD are in the order of several nm/s.
Direct observation of hopping and merging of single Au adatoms to form dimers on Si(111)-(7 × 7)
Authors: Zhang Lei , Jeon Yujin , Shim Hyungjoon , Lee Geunseop
Published: October 2012

Au single adatoms and dimers were imaged on Si(111)-(7 × 7) at different temperatures and bias voltages using a variable-temperature scanning tunneling microscope. At room temperature (RT), a single Au adatom induces sharp highlighted triangular features in the half unit cells (HUCs) of Si(111)-(7 × 7). These triangular features become fuzzy at temperatures lower than 225 K, as a result of the reduced moving speed of the single Au adatoms inside the HUCs. The formation of an Au adatom dimer was directly observed at RT when a single Au adatom in a HUC jumped into a neighboring HUC that already contained a single Au adatom. The Au adatom dimer appears either as a noisy feature in the central area of the HUC defined by three Si center adatoms or as a bright protrusion located close to a corner Si adatom site at RT. It was observed that a noisy feature also can change into a bright protrusion, inducing charge redistribution in the nearby Si adatoms in both the occupied and neighboring HUCs.
Fabrication of polymeric substrates with micro- and nanoscale topography bioimprinted at progressive cell morphologies
Authors: Murray Lynn M. , Nock Volker , Alkaisi Maan M. , Lee Joanne J. M. , Woodfield Tim B. F.
Published: October 2012

This work introduces a novel process for the fabrication of polymer cell culture substrates containing physical topography based on timepoint specific cell phenotype replicas. Bioimprinting of human nasal chondrocyte at different cell adhesion time points was used to demonstrate the nanoscale replication process. Atomic force microscopy confirmed morphology progression at 1, 6, 12, and 24 h timepoints corresponding to dedifferentiation of the chondrocytes to fibroblast-like phenotype. Topographical analysis of the imprinted substrates yielded an inverse relationship between surface coverage, increasing from 11% to 87%, and maximum average pattern depth, decreasing from 1.2 μm to 430 nm. Methacrylate bioimprint features were successively replicated into a transitional polydmethylsiloxane mold used as an intermediate for further replication into polystyrene by a high-throughput embossing method. Substrates fabricated with this process have applications in stem cell engineering, regenerative medicine, and implantable devices.
“Cheers for Rates of Change” — An Introductory Lab Used to Relate Graphs to Physical Systems
Authors: Forrest Doug , Whalen Mary Battershell
Published: October 2012

Students entering physics courses in high school have seen graphs for years in math and science classes, but often do not have a deep understanding of the physical meaning of the graphs. This introductory activity is designed to allow students to collect data for a real world or physical situation (the height versus volume of water held in everyday drinking glasses), and interpret the meaning of the graph and how it describes the physical situation. This activity is well suited for students who don't have much physics knowledge. It uses familiar objects to start developing the skills of making and interpreting graphs and then relating them to the physical situations they analyze. These skills are used heavily all year in our physics classes, which are based on the Modeling Instruction in Physics framework developed at Arizona State University.1
And the 2011 Nobel Prize in Physics Goes to …The Accelerating Universe!
Authors: Hobson Art
Published: October 2012

The 5000-year-old remains of Stonehenge, in England, testify to humankind's reverence for the stars. Humans hauled four-ton stones from as far away as 240 km to make these monuments. They are the remains of a larger structure used for religious purposes and to predict astronomical events such as solstices, equinoxes, and perhaps even eclipses, an impressive feat for people who did not use writing. Eclipses occur in an irregular and apparently random pattern that repeats itself only over a 56-year cycle. Even to have been aware that a repeated pattern exists required enormous dedication and attention to detail.
Acoustic Resonators
Authors: Greenslade Thomas B.
Published: October 2012

Recently my collection of historical physics teaching apparatus was given a group of 19th-century tuning forks on resonant boxes. Figure 1 shows the smallest fork sitting on the largest one. The large tuning fork oscillates at 128 Hz and has a resonator that is 57.9 cm long. The small fork has a frequency 10 times higher, but its resonator has a length of 11.0 cm instead of the 5.8 cm that simple scaling would suggest. How is this possible?
Analyzing spring pendulum phenomena with a smart-phone acceleration sensor
Authors: Kuhn Jochen , Vogt Patrik
Published: October 2012

This paper describes two further pendulum experiments using the acceleration sensor of a smartphone in this column (for earlier contributions concerning this topic, including the description of the operation and use of the acceleration sensor, see Refs. 1 and 2). In this paper we focus on analyzing spring pendulum phenomena. Therefore two spring pendulum experiments will be described in which a smartphone is used as a pendulum body and SPARKvue3 software is used in conjunction with an iPhone or an iPod touch, or the Accelogger4 app for an Android device.1,2 As described in Ref. 1, the values measured by the smartphone are subsequently exported to a spreadsheet application (e.g., MS Excel) for analysis.
“Small” schools versus “big” schools: Anecdotal notes of a second-year physics teacher
Authors: Pudder David
Published: October 2012

