bluuebunny/crossref_metadata_2025 huggingface dataset:
Dualtropic CXCR6/CCR5 Simian Immunodeficiency Virus (SIV) Infection of Sooty Mangabey Primary Lymphocytes: Distinct Coreceptor Use in Natural versus Pathogenic Hosts of SIV
Authors: Elliott Sarah T. C. , Wetzel Katherine S. , Francella Nicholas , Bryan Steven , Romero Dino C. , Riddick Nadeene E. , Shaheen Farida , Vanderford Thomas , Derdeyn Cynthia A. , Silvestri Guido , Paiardini Mirko , Collman Ronald G.
Published: June 2015

Natural-host sooty mangabeys (SM) infected with simian immunodeficiency virus (SIV) exhibit high viral loads but do not develop disease, whereas infection of rhesus macaques (RM) causes CD4
+
T cell loss and AIDS. Several mechanisms have been proposed to explain these divergent outcomes, including differences in cell targeting, which have been linked to low expression of the canonical SIV entry receptor CCR5 on CD4
+
T cells of SM and other natural hosts. We previously showed that infection and high-level viremia occur even in a subset of SM that genetically lack functional CCR5, which indicates that alternative entry coreceptors are used by SIV
in vivo
in these animals. We also showed that SM CXCR6 is a robust coreceptor for SIV
smm
in vitro
. Here we identify CXCR6 as a principal entry pathway for SIV in SM primary lymphocytes. We show that
ex vivo
SIV infection of lymphocytes from CCR5 wild-type SM is mediated by both CXCR6 and CCR5. In contrast, infection of RM lymphocytes is fully dependent on CCR5. These data raise the possibility that CXCR6-directed tropism in CCR5-low natural hosts may alter CD4
+
T cell subset targeting compared with that in nonnatural hosts, enabling SIV to maintain high-level replication without leading to widespread CD4
+
T cell loss.

IMPORTANCE
Natural hosts of SIV, such as sooty mangabeys, sustain high viral loads but do not develop disease, while nonnatural hosts, like rhesus macaques, develop AIDS. Understanding this difference may help elucidate mechanisms of pathogenesis. Natural hosts have very low levels of the SIV entry coreceptor CCR5, suggesting that restricted entry may limit infection of certain target cells, although it is unclear how the virus replicates so robustly. Here we show that in sooty mangabey lymphocytes, infection is mediated by the alternative entry coreceptor CXCR6, as well as CCR5. In rhesus macaque lymphocytes, however, infection occurs entirely through CCR5. The use of CXCR6 for entry, combined with very low CCR5 levels, may redirect the virus to different cell targets in natural hosts. It is possible that differential targeting may favor infection of nonessential cells and limit infection of critical cells in natural hosts, thus contributing to benign outcome of infection.
Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL
Authors: Kumar Rajnish , Pan Ruimin , Upadhyay Chitra , Mayr Luzia , Cohen Sandra , Wang Xiao-Hong , Balasubramanian Preetha , Nádas Arthur , Seaman Michael S. , Zolla-Pazner Susan , Gorny Miroslaw K. , Kong Xiang-Peng , Hioe Catarina E.
Published: June 2015

The V3 region of HIV-1 gp120 is important for virus-coreceptor interaction and highly immunogenic. Although most anti-V3 antibodies neutralize only the sensitive tier 1 viruses, anti-V3 antibodies effective against the more resistant viruses exist, and a better understanding of these antibodies and their epitopes would be beneficial for the development of novel vaccine immunogens against HIV. The HIV-1 isolate JRFL with its cryptic V3 is resistant to most V3-specific monoclonal antibodies (MAbs). However, the V3 MAb 2424 achieves 100% neutralization against JRFL. 2424 is encoded by IGHV3-53 and IGLV2-28 genes, a pairing rarely used by the other V3 MAbs. 2424 also has distinct binding and neutralization profiles. Studies of 2424-mediated neutralization of JRFL produced with a mannosidase inhibitor further revealed that its neutralizing activity is unaffected by the glycan composition of the virus envelope. To understand the distinct activity of 2424, we determined the crystal structure of 2424 Fab in complex with a JRFL V3 peptide and showed that the 2424 epitope is located at the tip of the V3 crown (307IHIGPGRAFYT319), dominated by interactions with HisP308, ProP313, and ArgP315. The binding mode of 2424 is similar to that of the well-characterized MAb 447-52D, although 2424 is more side chain dependent. The 2424 epitope is focused on the very apex of V3, away from nearby glycans, facilitating antibody access. This feature distinguishes the 2424 epitope from the other V3 crown epitopes and indicates that the tip of V3 is a potential site to target and incorporate into HIV vaccine immunogens.

