bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of c-rel-related transcripts in mouse hematopoietic tissues, fractionated lymphocyte populations, and cell lines.
Authors: Brownell E , Mathieson B , Young H A , Keller J , Ihle J N , Rice N R
Published: September 2015

A portion of the human cellular homolog of v-rel, the transforming gene of the leukemogenic retrovirus reticuloendotheliosis virus, strain T, was used to survey RNAs from several mouse tissues, selected lymphocyte populations, and hematopoietic cell lines for c-rel expression. Relatively high levels of a high-molecular-weight transcript were observed in peripheral B and T cells, whereas lower levels were detectable in functionally immature thymocytes. These results suggested that, unlike c-myb and c-ets, the c-rel proto-oncogene plays a role in later stages of lymphocyte differentiation.
Interaction between two different regulatory elements activates the murine alpha A-crystallin gene promoter in explanted lens epithelia.
Authors: Chepelinsky A B , Sommer B , Piatigorsky J
Published: September 2015

Previous experiments have indicated that 5' flanking DNA sequences (nucleotides-366 to +46) are capable of regulating the lens-specific transcription of the murine alpha A-crystallin gene. Here we have analyzed these 5' regulatory sequences by transfecting explanted embryonic chicken lens epithelia with different alpha A-crystallin-CAT (chloramphenicol acetyltransferase) hybrid genes (alpha A-crystallin promoter sequences fused to the bacterial CAT gene in the pSVO-CAT expression vector). The results indicated the presence of a proximal (-88 to +46) and a distal (-111 to -88) domain which must interact for promoter function. Deletion experiments showed that the sequence between -88 and -60 was essential for function of the proximal domain in the explanted epithelia. A synthetic oligonucleotide containing the sequence between -111 and -84 activated the proximal domain when placed in either orientation 57 base pairs upstream from position -88 of the alpha A-crystallin-CAT hybrid gene.
Maximal binding levels of an H1 histone gene-specific factor in S-phase correlate with maximal H1 gene transcription.
Authors: Dalton S , Wells J R
Published: September 2015

Levels of trans-acting factor (H1-SF) binding to the histone H1 gene-specific motif (5'-AAACACA-3' [L. S. Coles and J. R. E. Wells, Nucleic Acids Res. 13:585-594, 1985]) increase 12-fold from G1 to S-phase in synchronized cells and decrease again in G2 phase of the cell cycle. Since the H1 element is required for S-phase expression of H1 genes (S. Dalton and J. R. E. Wells, EMBO J. 7:49-56, 1988), it is likely that the increased levels of H1-SF binding component play an important role in S-phase regulation of H1 gene transcription.
Evidence for cooperation between cells during sporulation of the yeast Saccharomyces cerevisiae.
Authors: Jakubowski H , Goldman E
Published: September 2015

Diploid Saccharomyces cerevisiae cells heterozygous for the mating type locus (MATa/MAT alpha) undergo meiosis and sporulation when starved for nitrogen in the presence of a poor carbon source such as potassium acetate. Diploid yeast adenine auxotrophs sporulated well at high cell density (10(7) cells per ml) under these conditions but failed to differentiate at low cell density (10(5) cells per ml). The conditional sporulation-deficient phenotype of adenine auxotrophs could be complemented by wild-type yeast cells, by medium from cultures that sporulate at high cell density, or by exogenously added adenine (or hypoxanthine with some mutants). Adenine and hypoxanthine in addition to guanine, adenosine, and numerous nucleotides were secreted into the medium, each in its unique temporal pattern, by sporulating auxotrophic and prototrophic yeast strains. The major source of these compounds was degradation of RNA. The data indicated that differentiating yeast cells cooperate during sporulation in maintaining sufficiently high concentrations of extracellular purines which are absolutely required for sporulation of adenine auxotrophs. Yeast prototrophs, which also sporulated less efficiently at low cell density (10(3) cells per ml), reutilized secreted purines in preference to de novo-made purine nucleotides whose synthesis was in fact inhibited during sporulation at high cell density. Adenine enhanced sporulation of yeast prototrophs at low cell density. The behavior of adenine auxotrophs bearing additional mutations in purine salvage pathway genes (ade apt1, ade aah1 apt1, ade hpt1) supports a model in which secretion of degradation products, uptake, and reutilization of these products is a signal between cells synchronizing the sporulation process.
Developmental and tissue-specific expression of U4 small nuclear RNA genes.
Authors: Korf G M , Botros I W , Stumph W E
Published: September 2015

U4 RNA is one of several small nuclear RNAs involved in the splicing of mRNA precursors. The domestic chicken has two genes per haploid genome that are capable of encoding U4 RNA. The U4X RNA gene (which encodes a sequence variant of U4 RNA that was unknown prior to the cloning of the gene) and the U4B RNA gene were both expressed in vivo in each of seven adult and three embryonic chicken tissues examined. However, the ratio of U4B RNA to U4X RNA can vary more than sevenfold in both a tissue- and stage-specific manner.
The cell-specific elastase I enhancer comprises two domains.
Authors: Kruse F , Komro C T , Michnoff C H , MacDonald R J
Published: September 2015