Last spring I was just finishing up the second year of my teaching career. I was fortunate enough to be teaching physics and physical science at an academic magnet school located in southern West Virginia. The previous year, I had the opportunity to teach mathematics and science at a comprehensive high school located in northern West Virginia—close to the border of Pennsylvania. When I take a look back at my last two years of teaching, I can see many similarities and many differences. I see positives as well as negatives. However, if you were to ask me what the biggest difference was between last year and the one before, I would most certainly reply the size and locality of schools.
Pitch strength of noise-vocoded harmonic tone complexes in normal-hearing listeners
Authors: Shofner William P. , Campbell Jeannine
Published: October 2012

To study the role of harmonic structure in pitch perception, normal-hearing listeners were tested using noise-vocoded harmonic tone complexes. When tested in a magnitude judgment procedure using vocoded versions generated with 2–128 channels, judgments of pitch strength increased systematically as the number of channels increased and reflected acoustic cues based on harmonic peak-to-valley ratio, but not cues based on periodicity strength. When tested in a fundamental frequency discrimination task, listeners correctly recognized the direction of pitch change with as few as eight noise-vocoded channels. The results suggest that spectral processing contributes substantially to pitch perception in normal-hearing listeners.
A Dynamical-Systems View of Stem Cell Biology
Authors: Furusawa Chikara , Kaneko Kunihiko
Published: October 2012

During development, cells undergo a unidirectional course of differentiation that progressively decreases the number of cell types they can potentially become. Stem cells, however, keep their potential to both proliferate and differentiate. A very important issue then is to understand the characteristics that distinguish stem cells from other cell types and allow them to conduct stable proliferation and differentiation. Here, we review relevant dynamical-systems approaches to describe the state transition between stem and differentiated cells, with an emphasis on fluctuating and oscillatory gene expression levels, as these represent the specific properties of stem cells. Relevance between recent experimental results and dynamical-systems descriptions of stem cell differentiation is also discussed.
An Ancient Core Dynamo in Asteroid Vesta
Authors: Fu Roger R. , Weiss Benjamin P. , Shuster David L. , Gattacceca Jérôme , Grove Timothy L. , Suavet Clément , Lima Eduardo A. , Li Luyao , Kuan Aaron T.
Published: October 2012

Vesta to the Core

Vesta is one of the largest bodies in the main asteroid belt. Unlike most other asteroids, which are fragments of once larger bodies, Vesta is thought to have survived as a protoplanet since its formation at the beginning of the solar system (see the Perspective by
Binzel
, published online 20 September). Based on data obtained with the Gamma Ray and Neutron Detector aboard the Dawn spacecraft,

Prettyman
et al.

(p.
242
, published online 20 September) show that Vesta's reputed volatile-poor regolith contains substantial amounts of hydrogen delivered by carbonaceous chondrite impactors. Observations of pitted terrain on Vesta obtained by Dawn's Framing Camera and analyzed by

Denevi
et al.

(p.
246
, published online 20 September), provide evidence for degassing of volatiles and hence the presence of hydrated materials. Finally, paleomagnetic studies by

Fu
et al.

(p.
238
) on a meteorite originating from Vesta suggest that magnetic fields existed on the surface of the asteroid 3.7 billion years ago, supporting the past existence of a magnetic core dynamo.
Response to Comment on “Climatic Niche Shifts Are Rare Among Terrestrial Plant Invaders”
Authors: Guisan Antoine , Petitpierre Blaise , Broennimann Olivier , Kueffer Christoph , Randin Christophe , Daehler Curtis
Published: October 2012

Webber
et al
. take a critical view of our findings that niche expansions are rare in plant invaders, arguing mainly that we did not include nonanalog climates in our analyses. Yet, their concerns include misunderstandings and go beyond the scope of our study, which was purposely restricted to analog climates. We further explain why our results remain robust to other factors of niche dynamics in the native range. We conclude that the implications of our findings remain valid for projections of niche models in analog climates and that projections in nonanalog climates should be undertaken with care.
Strain Tuning of Individual Atomic Tunneling Systems Detected by a Superconducting Qubit
Authors: Grabovskij Grigorij J. , Peichl Torben , Lisenfeld Jürgen , Weiss Georg , Ustinov Alexey V.
Published: October 2012

Bend to Straighten

At low temperatures, the behavior of disordered solids, such as glasses, deviates from that of ordered crystals. The deviations may stem from the ability of some atomic entities to tunnel between two sites of almost identical energy, forming two low-energy states; such two-level systems (TLSs) are also thought to be a major contributor to the decoherence of superconducting qubits.