IMPORTANCEHIV/AIDS vaccines are crucial for controlling the HIV epidemics that continue to afflict millions of people worldwide. However, HIV vaccine development has been hampered by significant scientific challenges, one of which is the inability of HIV vaccine candidates evaluated thus far to elicit production of potent and broadly neutralizing antibodies. The V3 loop is one of the few immunogenic targets on the virus envelope glycoprotein that can induce neutralizing antibodies, but in many viruses, parts of V3 are inaccessible for antibody recognition. This study examined a V3-specific monoclonal antibody that can completely neutralize HIV-1 JRFL, a virus isolate resistant to most V3 antibodies. Our data reveal that this antibody recognizes the most distal tip of V3, which is not as occluded as other parts of V3. Hence, the epitope of 2424 is in one of the vulnerable sites on the virus that may be exploited in designing HIV vaccine immunogens.
The Great (Nuclear) Escape: New Insights into the Role of the Nuclear Egress Complex of Herpesviruses
Authors: Bigalke Janna M. , Heldwein Ekaterina E.
Published: June 2015

Herpesviruses are unusual among enveloped viruses because they bud twice yet acquire a single envelope. They are also the only known viruses that bud into the nuclear envelope. We discovered that the herpesvirus nuclear egress complex could bud membranes without the help of other proteins by forming a coat-like hexagonal scaffold inside the budding membrane. This finding raises the possibility that a phenotypically similar nuclear export of large RNAs is cargo driven.
Antimicrobial Tolerance in Biofilms
Authors: Stewart Philip S.
Published: June 2015

The tolerance of microorganisms in biofilms to antimicrobial agents is examined through a meta-analysis of literature data. A numerical tolerance factor comparing the rates of killing in the planktonic and biofilm states is defined to provide a quantitative basis for the analysis. Tolerance factors for biocides and antibiotics range over three orders of magnitude. This variation is not explained by taking into account the molecular weight of the agent, the chemistry of the agent, the substratum material, or the speciation of the microorganisms. Tolerance factors do depend on the areal cell density of the biofilm at the time of treatment and on the age of the biofilm as grown in a particular experimental system. This suggests that there is something that happens during biofilm maturation, either physical or physiological, that is essential for full biofilm tolerance. Experimental measurements of antimicrobial penetration times in biofilms range over orders of magnitude, with slower penetration (>12 min) observed for reactive oxidants and cationic molecules. These agents are retarded through the interaction of reaction, sorption, and diffusion. The specific physiological status of microbial cells in a biofilm contributes to antimicrobial tolerance. A conceptual framework for categorizing physiological cell states is discussed in the context of antimicrobial susceptibility. It is likely that biofilms harbor cells in multiple states simultaneously (e.g., growing, stress-adapted, dormant, inactive) and that this physiological heterogeneity is an important factor in the tolerance of the biofilm state.
Enteric Pathogens Exploit the Microbiota-generated Nutritional Environment of the Gut
Authors: Pacheco Alline R. , Sperandio Vanessa
Published: June 2015

Host bacterial associations have a profound impact on health and disease. The human gastrointestinal (GI) tract is inhabited by trillions of commensal bacteria that aid in the digestion of food and vitamin production and play crucial roles in human physiology. Disruption of these relationships and the structure of the bacterial communities that inhabit the gut can contribute to dysbiosis, leading to disease. This fundamental relationship between the host and microbiota relies on chemical signaling and nutrient availability and exchange. GI pathogens compete with the endogenous microbiota for a colonization niche (
1
,
2
). The ability to monitor nutrients and combine this information with the host physiological state is important for the pathogen to precisely program the expression of its virulence repertoire. A major nutrient source is carbon, and although the impact of carbon nutrition on the colonization of the gut by the microbiota has been extensively studied, the extent to which carbon sources affect the regulation of virulence factors by invading pathogens has not been fully defined. The GI pathogen enterohemorrhagic
E. coli
(EHEC) gages sugar sources as an important cue to regulate expression of its virulence genes. EHEC senses whether it is in a gluconeogenic versus a glycolytic environment, as well as fluctuations of fucose levels to fine tune regulation of its virulence repertoire.
Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria
Authors: Bobrovskyy Maksym , Vanderpool Carin K. , Richards Gregory R.
Published: June 2015

Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
Borrelia burgdorferi
: Carbon Metabolism and the Tick-Mammal Enzootic Cycle
Authors: Corona Arianna , Schwartz Ira
Published: June 2015

Borrelia burgdorferi
, the spirochetal agent of Lyme disease, is a zoonotic pathogen that is maintained in a natural cycle that typically involves mammalian reservoir hosts and a tick vector of the
Ixodes
species. During each stage of the enzootic cycle,
B. burgdorferi
is exposed to environments that differ in temperature, pH, small molecules, and most important, nutrient sources.
B. burgdorferi
has a highly restricted metabolic capacity because it does not contain a tricarboxylic acid cycle, oxidative phosphorylation, or any pathways for
de novo
biosynthesis of carbohydrates, amino acids, or lipids. Thus,
B. burgdorferi
relies solely on glycolysis for ATP production and is completely dependent on the transport of nutrients and cofactors from extracellular sources. Herein, pathways for carbohydrate uptake and utilization in
B. burgdorferi
are described. Regulation of these pathways during the different phases of the enzootic cycle is discussed. In addition, a model for differential control of nutrient flux through the glycolytic pathway as the spirochete transits through the enzootic cycle is presented.
The Fish Pathogen
Vibrio vulnificus
Biotype 2: Epidemiology, Phylogeny, and Virulence Factors Involved in Warm-Water Vibriosis
Authors: Amaro Carmen , Sanjuán Eva , Fouz Belén , Pajuelo David , Lee Chung-Te , Hor Lien-I , Barrera Rodolfo
Published: June 2015