Two separate domains within the 134-base-pair rat elastase I enhancer and a third domain at the enhancer-promoter boundary are required for selective expression in pancreatic acinar cells. The domains were detected by a series of 10-base-pair substitution mutations across the elastase I gene regulatory region from positions -200 to -61. The effect of each mutant on the pancreas-specific expression of a linked chloramphenicol acetyltransferase gene was assayed by transfection into pancreatic 266-6 acinar cells and control NIH/3T3 cells. The two enhancer domains are nonredundant, because mutations in either eliminated (greater than 100-fold reduction) expression in 266-6 cells. DNase I protection studies of the elastase I enhancer-promoter region with partially purified nuclear extracts from pancreatic tissue and 266-6 cells revealed nine discrete protected regions (footprints) on both DNA strands. One of three footprints that lie within the two functional domains of the enhancer contained a sequence, conserved among several pancreas-specific genes, which when mutated decreased linked chloramphenicol acetyltransferase expression up to 170-fold in 266-6 cells. This footprint may represent a binding site for one or more pancreas-specific regulatory proteins.
An oligomer complementary to c-myc mRNA inhibits proliferation of HL-60 promyelocytic cells and induces differentiation.
Authors: Holt J T , Redner R L , Nienhuis A W
Published: September 2015

To study the role of a nuclear proto-oncogene in the regulation of cell growth and differentiation, we inhibited HL-60 c-myc expression with a complementary antisense oligomer. This oligomer was stable in culture and entered cells, forming an intracellular duplex. Incubation of cells with the anti-myc oligomer decreased the steady-state levels of c-myc protein by 50 to 80%, whereas a control oligomer did not significantly affect the c-myc protein concentration. Direct inhibition of c-myc expression with the anti-myc oligomer was associated with a decreased cell growth rate and an induction of myeloid differentiation. Related antisense oligomers with 2- to 12-base-pair mismatches with c-myc mRNA did not influence HL-60 cells. Thus, the effects of the antisense oligomer exhibited sequence specificity, and furthermore, these effects could be reversed by hybridization competition with another complementary oligomer. Antisense inhibition of a nuclear proto-oncogene apparently bypasses cell surface events in affecting cell proliferation and differentiation.
Two-step stimulation of B lymphocytes to enter DNA synthesis: synergy between anti-immunoglobulin antibody and cytochalasin on expression of c-myc and a G1-specific gene.
Authors: Buckler A J , Rothstein T L , Sonenshein G E
Published: September 2015

Previously we demonstrated that stimulation of resting murine splenic B lymphocytes with goat anti-mouse immunoglobulin antibody (GaMIg) plus cytochalasin D (CD) led to DNA synthesis; GaMIg and CD added simultaneously, or GaMIg added before CD, induced this response (T. L. Rothstein, J. Immunol. 136:813-816, 1986). Cells similarly treated with GaMIg or CD alone did not enter S phase. Here we have measured the effects of this two-signal stimulation on the c-myc, 2F1, and gamma-actin genes. The expression of these growth-related genes is known to change either during the G0-to-G1 transition or in the G1 phase of the cell cycle. For the 2F1 and c-myc genes, neither the GaMIg nor CD stimulus alone led to a prolonged increase in mRNA levels, whereas GaMIg plus CD allowed for continuous elevated expression of these genes. Furthermore, GaMIg pretreatment rendered expression of the c-myc and 2F1 genes susceptible to subsequent action by CD. In contrast, CD alone was sufficient to produce changes in gamma-actin gene expression. Thus there are synergistic effects of competence- and progressionlike factors on the expression of the c-myc and 2F1 genes, and these effects correlate with the progression of B lymphocytes to DNA synthesis.
DNA-binding site for two skeletal actin promoter factors is important for expression in muscle cells.
Authors: Walsh K , Schimmel P
Published: September 2015

Two nuclear factors bind to the same site in the chicken skeletal actin promoter. Mutations in the footprint sequence which eliminate detectable binding decrease expression in transfected skeletal muscle cells by a factor of 25 to 50 and do not elevate the low expression in nonmuscle cells. These results show that the factor-binding site contributes to the activation of expression in muscle cells and that it alone does not contribute significantly to repress expression in nonmuscle cells.
Characterization of the human granulocyte-macrophage colony-stimulating factor promoter region by genetic analysis: correlation with DNase I footprinting.
Authors: Nimer S D , Morita E A , Martis M J , Wachsman W , Gasson J C
Published: September 2015