Grabovskij
et al.

(p.
232
) used mechanical strain to control the splitting between the energy levels of TLSs formed in the disordered barrier of the Josephson junction in a superconducting qubit. For some of the detected TLSs, the splitting exhibited the predicted minimum as a function of strain, verifying the TLS model of disordered solids.
Seeing Is Believing
Authors: Brooks Benjamin A.
Published: October 2012

Satellite data and computational modeling provide evidence for a spheroidal magma body rising within the crust below the Altiplano Plateau in the central Andes.
Observation of Resonances in Penning Ionization Reactions at Sub-Kelvin Temperatures in Merged Beams
Authors: Henson A. B. , Gersten S. , Shagam Y. , Narevicius J. , Narevicius E.
Published: October 2012

Relatively Cold

Temperature is essentially a measure of relative atomic or molecular motion. Low temperature does not necessarily imply a sample at absolute rest—what is important is for every member of the sample to be moving (or not moving) at the same velocity. Techniques for studying reactions under extreme cooling have nonetheless tended to focus on slowing down molecules.

Henson
et al.

(p.
234
) now demonstrate an alternative approach in which two beams of distinct gas-phase reagents are merged so as to continue forward with very little spread in their velocity. The interactions thus occur at millikelvin temperatures, revealing signatures of nonclassical dynamics such as oscillatory ionization probabilities with small shifts in energy.
Manipulators of the Quantum Realm Lauded
Authors: Cho Adrian
Published: October 2012

This year's Nobel Prize in physics honors Serge Haroche and David Wineland for creating delicate quantum states of individual particles and doing novel things with them.
New Arctic Research Vessel Ready to Make a Splash
Authors: Gramling Carolyn
Published: October 2012

Polar researchers will soon have their own ride to the icy waters of the Bering Sea and points north: the
Sikuliaq
, a $200 million, nearly 80-meter ship owned by the U.S. National Science Foundation.
Jack—Not Jill—Went up the Hill
Authors: Anandasabapathy Niroshana
Published: October 2012

A subtle gender bias by faculty members favors male over female candidates in science.
Clinical Validation of a Type-Specific Real-Time Quantitative Human Papillomavirus PCR against the Performance of Hybrid Capture 2 for the Purpose of Cervical Cancer Screening
Authors: Depuydt C. E. , Benoy I. H. , Beert J. F. A. , Criel A. M. , Bogers J. J. , Arbyn M.
Published: October 2012

To be acceptable for use in cervical cancer screening, a new assay that detects DNA of high-risk human papillomavirus (hrHPV) types must demonstrate high reproducibility and performance not inferior to that of a clinically validated HPV test. In the present study, a real-time quantitative PCR (qPCR) assay targeting the E6 and E7 genes of hrHPV was compared with Hybrid Capture 2 (hc2) in a Belgian cervical cancer screening setting. In women >30 years old, the sensitivity and specificity for intraepithelial neoplasias of grade 2 or worse (93 cases of cervical intraepithelial neoplasias of grade 2 or worse (CIN2+) and 1,207 cases of no CIN or CIN1) were 93.6% and 95.6%, respectively, and those of hc2 were 83.9% and 94.5%, respectively {relative sensitivity of qPCR/hc2 = 1.12 [95% confidence interval (CI), 1.01 to 1.23]; relative specificity = 1.01 [95% CI, 0.99 to 1.03]}. A score test showed that the sensitivity (
P
< 0.0001) and specificity (
P
< 0.0001) of the qPCR assay were not inferior to those of hc2 at the required thresholds of 90% and 98%, respectively. The overall agreement of hrHPV positivity between the two runs of the qPCR tests was 98.7% (95% CI, 97.5 to 99.4%), with a kappa value of 0.96 (95% CI, 0.83 to 1.00). The qPCR assay used in this study can be considered a reliable HPV assay that fulfills the clinical validation criteria defined for use in cervical cancer screening.
Alternative Sampling Methods for Detecting Bacterial Pathogens in Children with Upper Respiratory Tract Infections
Authors: van den Bergh Menno R. , Bogaert Debby , Dun Lideke , Vons Joline , Chu Mei Ling J. N. , Trzciński Krzysztof , Veenhoven Reinier H. , Sanders Elisabeth A. M. , Schilder Anne M. G.
Published: October 2012