Vibrio vulnificus
biotype 2 is the etiological agent of warm-water vibriosis, a disease that affects eels and other teleosts, especially in fish farms. Biotype 2 is polyphyletic and probably emerged from aquatic bacteria by acquisition of a transferable virulence plasmid that encodes resistance to innate immunity of eels and other teleosts. Interestingly, biotype 2 comprises a zoonotic clonal complex designated as serovar E that has extended worldwide. One of the most interesting virulence factors produced by serovar E is RtxA1
3
, a multifunctional protein that acts as a lethal factor for fish, an invasion factor for mice, and a survival factor outside the host. Two practically identical copies of
rtxA1

3

are present in all biotype 2 strains regardless of the serovar, one in the virulence plasmid and the other in chromosome II. The plasmid also contains other genes involved in survival and growth in eel blood:
vep07
, a gene for an outer membrane (OM) lipoprotein involved in resistance to eel serum and
vep20
, a gene for an OM receptor specific for eel-transferrin and, probably, other related fish transferrins. All the three genes are highly conserved within biotype 2, which suggests that they are under a strong selective pressure. Interestingly, the three genes are related with transferable plasmids, which emphasizes the role of horizontal gene transfer in the evolution of
V. vulnificus
in nutrient-enriched aquatic environments, such as fish farms.
Flare frequency, healthcare resource utilisation and costs among patients with gout in a managed care setting: a retrospective medical claims-based analysis
Authors: Jackson Robert , Shiozawa Aki , Buysman Erin K , Altan Aylin , Korrer Stephanie , Choi Hyon
Published: June 2015

Objectives

For most gout patients, excruciatingly painful gout attacks are the major clinical burden of the disease. The goal of this study was to assess the association of frequent gout flares with healthcare burden, and to quantify how much lower gout-related costs and resource use are for those with infrequent flares compared to frequent gout flares.

Design

Retrospective cohort study.

Setting

Administrative claims data from a large US health plan.

Participants

Patients aged 18 years or above, and with evidence of gout based on medical and pharmacy claims between January 2009 and April 2012 were eligible for inclusion. Patient characteristics were assessed during a 12-month baseline period.

Outcome measures

Frequency of gout flares, healthcare costs and resource utilisation were assessed in the 12 months following the first qualifying gout claim. Generalised linear models were employed to assess the impact of flare frequency on cost outcomes after adjusting for covariates.

Results

102 703 patients with gout met study inclusion criteria; 89 201 had 0–1 gout flares, 9714 had 2 flares, and 3788 had 3+ flares. Average counts of gout-related inpatient stays, emergency room visits and ambulatory visits were higher among patients with 2 or 3+ flares, compared to those with 0–1 flares (all p<0.001). Adjusted annual gout-related costs were $1804, $3014 and $4363 in those with 0–1, 2 and 3+ gout flares, respectively (p<0.001 comparing 0–1 flares to 2 or 3+ flares).

Conclusions

Gout-related costs and resource use were lower for those with infrequent flares, suggesting significant cost benefit to a gout management plan that has a goal of reducing flare frequency.
Gestational age and newborn size according to parental social mobility: an intergenerational cohort study
Authors: Gigante Denise P , Horta Bernardo L , Matijasevich Alicia , Loret de Mola Christian , Barros Aluisio J D , Santos Ina S , Barros Fernando C , Victora Cesar G
Published: June 2015

Background

We examined the associations between socioeconomic trajectories from birth to adulthood and gestational age and birth size in the next generation, using linked data from two population-based birth cohorts carried out in a Brazilian city. By comparing socioeconomic trajectories of mothers and fathers, we attempted to identify-specific effects of maternal and paternal socioeconomic trajectory on offspring birth weight, birth length, head circumference and gestational age at birth.

Methods

2 population-based birth cohort studies were carried out in 1982 and 2004 in Pelotas (Brazil); 156 mothers and 110 fathers from the earlier cohort had children in 2004. Gestational age and birth length, weight and head circumference were measured. Analyses were carried out separately for mothers and fathers. Mediation analyses assessed the role of birth weight and adult body mass index (BMI).

Results

Among mothers, but not for fathers, childhood poverty was strongly associated with smaller size in the next generation (about 400 g in weight and 1.5 cm in height) and shorter gestations (about 2 weeks). Adult poverty did not play a role. For mothers, the associations with gestational age, birth length and weight—but not with head circumference—persisted after adjusting for maternal birth weight and for the height and weight of the grandmother. Maternal birth weight did not mediate the observed associations, but high maternal BMI in adulthood was partly responsible for the association with gestational age.