T-cell activation induces expression of the hematopoietic growth factor granulocyte-macrophage colony-stimulating factor (GM-CSF). To define the molecular events involved in the induction of GM-CSF gene expression more clearly, we prepared and analyzed deletion mutants of GM-CSF promoter recombinant constructs. The results localized inducible expression to a 90-base-pair region (-53 to +37) which is active in uninfected and human T-cell leukemia virus-infected T-cell lines but not in resting or mitogen-stimulated B cells. DNase I footprinting experiments revealed protection of sequences contained within this region, including a repeated nucleotide sequence, CATT(A/T), which could serve as a core recognition sequence for a cellular transcription factor. Upstream of these GM-CSF promoter sequences is a 15-base-pair region (-193 to -179) which has negative regulatory activity in human T-cell leukemia virus-infected T cells. These studies revealed a complex pattern of regulation of GM-CSF expression in T cells; positive and negative regulatory sequences may play critical roles in controlling the expression of this potent granulopoietin in the bone marrow microenvironment and in localized inflammatory responses.
Inpatient Falls: Improving assessment, documentation, and management
Authors: Nelson Eleanor , Reynolds Patrick
Published: September 2015

A frequently occurring job during on-call and out-of-hours shifts is reviewing a patient following a fall with this often being the responsibility of the most junior and inexperienced doctors. Following a pilot audit we identified inconsistencies in medical assessment and documentation, with 50% of expected data points not recorded.

Failure to complete a thorough assessment can lead to missed injuries, prolonged length of stay, and litigation. Using the plan, do, study, act (PDSA) cycle model this project sought to address this through providing teaching to junior doctors and the development of a pro-forma.

Three style cycles of data collection were performed; a formal baseline dataset, after delivering a teaching session to new junior doctors and following the trial of the new fall pro-forma. We selected 15 to 17 patient notes to review at random during a one month period for each data collection cycle and compared the medical assessment to the standards outlined by the National Patient Safety Agency (NPSA) guidelines.[1]

There were two key areas of improvement identified following the teaching session and introduction of the proforma. Documentation of a fall history was improved by nearly 30% being recorded in 100% of cases after the interventions. Documentation of a thorough musculoskeletal examination was improved from being recorded in just 54% of cases to 77% of cases; it was recorded in 100% of the cases where the proforma was used.

The project demonstrated the need to improve documentation and assessment of a patient who has fallen. Initial data collection has shown that assessment and documentation were improved providing teaching to junior doctors and by use of the document. The pro-forma has since been incorporated into hospital policy and now forms the compulsory documentation expected of the doctors and nurses managing patients following a fall. Ensuring easy access to the proforma and re-auditing after editing the document will be the next steps.
The electronic properties and nonlinear optical responses of the intermediate structures in rolling graphene to carbon nanotubes
Authors: Hu Yang-Yang , Li Wei-Qi , Yang Li , Feng Ji-Kang , Tian Wei Quan
Published: September 2015

From the same piece of finite size graphene (F-graphene) sheet through different directions (zigzag edge or armchair edge), (4, 4) and (8, 0) carbon nanotube clips form. The electronic properties of the intermediate structures in the two rolling processes 44 (zigzag) and 80 (armchair) have been investigated using quantum chemistry method. The magnetism of the F-graphene sheet disappears with the rolling operation in 44, while it is maintained throughout the whole rolling operation in 80. Furthermore, the highest occupied molecular orbital (HOMO) α and HOMO β gradually extend to the whole framework from the zigzag edges with the rolling operation in 44, and they gradually localize to the lower and upper half of the framework in 80. Oxygen passivation along the opening of the intermediate structures effectively improves the nonlinear optical (NLO) response of the intermediate structures in both the zigzag and the armchair processes. Oxygen passivation along the armchair opening in 80 enhances the βtot value, yet does not bring essential changes to the electron transitions contributed to the NLO response. Oxygen passivation along the zigzag opening in 44 is able not only to enhance the βtot value but also to change the transition nature of electron excitations with a major contribution to the NLO response.
Expert perceptions of media reporting on a large-scale environmental risk issue: insights from mountain pine beetle management in Alberta, Canada
Authors: McFarlane Bonita L. , Parkins John R. , Romanowski Sharon
Published: September 2015

The media play a key role in communicating risk issues and serve as a link between experts and the public. In this study, we explore experts’ perspectives on the role of the media and media content with respect to a mountain pine beetle (MBP; Dendroctonus ponderosae Hopkins) epidemic in western Canada. We collected data using an internet-based survey of 59 MPB experts in 2009 and 1628 articles from local, regional, and national newspapers from 2000 to 2008. Survey findings show that experts do not have a favourable view of media reporting of MPB. In our media analysis, we found that the media are used effectively by experts to disseminate MPB risk information and to justify a swift response and control measures. Most articles reported information presented to them by government and industry. We conclude that the media played primarily an educational role and gave limited attention to fostering public dialogue on MPB management.
Characterization of the VP39 envelope protein from Singapore grouper iridovirus
Authors: Zhang Honglian , Zhou Sheng , Xia Liqun , Huang Xiaohong , Huang Youhua , Cao Jianhao , Qin Qiwei
Published: September 2015