Nasopharyngeal sampling is used for detecting bacteria commonly involved in upper respiratory tract infections, but it requires training and may not always be well tolerated. We sampled children (n= 66) of ages 0 to 4 years, with rhinorrhea, by using a nasopharyngeal swab, a nasal swab, and nose blowing/wiping into a paper tissue.Streptococcus pneumoniae,Haemophilus influenzae,Moraxella catarrhalis, andStaphylococcus aureuswere cultured at similar rates across methods with high concordance (80 to 97%), indicating that they are reliably detected by alternative means.
Japanese Encephalitis Virus Infects Neuronal Cells through a Clathrin-Independent Endocytic Mechanism
Authors: Kalia Manjula , Khasa Renu , Sharma Manish , Nain Minu , Vrati Sudhanshu
Published: October 2012

Japanese encephalitis virus (JEV) is a mosquito-borne pathogenic flavivirus responsible for acute viral encephalitis in humans. The cellular entry of JEV is poorly characterized in terms of molecular requirements and pathways. Here we present a systematic study of the internalization mechanism of JEV in fibroblasts and neuroblastoma cells. To verify the roles of distinct pathways of cell entry, we used fluorescently labeled virus particles, a combination of pharmacological inhibitors, RNA interference (RNAi), and dominant-negative (DN) mutants of regulatory proteins involved in endocytosis. Our study demonstrates that JEV infects fibroblasts in a clathrin-dependent manner, but it deploys a clathrin-independent mechanism to infect neuronal cells. The clathrin-independent pathway requires dynamin and plasma membrane cholesterol. Virus binding to neuronal cells leads to rapid actin rearrangements and an intact and dynamic actin cytoskeleton, and the small GTPase RhoA plays an important role in viral entry. Immunofluorescence analysis of viral colocalization with endocytic markers showed that JEV traffics through Rab5-positive early endosomes and that release of the viral nucleocapsid occurs at the level of the early and not the late endosomes.
Myeloid-Derived Suppressor Cells Regulate Natural Killer Cell Response to Adenovirus-Mediated Gene Transfer
Authors: Zhu Jiangao , Huang Xiaopei , Yang Yiping
Published: October 2012

The attendant innate and adaptive immune responses to viral vectors have posed a significant hurdle for clinical application of viral vector-mediated gene therapy. Previous studies have shown that natural killer (NK) cells play a critical role in innate immune elimination of adenoviral vectors in the liver. However, it is not clear how the NK cell response to adenoviral vectors is regulated. In this study, we identified a role for granulocytic myeloid-derived suppressor cells (G-MDSCs) in this process. We show that
in vivo
administration of adenoviral vectors results in rapid accumulation of G-MDSCs early during adenoviral infection.
In vivo
depletion of both MDSC populations, but not monocytic MDSCs (M-MDSCs) alone, resulted in accelerated clearance of adenoviral vectors in the liver. This was accompanied by enhanced NK cell proliferation and activation, suggesting a role for MDSCs, probably G-MDSCs, in suppressing NK cell activation and function
in vivo
. We further demonstrate
in vitro
that G-MDSCs, but not M-MDSCs, are responsible for the suppression of NK cell activation. In addition, we show that adenoviral infection activated G-MDSCs to produce higher levels of reactive oxygen species (ROS) and that G-MDSC-mediated suppression of NK cells is mediated by ROS, specifically, H
2
O
2
. This study demonstrates for the first time that the NK cell response to adenoviral vectors is negatively regulated by G-MDSCs and suggests that G-MDSC-based strategies could potentially improve the outcome of viral vector-mediated gene therapy.
An unusual case of abdominal distension: pneumoperitoneum secondary to pneumomediastinum in a patient with chronic obstructive pulmonary disease
Authors: Sturgeon Jonathan P , Collard Benjamin R B , Patel Arjun K K , Devoto Laurence
Published: October 2012

A 68-year-old lady with end-stage chronic obstructive pulmonary disease presented with vomiting and abdominal pain. On examination her abdomen was grossly distended, diffusely tender and hyper-resonant. Imaging showed dilated loops of bowel and free air in the abdomen with no intestinal perforation. The free abdominal air had come down from the thorax by dissecting down around the oesophagus. A pneumomediastinum was present in her chest, secondary to her extensive emphysematous disease. She was treated conservatively and her pneumomediastinum resolved several weeks later, with subsequent resumption of intestinal motility and return to premorbid function. Surgical intervention would not have helped her condition.
Crouzon syndrome: a social stigma
Authors: Pandey Neelisha , Pandey Ramesh Kumar , Singh Rajeev Kumar , Shah Naveen Kumar
Published: October 2012

Crouzon syndrome is a rare genetic disorder caused due to genetic mutations. It is characterised by partial hearing loss, dry eyes, strabismus and underdevelopment of the upper jaw with facial deformities and malocclusion. These facial deformities greatly affect the social and emotional development of the affected child. The present case report highlights the social problems faced by a child suffering with Crouzon syndrome.
A NOVEL AND PRACTICAL SYSTEM FOR VERIFYING SIGNATURES ON PERSIAN HANDWRITTEN BANK CHECKS
Authors: FOROOZANDEH ATEFEH , AKBARI YOUNES , JALILI MOHAMMAD J. , SADRI JAVAD
Published: October 2012