Conclusions

Strong effects of early poverty on gestational age and birth size in the next generation were observed among mothers, but not among fathers. These findings suggest a specific maternal effect of socioeconomic trajectory, and in particular of early poverty on offspring size and duration of pregnancy.
Shaft resistance of driven cast-in-situ piles in sand
Authors: Flynn Kevin N. , McCabe Bryan A.
Published: June 2015

Driven cast-in-situ (DCIS) piles are classified as a large displacement pile, despite sharing certain aspects of their construction with replacement pile types. However, there are relatively few case histories of load tests on DCIS piles in the literature to verify the assumption that they behave as large displacement piles. In particular, the shaft resistance of DCIS piles in sand is uncertain due to the complex interaction between the freshly cast concrete and surrounding displaced soil after extraction of the steel installation tube. This paper describes the installation, curing, and maintained compression load testing of three temporary-cased DCIS test piles at a uniform sand site near Coventry, United Kingdom. The piles were instrumented with vibrating wire strain gauges to enable accurate measurement of the local shear stress generated on the pile shaft during maintained compression loading. The tests showed that the peak average and local shear stresses tended to mobilize at greater shaft displacements than traditional preformed displacement piles during loading. A clear reduction in normalized local shear stresses (and hence radial effective stress) at failure with distance from the pile base, i.e., friction fatigue, was evident for all piles, implying that radial stresses generated during driven installation of the steel tube are not erased upon concreting and tube withdrawal. Furthermore, the inferred normalized radial effective stresses at failure were remarkably similar to those reported for traditional preformed displacement piles in the literature.
Role of thioredoxin nitration in bleomycin-induced pulmonary fibrosis in rats
Authors: Wang Lei , Song Yimin , Li Xiankui , Guo Haizhou , Zhang Guojun
Published: June 2015

Oxidant stimulation has been suggested to play an important role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). Our study aimed to investigate the role and mechanisms of thioredoxin (Trx) nitration during the development of IPF. A rat model of IPF was established by intratracheal instillation of bleomycin (BLM). Male Wistar rats were randomly distributed among the control group and BLM-treated group, in which rats were intratracheally instilled with a single dose of BLM (5.0 mg/kg body mass in 1.0 mL phosphate-buffered saline). At 7 or 28 days after instillation the rats were euthanized. Histopathological and biochemical examinations were performed. The activity and protein level of thioredoxin were assessed. The thioredoxin nitration level was determined using immunoprecipitation and immunoblotting techniques. Our results demonstrated that protein tyrosine nitration increased in the BLM-treated group compared with the control group. Trx activity decreased in the BLM group compared with control group, whereas Trx expression and nitration level increased dramatically in the BLM group compared with the control group. Our results indicated that Trx nitration might be involved in the pathogenesis of IPF.
Cortisol and catecholamine responses to social context and a chemical alarm signal in juvenile lake sturgeon,Acipenserfulvescens
Authors: Hare Alexander J. , Waheed Ahmed , Hare James F. , Anderson W. Gary
Published: June 2015

We examined potential benefits of group living in juvenile lake sturgeon (Acipenser fulvescens Rafinesque, 1817) and whether those benefits applied equally to associations with conspecific and allospecific individuals. In the first experiment, one focal lake sturgeon was placed with either seven size-matched conspecifics, allospecifics, or in isolation and given a 30 s air exposure. In the second experiment, one focal lake sturgeon was placed with either seven conspecifics or in isolation and was exposed to a conspecific skin homogenate as a potential alarm substance or a control of distilled water. Cortisol, norepinephrine, and epinephrine levels were measured before and after exposure in each experiment via an indwelling cannula in the caudal sinus. In the first experiment, lake sturgeon held with allospecifics and in isolation had a significantly longer norepinephrine response. Furthermore, plasma norepinephrine concentration in the focal lake sturgeon in the allospecific treatment was significantly higher than the other treatments following air exposure. In the second experiment, there was no behavioural or hormonal response to the introduction of conspecific skin homogenate, yet isolated fish had elevated baseline norepinephrine and cortisol levels. Finally, comparison of baseline levels of all three hormones between two ages of juveniles indicated an effect of age on baseline epinephrine levels. Our findings confirm the potential physiological benefit of group living in lake sturgeon and suggest an ontogenetic shift in both the behavioural response to potential stressors and the baseline hormonal levels that may influence fitness.
Local varying-alpha theories
Authors: Barrow John D. , Magueijo João
Published: June 2015