Singapore grouper iridovirus (SGIV) is a major pathogen that causes heavy economic losses to the grouper aquaculture industry in China and Southeast Asian countries. In the present study, a viral envelope protein, VP39, encoded by SGIV ORF39L, was identified and characterized. SGIV ORF39L was found in all sequenced iridoviruses and is now considered to be a core gene of the family Iridoviridae. ORF39L was classified as a late gene during in vitro infection using reverse transcription–polymerase chain reaction, western blotting, and a drug inhibition analysis. An indirect immunofluorescence assay revealed that the VP39 protein was confined to the cytoplasm, especially at viral assembly sites. Western blot and matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry analyses suggested that VP39 is an envelope protein. Immunogold electron microscopy further confirmed that VP39 is a viral envelope protein. Furthermore, a mouse anti-VP39 polyclonal antibody exhibited SGIV-neutralizing activity in vitro, suggesting that VP39 is involved in SGIV infection. Taken together, the current data suggest that VP39 represents a conserved envelope protein of iridoviruses that contributes to viral infection.
Analyses of alpha–alpha elastic scattering data in the energy range 53.4–119.9 MeV
Authors: Shehadeh Z.F.
Published: September 2015

The differential and reaction cross sections for alpha–alpha elastic scattering at energies ranging from 50 to 120 MeV (lab. system) have been clearly explained for the first time, by using a new optical potential type. This potential, which is different from all other proposed potentials, is composed of two real parts: one is an attractive squared Woods–Saxon and the other is a repulsive core of the Woods–Saxon form in addition to a surface Woods–Saxon form for the imaginary part. The nature of the real part has been determined from available phase shifts through using inverse scattering theory for the identical particles at a fixed energy, adopting the framework of the Schrödinger equation. It is found that the repulsive real part is essential for improving the fit to the measured elastic differential cross sections, and in explaining the kink that appears at r < 1.0 fm in the shape of the real part of the potential. Using this new potential, our calculated reaction cross sections are in reasonable agreement with the ones reported by both Darriulat et al. (Phys. Rev. 137, B315 (1965). doi:10.1103/PhysRev.137.B315) and Brown and Tang (Nucl. Phys. A, 170, 225 (1971). doi:10.1016/0375-9474(71)90633-6 ).
Note on uncertainty relations in doubly special relativity and gravity’s rainbow
Authors: Son Edwin J. , Kim Wontae
Published: September 2015

We present commutation relations depending on the rainbow functions which are slightly different from the well-known results. However, the advantage of these new commutation relations are compatible with the calculation of the Hawking temperature in the rainbow Schwarzschild black hole.
Approximating Chaotic Attractors by Period-Three Cycles in Discrete Stochastic Systems
Authors: Bashkirtseva Irina , Ryashko Lev
Published: September 2015

We study a distribution of random states forced outwards of the general deterministic attractor (regular or chaotic) for one-dimensional discrete-time systems with unimodal map. To approximate this distribution, we replace the original system by the appropriate modeling system with stable 3-cycle and use the stochastic sensitivity function technique. Constructive abilities of the suggested approach are demonstrated in the analysis of noise-induced transitions from chaos to order.
Ten shades of black
Authors: Hod Shahar
Published: September 2015

The holographic principle has taught us that, as far as their entropy content is concerned, black holes in (3 + 1)-dimensional curved spacetimes behave as ordinary thermodynamic systems in flat (2 + 1)-dimensional spacetimes. In this paper, we point out that the opposite behavior can also be observed in black-hole physics. To show this we study the quantum Hawking evaporation of near-extremal Reissner–Nordström (RN) black holes. We first point out that the black-hole radiation spectrum departs from the familiar radiation spectrum of genuine (3 + 1)-dimensional perfect black-body emitters. In particular, the would be black-body thermal spectrum is distorted by the curvature potential which surrounds the black-hole and effectively blocks the emission of low-energy quanta. Taking into account the energy-dependent gray-body factors which quantify the imprint of passage of the emitted radiation quanta through the black-hole curvature potential, we reveal that the (3 + 1)-dimensional black holes effectively behave as perfect black-body emitters in a flat (9 + 1)-dimensional spacetime.
Observational hints of a pre-inflationary scale?
Authors: Gruppuso A. , Sagnotti A.
Published: September 2015

We argue that the lack of power exhibited by cosmic microwave background (CMB) anisotropies at large angular scales might be linked to the onset of inflation. We highlight observational features and theoretical hints that support this view, and present a preliminary estimate of the physical scale that would underlie the phenomenon.
Heavy-tailed features and dependence in limit order book volume profiles in futures markets
Authors: Richards Kylie-Anne , Peters Gareth W. , Dunsmuir William
Published: September 2015

This paper investigates fundamental stochastic attributes of the random structures of the volume profiles of the limit order book. We find statistical evidence that heavy-tailed sub-exponential volume profiles occur on the limit order book and these features are best captured via the generalized Pareto distribution MLE method. In futures exchanges, the heavy tail features are not asset class dependent and occur on ultra or mid-range high frequency. Volume forecasting models should account for heavy tails, time varying parameters and long memory. In application, utilizing the generalized Pareto distribution to model volume profiles allows one to avoid over-estimating the round trip cost of trading.
Enhancing the Reliability of MLC NAND Flash Memory Systems by Read Channel Optimization
Authors: Papandreou Nikolaos , Parnell Thomas , Pozidis Haralampos , Mittelholzer Thomas , Eleftheriou Evangelos , Camp Charles , Griffin Thomas , Tressler Gary , Walls Andrew
Published: September 2015