A novel system for verifying signatures on Persian handwritten bank checks is presented, in this paper. The presented system includes two main phases called: training and verification phases. At first, the system is trained using some genuine signatures provided by each customer in training phase. Then verifying the signatures on incoming checks is carried out in the verification phase. Feature extraction step is conducted based on a new approach that uses Multitresolution box-counting (MRBC) method for estimating the fractal dimension of signatures. Here, signature verification is modeled as testing hypothesis, and decision about acceptance or rejection of signatures on incoming checks is carried out using Kolmogorov–Smirnov test. The presented system has been tested on two databases: our new created database and NISDCC database which was used for ICDAR 2009 signature verification competition. Our database has 1000 genuine signatures provided by 100 participants and 200 skilled forgeries copied from genuine samples by five forgers. In total our database includes 1200 Persian signatures. Obtained results show promising performance of the presented system for its application on Persian banks.
2-BRIDGE NUMBERS OF TORUS KNOTS
Authors: MATSUDA HIROSHI
Published: October 2012

The 2-bridge number of knots was introduced by Hass, Rubinstein and Thompson [Knots and k-width, Geom. Dedicata143 (2009) 7–18] as a natural generalization of the bridge number introduced by Schubert [Über eine numerisch knoteninvariante, Math. Z.61 (1954) 245–288]. We show that the 2-bridge number of a torus knot of type (p, q) is (p - 1)q + 2 if 1 < p < q.
Managing software development in globally distributed teams
Authors: Cusumano Michael A.
Published: October 2012

Surveying the basic elements needed for globally distributed teams to function smoothly and efficiently.
The myths and truths of wireless security
Authors: Loo Alfred
Published: October 2012

Technology will never cure all wireless security ills. It will take a coordinated effort involving corporations, manufacturers, employers, and end users to fight the fight.
Record matching in digital library metadata
Authors: Kan Min-Yen , Tan Yee Fan
Published: October 2012

Using evidence from external sources to create more accurate matching systems.
Understanding sources of inefficiency in general-purpose chips
Authors: Hameed Rehan , Qadeer Wajahat , Wachs Megan , Azizi Omid , Solomatnikov Alex , Lee Benjamin C. , Richardson Stephen , Kozyrakis Christos , Horowitz Mark
Published: October 2012

Due to their high volume, general-purpose processors, and now chip multiprocessors (CMPs), are much more cost effective than ASICs, but lag significantly in terms of performance and energy efficiency. This paper explores the sources of these performance and energy overheads in general-purpose processing systems by quantifying the overheads of a 720p HD H.264 encoder running on a general-purpose CMP system. It then explores methods to eliminate these overheads by transforming the CPU into a specialized system for H.264 encoding. We evaluate the gains from customizations useful to broad classes of algorithms, such as SIMD units, as well as those specific to particular computation, such as customized storage and functional units.

The ASIC is 500x more energy efficient than our original four-processor CMP. Broadly applicable optimizations improve performance by 10x and energy by 7x. However, the very low energy costs of actual core ops (100s fJ in 90nm) mean that over 90% of the energy used in these solutions is still "overhead". Achieving ASIC-like performance and efficiency requires algorithm-specific optimizations. For each sub-algorithm of H.264, we create a large, specialized functional unit that is capable of executing 100s of operations per instruction. This improves performance and energy by an additional 25x and the final customized CMP matches an ASIC solution's performance within 3x of its energy and within comparable area.
High performance cache replacement using re-reference interval prediction (RRIP)
Authors: Jaleel Aamer , Theobald Kevin B. , Steely Simon C. , Emer Joel
Published: October 2012

Practical cache replacement policies attempt to emulate optimal replacement by predicting the re-reference interval of a cache block. The commonly used LRU replacement policy always predicts a near-immediate re-reference interval on cache hits and misses. Applications that exhibit a distant re-reference interval perform badly under LRU. Such applications usually have a working-set larger than the cache or have frequent bursts of references to non-temporal data (called scans). To improve the performance of such workloads, this paper proposes cache replacement using Re-reference Interval Prediction (RRIP). We propose Static RRIP (SRRIP) that is scan-resistant and Dynamic RRIP (DRRIP) that is both scan-resistant and thrash-resistant. Both RRIP policies require only 2-bits per cache block and easily integrate into existing LRU approximations found in modern processors. Our evaluations using PC games, multimedia, server and SPEC CPU2006 workloads on a single-core processor with a 2MB last-level cache (LLC) show that both SRRIP and DRRIP outperform LRU replacement on the throughput metric by an average of 4% and 10% respectively. Our evaluations with over 1000 multi-programmed workloads on a 4-core CMP with an 8MB shared LLC show that SRRIP and DRRIP outperform LRU replacement on the throughput metric by an average of 7% and 9% respectively. We also show that RRIP outperforms LFU, the state-of the art scan-resistant replacement algorithm to-date. For the cache configurations under study, RRIP requires 2X less hardware than LRU and 2.5X less hardware than LFU.
The virtual write queue
Authors: Stuecheli Jeffrey , Kaseridis Dimitris , Daly David , Hunter Hillery C. , John Lizy K.
Published: October 2012