In a recent paper, we demonstrated how the simplest model for varying-alpha may be interpreted as the effect of a dielectric material, generalized to be consistent with Lorentz invariance. Unlike normal dielectrics, such a medium cannot change the speed of light, and its dynamics obey a Klein–Gordon equation. This work immediately suggests an extension of the standard theory, even if we require compliance with Lorentz invariance. Instead of a wave equation, the dynamics may satisfy a local algebraic relation involving the permittivity and the properties of the electromagnetic (EM) field, in analogy with more conventional dielectric (but still preserving Lorentz invariance). We develop the formalism for such theories and investigate some phenomenological implications. The problem of the divergence of the classical self-energy can be solved, or at least softened, in this framework. Some interesting new cosmological solutions for the very early universe are found, including the possibility of a bounce, inflation and expansion with a loitering phase, all of which are induced by early variations in alpha.
The statistical and dynamics properties of hard-sphere polymer chains
Authors: Huang Zi-Wen , Hou Ji-Xuan , Xie Chun , Zhang Hao
Published: June 2015

We investigated a highly coarse-grained polymer model — hard-sphere (HS) model. This model is characterized by its time-saving computation and strictly guaranteed uncrossability of polymer chains. Regarding the statistical and dynamic properties of HS model, our simulating results perfectly coincide with pre-existing scaling theory. Additionally, we point out that the power exponent of scaling relationship between its relaxation time and chain length is 2.2.
A Pairwise Naïve Bayes Approach to Bayesian Classification
Authors: Asafu-Adjei Josephine K. , Betensky Rebecca A.
Published: June 2015

Despite the relatively high accuracy of the naïve Bayes (NB) classifier, there may be several instances where it is not optimal, i.e. does not have the same classification performance as the Bayes classifier utilizing the joint distribution of the examined attributes. However, the Bayes classifier can be computationally intractable due to its required knowledge of the joint distribution. Therefore, we introduce a "pairwise naïve" Bayes (PNB) classifier that incorporates all pairwise relationships among the examined attributes, but does not require specification of the joint distribution. In this paper, we first describe the necessary and sufficient conditions under which the PNB classifier is optimal. We then discuss sufficient conditions for which the PNB classifier, and not NB, is optimal for normal attributes. Through simulation and actual studies, we evaluate the performance of our proposed classifier relative to the Bayes and NB classifiers, along with the HNB, AODE, LBR and TAN classifiers, using normal density and empirical estimation methods. Our applications show that the PNB classifier using normal density estimation yields the highest accuracy for data sets containing continuous attributes. We conclude that it offers a useful compromise between the Bayes and NB classifiers.
An Efficient Coupled-Mode Formulation for Acoustic Propagation in Inhomogeneous Waveguides
Authors: Yang Chunmei , Luo Wenyu , Zhang Renhe , Lyu Liangang , Qiao Fangli
Published: June 2015

The direct-global-matrix coupled-mode model (DGMCM) for sound propagation in range-dependent waveguides was recently developed by Luo et al. [A numerically stable coupled-mode formulation for acoustic propagation in range-dependent waveguides, Sci. China G: Phys. Mech. Astron. 55 (2012) 572–588]. A brief review of the formulation and characteristics of this model is given. This paper extends this model to deal with realistic problems involving an inhomogeneous water column and a penetrable sloping bottom. To this end, the normal mode model KRAKEN is adopted to provide local modal solutions and their associated coupling matrices. As a result, the extended DGMCM model is capable of providing full two-way solutions to two-dimensional (2D) realistic problems with a depth- and range-dependent sound speed profile as well as a penetrable sloping bottom. To validate this model, it is first applied to a benchmark problem of sound propagation in a plane-parallel waveguide with a depth- and range-dependent sound speed profile, and then it is applied to a problem involving both an inhomogeneous water column and a sloping bottom. Comparisons with the analytical solution proposed by DeSanto and with the numerical model COUPLE are also provided, which show that the extended DGMCM model is accurate and efficient and hence can serve as a benchmark for realistic problems of sound propagation in an inhomogeneous waveguide.
Knowledge-based reasoning to annotate noncoding RNA using multi-agent system
Authors: Arruda Wosley C. , Souza Daniel S. , Ralha Célia G. , Walter Maria Emilia M. T. , Raiol Tainá , Brigido Marcelo M. , Stadler Peter F.
Published: June 2015

Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since characteristics and signals of ncRNAs are not entirely known, researchers use different computational tools together with their biological knowledge to predict putative ncRNAs. In this context, this work presents ncRNA-Agents, a multi-agent system to annotate ncRNAs based on the output of different tools, using inference rules to simulate biologists’ reasoning. Experiments with data from the fungus Saccharomyces cerevisiae allowed to measure the performance of ncRNA-Agents, with better sensibility, when compared to Infernal, a widely used tool for annotating ncRNA. Besides, data of the Schizosaccharomyces pombe and Paracoccidioides brasiliensis fungi identified novel putative ncRNAs, which demonstrated the usefulness of our approach. NcRNA-Agents can be be found at: http://www.biomol.unb.br/ncrna-agents .
Magnetic susceptibility application: a window onto ancient environments and climatic variations: foreword
Authors: Da Silva A. C. , Whalen M. T. , Hladil J. , Chadimova L. , Chen D. , Spassov S. , Boulvain F. , Devleeschouwer X.
Published: June 2015