NAND flash memory is not only the ubiquitous storage medium in consumer applications but has also started to appear in enterprise storage systems as well. MLC and TLC flash technology made it possible to store multiple bits in the same silicon area as SLC, thus reducing the cost per amount of data stored. However, at current sub-20nm technology nodes, MLC flash devices fail to provide the levels of raw reliability, mainly cycling endurance, that are required by typical enterprise applications. Advanced signal processing and coding schemes are needed to improve the flash bit error rate and thus elevate the device reliability to the desired level. In this article, we report on the use of adaptive voltage thresholds and cell-to-cell interference cancellation in the read operation of NAND flash devices. We discuss how the optimal read voltage thresholds can be determined and assess the benefit of cancelling cell-to-cell interference in terms of cycling endurance, data retention, and resilience to read disturb.
Component-Based Synthesis of Embedded Systems Using Satisfiability Modulo Theories
Authors: Peter Steffen , Givargis Tony
Published: September 2015

Constraint programming solvers, such as Satisfiability Modulo Theory (SMT) solvers, are capable tools in finding preferable configurations for embedded systems from large design spaces. However, constructing SMT constraint programs is not trivial, in particular for complex systems that exhibit multiple viewpoints and models. In thisarticle we propose CoDeL: a component-based description language that allows system designers to express components as reusable building blocks of the system with their parameterizable properties, models, and interconnectivity. Systems are synthesized by allocating, connecting, and parameterizing the components to satisfy the requirements of an application. We present an algorithm that transforms component-based design spaces, expressible in CoDeL, to an SMT program, which, solved by state-of-the-art SMT solvers, determines the satisfiability of the synthesis problem, and delivers a correct-by-construction system configuration. Evaluation results for use cases in the domain of scheduling and mapping of distributed real-time processes confirm, first, the performance gain of SMT compared to traditional design space exploration approaches, second, the usability gains by expressing design problems in CoDeL, and third, the capability of the CoDeL/SMT approach to support the design of embedded systems.
An Improved Methodology for Resilient Design Implementation
Authors: Kahng Andrew B. , Kang Seokhyeong , Li Jiajia , Pineda De Gyvez Jose
Published: September 2015

Resilient design techniques are used to (i) ensure correct operation under dynamic variations and to (ii) improve design performance (e.g., timing speculation). However, significant overheads (e.g., 16% and 14% energy penalties due to throughput degradation and additional circuits) are incurred by existing resilient design techniques. For instance, resilient designs require additional circuits to detect and correct timing errors. Further, when there is an error, the additional cycles needed to restore a previous correct state degrade throughput, which diminishes the performance benefit of using resilient designs. In this work, we describe an improved methodology for resilient design implementation to minimize the costs of resilience in terms of power, area, and throughput degradation. Our methodology uses two levers: selective-endpoint optimization (i.e., sensitivity-based margin insertion) and clock skew optimization. We integrate the two optimization techniques in an iterative optimization flow which comprehends toggle rate information and the trade-off between cost of resilience and margin on combinational paths. Since the error-detection network can result in up to 9% additional wirelength cost, we also propose a matching-based algorithm for construction of the error-detection network to minimize this resilience overhead. Further, our implementations comprehend the impacts of signoff corners (in particular, hold constraints, and use of typical vs. slow libraries) and process variation, which are typically omitted in previous studies of resilience trade-offs. Our proposed flow achieves energy reductions of up to 21% and 10% compared to a conventional (with only margin used to attain robustness) design and a brute-force implementation (i.e., a typical resilient design, where resilient endpoints are (greedily) instantiated at timing-critical endpoints), respectively. We show that these benefits increase in the context of an adaptive voltage scaling strategy.
An Application Adaptation Approach to Mitigate the Impact of Dynamic Thermal Management on Video Encoding
Authors: Mirtar Ali , Dey Sujit , Raghunathan Anand
Published: September 2015

Due to limitations of cooling methods such as using fan and heat sink, dynamic thermal management (DTM) is being widely adopted to manage the temperature of computing systems. However, application of DTM can reduce the system performance and thereby affect the quality of real-time applications. Real-time video encoding, which has high computational need and hard deadlines, is a commonly used application that can be severely affected by the usage of DTM. We study the effect of DTM on a widely used H.264 video encoder and formulate a multidimensional optimization problem to maximize video quality and minimize bit rate while ensuring that the video encoder can run in real time in spite of DTM effects. We model the effects of adapting encoding parameters on video quality, bit rate, and encoder speed. We propose a dynamic application adaptation method to efficiently solve the optimization problem by optimally adapting the encoding parameters in response to DTM effects. In addition, we show that the proposed dynamic application adaptation method would reduce the need for cooling methods such as forced convection cooling. We implement the proposed approach on an Intel® Core™ 2 Duo platform where dynamic voltage and frequency scaling (DVFS) is used for DTM. Our measurements with several videos reveal that when DTM is applied, the video quality is affected significantly. However, using the proposed adaptation algorithm, the encoder can run in real time, and the quality loss is minimized with only a marginal increase in the bit rate.
FOLD
Authors: Pomeranz Irith
Published: September 2015