In computer architecture, caches have primarily been viewed as a means to hide memory latency from the CPU. Cache policies have focused on anticipating the CPU's data needs, and are mostly oblivious to the main memory. In this paper, we demonstrate that the era of many-core architectures has created new main memory bottlenecks, and mandates a new approach: coordination of cache policy with main memory characteristics. Using the cache for memory optimization purposes, we propose a
Virtual Write Queue
which dramatically expands the memory controller's visibility of processor behavior, at low implementation overhead. Through memory-centric modification of existing policies, such as scheduled writebacks, this paper demonstrates that performance limiting effects of highly-threaded architectures can be overcome. We show that through awareness of the physical main memory layout and by focusing on writes, both read and write average latency can be shortened, memory power reduced, and overall system performance improved. Through full-system cycle-accurate simulations of SPEC cpu2006, we demonstrate that the proposed
Virtual Write Queue
achieves an average 10.9% system-level throughput improvement on memory-intensive workloads, along with an overall reduction of 8.7% in memory power across the whole suite.
Reducing cache power with low-cost, multi-bit error-correcting codes
Authors: Wilkerson Chris , Alameldeen Alaa R. , Chishti Zeshan , Wu Wei , Somasekhar Dinesh , Lu Shih-lien
Published: October 2012

Technology advancements have enabled the integration of large on-die embedded DRAM (eDRAM) caches. eDRAM is significantly denser than traditional SRAMs, but must be periodically refreshed to retain data. Like SRAM, eDRAM is susceptible to device variations, which play a role in determining refresh time for eDRAM cells. Refresh power potentially represents a large fraction of overall system power, particularly during low-power states when the CPU is idle. Future designs need to reduce cache power without incurring the high cost of flushing cache data when entering low-power states.

In this paper, we show the significant impact of variations on refresh time and cache power consumption for large eDRAM caches. We propose Hi-ECC, a technique that incorporates multi-bit error-correcting codes to significantly reduce refresh rate. Multi-bit error-correcting codes usually have a complex decoder design and high storage cost. Hi-ECC avoids the decoder complexity by using strong ECC codes to identify and disable sections of the cache with multi-bit failures, while providing efficient single-bit error correction for the common case. Hi-ECC includes additional optimizations that allow us to amortize the storage cost of the code over large data words, providing the benefit of multi-bit correction at same storage cost as a single-bit error-correcting (SECDED) code (2% overhead). Our proposal achieves a 93% reduction in refresh power vs. a baseline eDRAM cache without error correcting capability, and a 66% reduction in refresh power vs. a system using SECDED codes.
Use ECP, not ECC, for hard failures in resistive memories
Authors: Schechter Stuart , Loh Gabriel H. , Strauss Karin , Burger Doug
Published: October 2012

As leakage and other charge storage limitations begin to impair the scalability of DRAM, non-volatile resistive memories are being developed as a potential replacement. Unfortunately, current error correction techniques are poorly suited to this emerging class of memory technologies. Unlike DRAM, PCM and other resistive memories have wear lifetimes, measured in writes, that are sufficiently short to make cell failures common during a system's lifetime. However, resistive memories are much less susceptible to transient faults than DRAM. The Hamming-based ECC codes used in DRAM are designed to handle transient faults with no effective lifetime limits, but ECC codes applied to resistive memories would wear out faster than the cells they are designed to repair. This paper evaluates
Error-Correcting Pointers
(ECP), a new approach to error correction optimized for memories in which errors are the result of permanent cell failures that occur, and are immediately detectable, at write time. ECP corrects errors by permanently encoding the locations of failed cells into a table and assigning cells to replace them. ECP provides longer lifetimes than previously proposed solutions with equivalent overhead. What's more, as the level of variance in cell lifetimes increases -- a likely consequence of further scalaing -- ECP's margin of improvement over existing schemes increases.
Morphable memory system
Authors: Qureshi Moinuddin K. , Franceschini Michele M. , Lastras-Montaño Luis A. , Karidis John P.
Published: October 2012