Magnetic susceptibility (MS) is a powerful tool, which is being applied increasingly on sedimentary rocks to constrain stratigraphic correlations, or as a palaeo-environmental or palaeo-climatic tool. The origin of the magnetic minerals responsible for the variations in MS can be linked to various phenomena such as detrital inputs, pedogenesis, bacterial precipitation or diagenesis. Therefore, it is critical to improve our knowledge of the origin of the MS signal in order to apply it for correlations or as a proxy. Here, we present a synthesis of the techniques that can be applied to get a better understanding of the origin of the MS signal, through comparison with other palaeo-environmental proxies, through magnetic measurements or through dissolution and direct observation of the extracted minerals. We also propose an overview of the different techniques applied in order to use MS as a correlation tool, and we show various examples of successful applications of MS as a recorder of change in past sea-level and climate. We also present the main results and activities of the IGCP-580 project ‘Application of magnetic susceptibility as a palaeo-climatic proxy on Palaeozoic sedimentary rocks and characterization of the magnetic signal’.
Incentives in Large Random Two-Sided Markets
Authors: Immorlica Nicole , Mahdian Mohammad
Published: June 2015

Many centralized two-sided markets form a matching between participants by running a stable matching algorithm. It is a well-known fact that no matching mechanism based on a stable matching algorithm can guarantee truthfulness as a dominant strategy for participants. However, we show that in a probabilistic setting where the preference lists on one side of the market are composed of only a constant (independent of the size of the market) number of entries, each drawn from an arbitrary distribution, the number of participants that have more than one stable partner is vanishingly small. This proves (and generalizes) a conjecture of Roth and Peranson [1999]. As a corollary of this result, we show that, with high probability, the truthful strategy is the best response for a random player when the other players are truthful. We also analyze equilibria of the deferred acceptance stable matching game. We show that the game with complete information has an equilibrium in which, in expectation, a (1−
o
(1)) fraction of the strategies are truthful. In the more realistic setting of a game of incomplete information, we will show that the set of truthful stratiegs form a (1+
o
(1))-approximate Bayesian-Nash equilibrium for uniformly random preferences. Our results have implications in many practical settings and are inspired by the work of Roth and Peranson [1999] on the National Residency Matching Program.
An Improved Competitive Algorithm for Reordering Buffer Management
Authors: Avigdor-Elgrabli Noa , Rabani Yuval
Published: June 2015

We design and analyze an online reordering buffer management algorithm with improved
O
(log 
k
/log log 
k
) competitive ratio for nonuniform costs, where
k
is the buffer size. This improves on the best previous result (even for uniform costs) of Englert and Westermann (2005) giving
O
(log 
k
) competitive ratio, which was also the best (offline) polynomial time approximation guarantee for this problem. Our analysis is based on an intricate dual fitting argument using a linear programming relaxation for the problem that we introduce in this article.
The future of computer science and engineering is in your hands
Authors: Kumar Vijay , Kalil Thomas A.
Published: June 2015

How government service can profoundly influence computer science research and education.
Unifying logic and probability
Authors: Russell Stuart
Published: June 2015

Open-universe probability models show merit in unifying efforts.
Design of Ultra-Low Power Scalable-Throughput Many-Core DSP Applications
Authors: Srivastav Meeta , Ehteshamuddin Mohammed , Stegner Kyle , Nazhandali Leyla
Published: June 2015

We propose a system-level solution in designing process variation aware (PVA) scalable-throughput many-core systems for energy constrained applications. In our proposed methodology, we leverage the benefits of voltage scaling for obtaining energy efficiency while compensating for the loss in throughput by exploiting parallelism present in various DSP designs. We demonstrate that such a hybrid method consumes 6.27%- 28.15% less power as compared to simple dynamic voltage scaling over different workload environments. Design details of a prototype chip fabricated on 90
nm
technology node and its findings are presented. Chip consists of 8 homogeneous FIR cores, which are capable of running from near-threshold to nominal voltages. In our 20 chip population, we observe 7% variation in speed among the cores at nominal voltage (0.9V) and 26% at near threshold voltage (0.55V). We also observe 54% variation in power consumption of the cores. For any desired throughput, the optimum number of cores and their optimum operating voltage is chosen based on the speed and power characteristics of the cores present inside the chip. We will also present analysis on energy-efficiency of such systems based on changes in ambient temperature.
A Methodology to Recover RTL IP Functionality for Automatic Generation of SW Applications
Authors: Bombieri Nicola , Fummi Franco , Vinco Sara
Published: June 2015

With the advent of heterogeneous multiprocessor system-on-chips (MPSoCs), hardware/software partitioning is again on the rise both in research and in product development. In this new scenario, implementing intellectual-property (IP) blocks as SW applications rather than dedicated HW is an increasing trend to fully exploit the computation power provided by the MPSoC CPUs. On the other hand, whole libraries of IP blocks are available as RTL descriptions, most of them without a corresponding high-level SW implementation. In this context, this article presents a methodology to automatically generate SW applications in C++, by starting from existing RTL IPs implemented in hardware description language (HDL). The methodology exploits an abstraction algorithm to eliminate implementation details typical of HW descriptions (such as cycle-accurate functionality and data types) to guarantee relevant performance of the generated code. The experimental results show that, in many cases, the C++ code automatically generated in a few seconds with the proposed methodology is as efficient as the corresponding code manually implemented from scratch.
Explaining Software Failures by Cascade Fault Localization
Authors: Yi Qiuping , Yang Zijiang , Liu Jian , Zhao Chen , Wang Chao
Published: June 2015