This article introduces a new approach to extreme static test compaction for functional test sequences that modifies the sequence in order to enhance the ability to omit test vectors from it and thus compact it. In the new approach, modification of the sequence and omission of test vectors from it are tightly coupled by focusing both subprocedures on subsequences of limited lengths. In a new process that is referred to as folding, a subsequence is partitioned into two halves, and the goal of the modification is to ensure that the two halves are as similar as possible. With similar halves, the expectation is that it will be possible to omit test vectors from the subsequence. Experimental results demonstrate that the procedure produces extremely short functional test sequences for benchmark circuits.
Architecting the Last-Level Cache for GPUs using STT-RAM Technology
Authors: Samavatian Mohammad Hossein , Arjomand Mohammad , Bashizade Ramin , Sarbazi-Azad Hamid
Published: September 2015

Future GPUs should have larger L2 caches based on the current trends in VLSI technology and GPU architectures toward increase of processing core count. Larger L2 caches inevitably have proportionally larger power consumption. In this article, having investigated the behavior of GPGPU applications, we present an efficient L2 cache architecture for GPUs based on STT-RAM technology. Due to its high-density and low-power characteristics, STT-RAM technology can be utilized in GPUs where numerous cores leave a limited area for on-chip memory banks. They have, however, two important issues, high energy and latency of write operations, that have to be addressed. Low retention time STT-RAMs can reduce the energy and delay of write operations. Nevertheless, employing STT-RAMs with low retention time in GPUs requires a thorough study on the behavior of GPGPU applications. Based on this investigation, we have architectured a two-part STT-RAM-based L2 cache with low-retention (LR) and high-retention (HR) parts. The proposed two-part L2 cache exploits a dynamic threshold regulator (DTR) to efficiently regulate the write threshold for migration of the data blocks from HR to LR, based on the behavior of the applications. Also, a Data and Access type Aware Cache Search mechanism (DAACS) is hired for handling the search of the requested data blocks in two parts of the cache. The STT-RAM L2 cache architecture proposed in this article can improve IPC by up to 171% (20% on average), and reduce the average consumed power by 28.9% compared to a conventional L2 cache architecture with equal on-chip area.
Diversionary Comments under Blog Posts
Authors: Wang Jing , Yu Clement T. , Yu Philip S. , Liu Bing , Meng Weiyi
Published: September 2015

There has been a recent swell of interest in the analysis of blog comments. However, much of the work focuses on detecting comment spam in the blogsphere. An important issue that has been neglected so far is the identification of diversionary comments. Diversionary comments are defined as comments that divert the topic from the original post. A possible purpose is to distract readers from the original topic and draw attention to a new topic. We categorize diversionary comments into five types based on our observations and propose an effective framework to identify and flag them. To the best of our knowledge, the problem of detecting diversionary comments has not been studied so far. We solve the problem in two different ways: (i) rank all comments in descending order of being diversionary and (ii) consider it as a classification problem. Our evaluation on 4,179 comments under 40 different blog posts from Digg and Reddit shows that the proposed method achieves the high mean average precision of 91.9% when the problem is considered as a ranking problem and 84.9% of F-measure as a classification problem. Sensitivity analysis indicates that the effectiveness of the method is stable under different parameter settings.
Estimating Clustering Coefficients and Size of Social Networks via Random Walk
Authors: Katzir Liran , Hardiman Stephen J.
Published: September 2015

This work addresses the problem of estimating social network measures. Specifically, the measures at hand are the network average and global clustering coefficients and the number of registered users. The algorithms at hand (1) assume no prior knowledge about the network and (2) access the network using only the publicly available interface. More precisely, this work provides (a) a unified approach for clustering coefficients estimation and (b) a new network size estimator. The unified approach for the clustering coefficients yields the first external access algorithm for estimating the global clustering coefficient. The new network size estimator offers improved accuracy compared to prior art estimators.