Phase Change Memory (PCM) is emerging as a scalable and power efficient technology to architect future main memory systems. The scalability of PCM is enhanced by the property that PCM devices can store multiple bits per cell. While such Multi-Level Cell (MLC) devices can offer high density, this benefit comes at the expense of increased read latency, which can cause significant performance degradation. This paper proposes
Morphable Memory System (MMS)
, a robust architecture for efficiently incorporating MLC PCM devices in main memory. MMS is based on observation that memory requirement varies between workloads, and systems are typically over-provisioned in terms of memory capacity. So, during a phase of low memory usage, some of the MLC devices can be operated at fewer bits per cell to obtain lower latency. When the workload requires full memory capacity, these devices can be restored to high density MLC operation to have full main-memory capacity. We provide the runtime monitors, the hardware-OS interface, and the detailed mechanism for implementing MMS. Our evaluations on an 8-core 8GB MLC PCM-based system show that MMS provides, on average, low latency access for 95% of all memory requests, thereby improving overall system performance by 40%.
An integrated GPU power and performance model
Authors: Hong Sunpyo , Kim Hyesoon
Published: October 2012

GPU architectures are increasingly important in the multi-core era due to their high number of parallel processors. Performance optimization for multi-core processors has been a challenge for programmers. Furthermore, optimizing for power consumption is even more difficult. Unfortunately, as a result of the high number of processors, the power consumption of many-core processors such as GPUs has increased significantly.

Hence, in this paper, we propose an integrated power and performance (IPP) prediction model for a GPU architecture to predict the optimal number of active processors for a given application. The basic intuition is that when an application reaches the peak memory bandwidth, using more cores does not result in performance improvement.

We develop an empirical power model for the GPU. Unlike most previous models, which require measured execution times, hardware performance counters, or architectural simulations, IPP predicts execution times to calculate dynamic power events. We then use the outcome of IPP to control the number of running cores. We also model the increases in power consumption that resulted from the increases in temperature.

With the predicted optimal number of active cores, we show that we can save up to 22.09%of runtime GPU energy consumption and on average 10.99% of that for the five memory bandwidth-limited benchmarks.
Energy proportional datacenter networks
Authors: Abts Dennis , Marty Michael R. , Wells Philip M. , Klausler Peter , Liu Hong
Published: October 2012

Numerous studies have shown that datacenter computers rarely operate at full utilization, leading to a number of proposals for creating servers that are
energy proportional
with respect to the computation that they are performing.

In this paper, we show that as servers themselves become more energy proportional, the datacenter network can become a significant fraction (up to 50%) of cluster power. In this paper we propose several ways to design a high-performance datacenter network whose power consumption is more proportional to the amount of traffic it is moving -- that is, we propose
energy proportional datacenter networks
.

We first show that a flattened butterfly topology itself is inherently more power efficient than the other commonly proposed topology for high-performance datacenter networks. We then exploit the characteristics of modern plesiochronous links to adjust their power and performance envelopes dynamically. Using a network simulator, driven by both synthetic workloads and production datacenter traces, we characterize and understand design tradeoffs, and demonstrate an 85% reduction in power --- which approaches the ideal energy-proportionality of the network.

Our results also demonstrate two challenges for the designers of future network switches: 1) We show that there is a significant power advantage to having independent control of each unidirectional channel comprising a network link, since many traffic patterns show very asymmetric use, and 2) system designers should work to optimize the high-speed channel designs to be more energy efficient by choosing optimal data rate and equalization technology. Given these assumptions, we demonstrate that energy proportional datacenter communication is indeed possible.
IVEC
Authors: Huang Ruirui , Suh G. Edward
Published: October 2012

This paper proposes a unified off-chip memory integrity protection scheme, named IVEC. Today, a system needs two independent mechanisms in order to protect the memory integrity from both physical attacks and random errors. Integrity verification schemes detect malicious tampering of memory while error correcting codes (ECC) detect and correct random errors. IVEC enables both detection of malicious attacks for security and correction of random errors for reliability at the same time by extending the integrity verification techniques. Analytical and experimental studies show that IVEC can correct single-bit errors and even multi-bit errors from one DRAM chip within a cache block read without any additional ECC bits, when the integrity verification is also required for security, effectively removing the memory and bandwidth overheads (12.5%) of typical ECC schemes. Alternatively, with parity bits, IVEC can provide even stronger error correction capabilities comparable to the traditional chip-kill correct, still with less overheads. For both cases, IVEC can use standard non-ECC DIMMs.
Evaluating Interconnect and Virtualization Performance forHigh Performance Computing
Authors: Ramakrishnan Lavanya , Canon R. Shane , Muriki Krishna , Sakrejda Iwona , Wright Nicholas J.
Published: October 2012