During software debugging, a significant amount of effort is required for programmers to identify the root cause of a manifested failure. In this article, we propose a cascade fault localization method to help speed up this labor-intensive process via a combination of weakest precondition computation and constraint solving. Our approach produces a cause tree, where each node is a potential cause of the failure and each edge represents a casual relationship between two causes. There are two main contributions of this article that differentiate our approach from existing methods. First, our method systematically computes all potential causes of a failure and augments each cause with a proper context for ease of comprehension by the user. Second, our method organizes the potential causes in a tree structure to enable
on-the-fly
pruning based on domain knowledge and feedback from the user. We have implemented our new method in a software tool called CaFL, which builds upon the LLVM compiler and KLEE symbolic virtual machine. We have conducted experiments on a large set of public benchmarks, including real applications from GNU Coreutils and Busybox. Our results show that in most cases the user has to examine only a small fraction of the execution trace before identifying the root cause of the failure.
Aging- and Variation-Aware Delay Monitoring Using Representative Critical Path Selection
Authors: Firouzi Farshad , Ye Fangming , Chakrabarty Krishnendu , Tahoori Mehdi B.
Published: June 2015

Process together with runtime variations in temperature and voltage, as well as transistor aging, degrade path delay and may eventually induce circuit failure due to timing variations. Therefore, in-field tracking of path delays is essential, and to respond to this need, several delay sensor designs have been proposed in the literature. However, due to the significant overhead of these sensors and the large number of critical paths in today's IC, it is infeasible to monitor the delay of every critical path in silicon. We present an aging- and variationaware representative path selection technique based on machine learning that allows to measure the delay of a small set of paths and infer the delay of a larger pool of paths that are likely to fail due to delay variations. Simulation results for benchmark circuits highlight the accuracy of the proposed approach for predicting critical-path delay based on the selected representative paths.
SECRET
Authors: Lin Chung-Hsiang , Shen De-Yu , Chen Yi-Jung , Yang Chia-Lin , Wang Cheng-Yuan Michael
Published: June 2015

DRAMs are used as the main memory in most computing systems today. Studies show that DRAMs contribute to a significant part of overall system power consumption. One of the main challenges in low-power DRAM design is the inevitable refresh process. Due to process variation, memory cells exhibit retention time variations. Current DRAMs use a single refresh period determined by the cell with the largest leakage. Since prolonging refresh intervals introduces retention errors, a set of previous works adopt conventional error-correcting code (ECC) to correct retention errors. However, these approaches introduce significant area and energy overheads. In this article, we propose a novel error correction framework for retention errors in DRAMs, called
SECRET
(selective error correction for refresh energy reduction). The key observations we make are that retention errors are hard errors rather than soft errors, and only few DRAM cells have large leakage. Therefore, instead of equipping error correction capability for all memory cells as existing ECC schemes, we only allocate error correction information to leaky cells under a refresh interval. Our SECRET framework contains two parts: an offline phase to identify memory cells with retention errors given a target error rate and a low-overhead error correction mechanism. The experimental results show that among all test cases performed, the proposed SECRET framework can reduce refresh power by 87.2% and overall DRAM power up to 18.57% with negligible area and performance overheads.
Intercepting Functions for Memoization
Authors: Suresh Arjun , Swamy Bharath Narasimha , Rohou Erven , Seznec André
Published: June 2015

Memoization is the technique of saving the results of executions so that future executions can be omitted when the input set repeats. Memoization has been proposed in previous literature at the instruction, basic block, and function levels using hardware, as well as pure software--level approaches including changes to programming language.

In this article, we focus on software memoization for procedural languages such as C and Fortran at the granularity of a function. We propose a simple linker-based technique for enabling software memoization of any dynamically linked pure function by function interception and illustrate our framework using a set of computationally expensive pure functions—the transcendental functions. Transcendental functions are those that cannot be expressed in terms of a finite sequence of algebraic operations (trigonometric functions, exponential functions, etc.) and hence are computationally expensive.

Our technique does not need the availability of source code and thus can even be applied to commercial applications, as well as applications with legacy codes. As far as users are concerned, enabling memoization is as simple as setting an environment variable. Our framework does not make any specific assumptions about the underlying architecture or compiler toolchains and can work with a variety of current architectures. We present experimental results for a x86-64 platform using both gcc and icc compiler toolchains, and an ARM Cortex-A9 platform using gcc. Our experiments include a mix of real-world programs and standard benchmark suites: SPEC and Splash2x. On standard benchmark applications that extensively call the transcendental functions, we report memoization benefits of up to 50% on Intel Ivy Bridge and up to 10% on ARM Cortex-A9.