Our approach is to view a social network as an undirected graph and use the public interface to retrieve a random walk. To estimate the clustering coefficient, the connectivity of each node in the random walk sequence is tested in turn. We show that the error drops exponentially in the number of random walk steps. For the network size estimation we offer a generalized view of prior art estimators that in turn yields an improved estimator. All algorithms are validated on several publicly available social network datasets.
A Document Retrieval Model Based on Digital Signal Filtering
Authors: Costa Alberto , Buccio Emanuele Di , Melucci Massimo
Published: September 2015

Information retrieval (IR) systems are designed, in general, to satisfy the information need of a user who expresses it by means of a query, by providing him with a subset of documents selected from a collection and ordered by decreasing relevance to the query. Such systems are based on IR models, which define how to represent the documents and the query, as well as how to determine the relevance of a document for a query. In this article, we present a new IR model based on concepts taken from both IR and digital signal processing (like Fourier analysis of signals and filtering). This allows the whole IR process to be seen as a physical phenomenon, where the query corresponds to a signal, the documents correspond to filters, and the determination of the relevant documents to the query is done by filtering that signal. Tests showed that the quality of the results provided by this IR model is comparable with the state-of-the-art.
Visualizing Sets with Linear Diagrams
Authors: Rodgers Peter , Stapleton Gem , Chapman Peter
Published: September 2015

This paper presents the first design principles that optimize the visualization of sets using linear diagrams. These principles are justified through empirical studies that evaluate the impact of graphical features on task performance. Linear diagrams represent sets using straight line segments, with line overlaps corresponding to set intersections. This study builds on recent empirical research, which establishes that linear diagrams can be superior to prominent set visualization techniques, namely Euler and Venn diagrams. We address the problem of how to best visualize overlapping sets using linear diagrams. To solve the problem, we investigate which graphical features of linear diagrams significantly impact user task performance. To this end, we conducted seven crowdsourced empirical studies involving a total of 1,760 participants. These studies allowed us to identify the following design principles, which significantly aid task performance: use a minimal number of line segments, use guidelines where overlaps start and end, and draw lines that are thin as opposed to thick bars. We also evaluated the following graphical properties that did not significantly impact task performance: color, orientation, and set order. The results are brought to life through a freely available software implementation that automatically draws linear diagrams with user-controlled graphical choices. An important consequence of our research is that users are now able to create effective visualizations of sets automatically, thus improving human--computer interaction.
From Security Protocols to Pushdown Automata
Authors: Chrétien Rémy , Cortier Véronique , Delaune Stéphanie
Published: September 2015

Formal methods have been very successful in analyzing security protocols for reachability properties such as secrecy or authentication. In contrast, there are very few results for equivalence-based properties, crucial for studying, for example, privacy-like properties such as anonymity or vote secrecy.

We study the problem of checking equivalence of security protocols for an unbounded number of sessions. Since replication leads very quickly to undecidability (even in the simple case of secrecy), we focus on a limited fragment of protocols (standard primitives but pairs, one variable per protocol’s rules) for which the secrecy preservation problem is known to be decidable. Surprisingly, this fragment turns out to be undecidable for equivalence. Then, restricting our attention to deterministic protocols, we propose the first decidability result for checking equivalence of protocols for an unbounded number of sessions. This result is obtained through a characterization of equivalence of protocols in terms of equality of languages of (generalized, real-time) deterministic pushdown automata. We further show that checking for equivalence of protocols is actually equivalent to checking for equivalence of generalized, real-time deterministic pushdown automata.

Very recently, the algorithm for checking for equivalence of deterministic pushdown automata has been implemented. We have implemented our translation from protocols to pushdown automata, yielding the first tool that decides equivalence of (some class of) protocols, for an unbounded number of sessions. As an application, we have analyzed some protocols of the literature including a simplified version of the basic access control (BAC) protocol used in biometric passports.
In defense of IBM
Authors: Cusumano Michael A.
Published: September 2015

The ability to adjust to various technical and business disruptions has been essential to IBM's success during the past century.
Storming the cubicle
Authors: Neville-Neil George V.
Published: September 2015

Acquisitive redux
Thinking thoughts
Authors: Armour Phillip G.
Published: September 2015

On brains and bytes.
Computing is history
Authors: Misa Thomas J.
Published: September 2015

Reflections on the past to inform the future.
On the Decidability of Elementary Modal Logics
Authors: Michaliszyn Jakub , Otop Jan , Kieroński Emanuel
Published: September 2015

We consider the satisfiability problem for modal logic over first-order definable classes of frames. We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is either NP-complete or PS
pace
-complete, and global satisfiability is NP-complete, PS
pace
-complete, or E
xp
T
ime
-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability.
Inside the Social Network's (Datacenter) Network
Authors: Roy Arjun , Zeng Hongyi , Bagga Jasmeet , Porter George , Snoeren Alex C.
Published: September 2015

Large cloud service providers have invested in increasingly larger datacenters to house the computing infrastructure required to support their services. Accordingly, researchers and industry practitioners alike have focused a great deal of effort designing network fabrics to efficiently interconnect and manage the traffic within these datacenters in performant yet efficient fashions. Unfortunately, datacenter operators are generally reticent to share the actual requirements of their applications, making it challenging to evaluate the practicality of any particular design.