Scientists are increasingly considering cloud computing platforms to satisfy their computational needs. Previous work has shown that virtualized cloud environments can have significant performance impact. However there is still a limited understanding of the nature of overheads and the type of applications that might do well in these environments. In this paper we detail benchmarking results that characterize the virtualization overhead and its impact on performance. We also examine the performance of various interconnect technologies with a view to understanding the performance impacts of various choices. Our results show that virtualization can have a significant impact upon performance, with at least a 60% performance penalty. We also show that less capable interconnect technologies can have a significant impact upon performance of typical HPC applications. We also evaluate the performance of the Amazon Cluster compute instance and show that it performs approximately equivalently to a 10G Ethernet cluster at low core counts.
Towards efficient GPU sharing on multicore processors
Authors: Wang Lingyuan , Huang Miaoqing , El-Ghazawi Tarek
Published: October 2012

Scalable systems employing a mix of GPUs with CPUs are becoming increasingly prevalent in high-performance computing. The presence of such accelerators introduces significant challenges and complexities to both language developers and end users. This paper provides a close study of efficient coordination mechanisms to handle parallel requests from multiple hosts of control to a GPU under hybrid programming. Using a set of microbenchmarks and applications on a GPU cluster, we show that thread and process-based context hosting have different tradeoffs. Experimental results on application benchmarks suggest that both thread-based context funneling and process-based context switching natively perform similarly on the latest Fermi GPUs, while manually guided context funneling is currently the best way to achieve optimal performance.
Bioengineering Methods for Analysis of Cells In Vitro
Authors: Underhill Gregory H. , Peter Galie , Chen Christopher S. , Bhatia Sangeeta N.
Published: October 2012

Efforts in the interdisciplinary field of bioengineering have led to innovative methods for investigating the complexities of cell responses in vitro. These approaches have emphasized the reduction of complex multicomponent cellular microenvironments into distinct individual signals as a means to both (a) better construct mimics of in vivo microenvironments and (b) better deconstruct microenvironments to study them. Microtechnology tools, together with advances in biomaterials, have been fundamental to this progress by enabling the tightly controlled presentation of environmental cues and the improved systematic analysis of cellular perturbations. In this review, we describe bioengineering approaches for controlling and measuring cell-environmental interactions in vitro, including strategies for high-throughput analysis. We also describe the mechanistic insights gained by the use of these novel tools, with associated applications ranging from fundamental biological studies, in vitro modeling of in vivo processes, and cell-based therapies.
Cardiac Regenerative Capacity and Mechanisms
Authors: Kikuchi Kazu , Poss Kenneth D.
Published: October 2012

The heart holds the monumental yet monotonous task of maintaining circulation. Although cardiac function is critical to other organs and to life itself, mammals are not equipped with significant natural capacity to replace heart muscle that has been lost by injury. This deficiency plays a role in leaving millions worldwide vulnerable to heart failure each year. By contrast, certain other vertebrate species such as zebrafish are strikingly good at heart regeneration. A cellular and molecular understanding of endogenous regenerative mechanisms and advances in methodology to transplant cells together project a future in which cardiac muscle regeneration can be therapeutically stimulated in injured human hearts. This review focuses on what has been discovered recently about cardiac regenerative capacity and how natural mechanisms of heart regeneration in model systems are stimulated and maintained.
Apical targeting of the P2Y4 receptor is directed by hydrophobic and basic residues in the cytoplasmic tail
Authors: DuBose D. Ross , Wolff Samuel C. , Qi Ai-Dong , Naruszewicz Izabela , Nicholas Robert A.
Published: October 2012

The P2Y4 receptor is selectively targeted to the apical membrane in polarized epithelial cell lines and has been shown to play a key role in intestinal chloride secretion. In this study, we delimit a 23 amino acid sequence within the P2Y4 receptor C-tail that directs its apical targeting. Using a mutagenesis approach, we found that four hydrophobic residues near the COOH-terminal end of the signal are necessary for apical sorting, whereas two basic residues near the NH2-terminal end of the signal are involved to a lesser extent. Interestingly, mutation of the key hydrophobic residues results in a basolateral enrichment of the receptor construct, suggesting that the apical targeting sequence may prevent insertion or disrupt stability of the receptor at the basolateral membrane. The signal is not sequence specific, as an inversion of the 23 amino acid sequence does not disrupt apical targeting. We also show that the apical targeting sequence is an autonomous signal and is capable of redistributing the normally basolateral P2Y12 receptor, suggesting that the apical signal is dominant over the basolateral signal in the main body of the P2Y12 receptor. The targeting sequence is unique to the P2Y4 receptor, and sequence alignments of the COOH-terminal tail of mammalian orthologs reveal that the hydrophobic residues in the targeting signal are highly conserved. These data define the novel apical sorting signal of the P2Y4 receptor, which may represent a common mechanism for trafficking of epithelial transmembrane proteins.