Memoization was able to regain a performance loss of 76% in bwaves due to a known performance bug in the GNU implementation of the
pow
function. The same benchmark on ARM Cortex-A9 benefited by more than 200%.
Section-Based Program Analysis to Reduce Overhead of Detecting Unsynchronized Thread Communication
Authors: Das Madan , Southern Gabriel , Renau Jose
Published: June 2015

Most systems that test and verify parallel programs, such as deterministic execution engines, data race detectors, and software transactional memory systems, require instrumenting loads and stores in an application. This can cause a very significant runtime and memory overhead compared to executing uninstrumented code. Multithreaded programming typically allows any thread to perform loads and stores to any location in the process’s address space independently, and such tools monitor all these memory accesses. However, many of the addresses in these unsynchronized memory accesses are only used by a single thread and do not affect other executing threads.

We propose Section-Based Program Analysis (SBPA), a novel way to decompose the program into disjoint code sections to identify and eliminate instrumenting such loads and stores during program compilation so that the program runtime overhead is significantly reduced. Our analysis includes improvements to pointer analysis and uses a few user directives to increase the effectiveness of SBPA further. We implemented SBPA for a deterministic execution runtime environment and were able to eliminate 51% of dynamic memory access instrumentations. When combined with directives, such reduction increased to 63%. We also integrated SBPA with ThreadSanitizer, a state-of-the-art dynamic race detector, and achieved a speedup of 2.43 (2.74 with directives) on a geometric mean basis.
Growing pains for deep learning
Authors: Edwards Chris
Published: June 2015

Neural networks, which support online image search and speech recognition, eventually will drive more advanced services.
SIGIR 2014
Authors: Halvey Martin , Villa Robert , Clough Paul D.
Published: June 2015

On July 11th 2014 the First Workshop on the Gathering Efficient Assessments of Relevance (GEAR 2014) was held as part of the SIGIR 2014 conference at the Gold Coast, Australia. An invited talk was given by Dr Nicola Ferro. Three full papers were presented, in addition to a design activity which lead to a lively discussion on gathering relevance assessments. This contribution discusses the events of the workshop.
Report on the Seventh Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR'14)
Authors: Alonso Omar , Kamps Jaap , Karlgren Jussi
Published: June 2015

There is an increasing amount of structure on the Web as a result of modern Web languages, user tagging and annotation, emerging robust NLP tools, and an ever growing volume of linked data. These meaningful, semantic, annotations hold the promise to significantly enhance information access, by enhancing the depth of analysis of today's systems. The goal of the ESAIR'14 workshop remained to advance the general research agenda on this core problem, with an explicit focus on one of the most challenging aspects to address in the coming years. The main remaining challenge is on the user's side---the potential of rich document annotations can only be realized if matched by more articulate queries exploiting these powerful retrieval cues---and a more dynamic approach is emerging by exploiting new forms of query autosuggest. How can the query suggestion paradigm be used to encourage searcher to articulate longer queries, with concepts and relations linking their statement of request to existing semantic models? How do entity results and social network data in "graph search" change the classic division between searchers and information and lead to extreme personalization---are you the query? How to leverage transaction logs and recommendation, and how adaptive should we make the system? What are the privacy ramifications and the UX aspects---how to not creep out users.

There was a strong feeling that we made substantial progress. Specifically, the discussion contributed to our understanding of the way forward. First, for notable (head, shoulder, but not tail) entities in semantic search we have reached the level of quality at minimal costs allowing for deployment in major web search engines---the dream has become a reality. Second, entity detection is moving fast into domain specific, personal, and business domains, and has become a vital component for a range of applications. Third, semantic web has exchanged logic for machine learning approaches, and machine learning is the natural unification of semantic web and information retrieval approaches.
Exploiting Implicit User Activity for Media Recommendation
Authors: Trevisiol Michele
Published: June 2015

This thesis explores in depth how to exploit the user browsing behavior, and in particular the referrer URL, to understand the interest of the users. The aim is, first, to understand the preferences of the users from their navigation patterns, i.e., from the implicit actions of the users. Then, to exploit this information to personalize the content offered by the service provider. The key findings from our studies allowed us to propose innovative solutions to perform recommendation and ranking of media content. We show how the browsing logs are extremely meaningful also for cold-start problem -- estimating the preferences of newcomers.
From Liking to Loyalty
Authors: Krishen Anjala S. , Trembath Leanne , Muthaly Siva
Published: June 2015

Building on existing models and social influence theory, we propose a hybrid social network affinity model which focuses on developing lasting relationships between consumers and social networking firms. Our model incorporates both rational and social influence motivations as antecedents to satisfaction and loyalty. Based on 352 adult respondents, we utilize a partial least squares structural equation method, and find that social network affinity is an important predictor of satisfaction and loyalty within a social network. In addition to other implications, our study indicates that social networking firms must build a sense of belonging, encourage interactivity, and offer ways to develop an emotional connection for their consumers.