Moreover, the limited large-scale workload information available in the literature has, for better or worse, heretofore largely been provided by a single datacenter operator whose use cases may not be widespread. In this work, we report upon the network traffic observed in some of Facebook's datacenters. While Facebook operates a number of traditional datacenter services like Hadoop, its core Web service and supporting cache infrastructure exhibit a number of behaviors that contrast with those reported in the literature. We report on the contrasting locality, stability, and predictability of network traffic in Facebook's datacenters, and comment on their implications for network architecture, traffic engineering, and switch design.
Poptrie
Authors: Asai Hirochika , Ohara Yasuhiro
Published: September 2015

Internet of Things leads to routing table explosion. An inexpensive approach for IP routing table lookup is required against ever growing size of the Internet. We contribute by a fast and scalable software routing lookup algorithm based on a multiway trie, called Poptrie. Named after our approach to traversing the tree, it leverages the population count instruction on bit-vector indices for the descendant nodes to compress the data structure within the CPU cache. Poptrie outperforms the state-of-the-art technologies, Tree BitMap, DXR and SAIL, in all of the evaluations using random and real destination queries on 35 routing tables, including the real global tier-1 ISP's full-route routing table. Poptrie peaks between 174 and over 240 Million lookups per second (Mlps) with a single core and tables with 500--800k routes, consistently 4--578% faster than all competing algorithms in all the tests we ran. We provide the comprehensive performance evaluation, remarkably with the CPU cycle analysis. This paper shows the suitability of Poptrie in the future Internet including IPv6, where a larger route table is expected with longer prefixes.
Network-Aware Scheduling for Data-Parallel Jobs
Authors: Jalaparti Virajith , Bodik Peter , Menache Ishai , Rao Sriram , Makarychev Konstantin , Caesar Matthew
Published: September 2015

To reduce the impact of network congestion on big data jobs, cluster management frameworks use various heuristics to schedule compute tasks and/or network flows. Most of these schedulers consider the job input data fixed and greedily schedule the tasks and flows that are ready to run. However, a large fraction of production jobs are recurring with predictable characteristics, which allows us to plan ahead for them. Coordinating the placement of data and tasks of these jobs allows for significantly improving their network locality and freeing up bandwidth, which can be used by other jobs running on the cluster. With this intuition, we develop Corral, a scheduling framework that uses characteristics of future workloads to determine an offline schedule which (i) jointly places data and compute to achieve better data locality, and (ii) isolates jobs both spatially (by scheduling them in different parts of the cluster) and temporally, improving their performance. We implement Corral on Apache Yarn, and evaluate it on a 210 machine cluster using production workloads. Compared to Yarn's capacity scheduler, Corral reduces the makespan of these workloads up to 33% and the median completion time up to 56%, with 20-90% reduction in data transferred across racks.
BackFi
Authors: Bharadia Dinesh , Joshi Kiran Raj , Kotaru Manikanta , Katti Sachin
Published: September 2015

We present BackFi, a novel communication system that enables high throughput, long range communication between very low power backscatter devices and WiFi APs using ambient WiFi transmissions as the excitation signal. Specifically, we show that it is possible to design devices and WiFi APs such that the WiFi AP in the process of transmitting data to normal WiFi clients can decode backscatter signals which the devices generate by modulating information on to the ambient WiFi transmission. We show via prototypes and experiments that it is possible to achieve communication rates of up to 5 Mbps at a range of 1 m and 1 Mbps at a range of 5 meters. Such performance is an order to three orders of magnitude better than the best known prior WiFi backscatter system [27,25]. BackFi design is energy efficient, as it relies on backscattering alone and needs insignificant power, hence the energy consumed per bit is small.
Rollback-Recovery for Middleboxes
Authors: Sherry Justine , Gao Peter Xiang , Basu Soumya , Panda Aurojit , Krishnamurthy Arvind , Maciocco Christian , Manesh Maziar , Martins João , Ratnasamy Sylvia , Rizzo Luigi , Shenker Scott
Published: September 2015

Network middleboxes must offer high availability, with automatic failover when a device fails. Achieving high availability is challenging because failover must correctly restore lost state (e.g., activity logs, port mappings) but must do so quickly (e.g., in less than typical transport timeout values to minimize disruption to applications) and with little overhead to failure-free operation (e.g., additional per-packet latencies of 10-100s of us). No existing middlebox design provides failover that is correct, fast to recover, and imposes little increased latency on failure-free operations. We present a new design for fault-tolerance in middleboxes that achieves these three goals. Our system, FTMB (for Fault-Tolerant MiddleBox), adopts the classical approach of "rollback recovery" in which a system uses information logged during normal operation to correctly reconstruct state after a failure. However, traditional rollback recovery cannot maintain high throughput given the frequent output rate of middleboxes. Hence, we design a novel solution to record middlebox state which relies on two mechanisms: (1) 'ordered logging', which provides lightweight logging of the information needed after recovery, and (2) a `parallel release' algorithm which, when coupled with ordered logging, ensures that recovery is always correct. We implement ordered logging and parallel release in Click and show that for our test applications our design adds only 30$\mu$s of latency to median per packet latencies. Our system introduces moderate throughput overheads (5-30%) and can reconstruct lost state in 40-275ms for practical systems.