bluuebunny/crossref_metadata_2025 huggingface dataset:
ISG15 Is Upregulated in Respiratory Syncytial Virus Infection and Reduces Virus Growth through Protein ISGylation
Authors: González-Sanz Rubén , Mata Manuel , Bermejo-Martín Jesús , Álvarez Amparo , Cortijo Julio , Melero José A. , Martínez Isidoro
Published: January 2016

Human respiratory syncytial virus (RSV), for which neither a vaccine nor an effective therapeutic treatment is currently available, is the leading cause of severe lower respiratory tract infections in children. Interferon-stimulated gene 15 (ISG15) is a ubiquitin-like protein that is highly increased during viral infections and has been reported to have an antiviral or a proviral activity, depending on the virus. Previous studies from our laboratory demonstrated strong ISG15 upregulation during RSV infectionin vitro. In this study, an in-depth analysis of the role of ISG15 in RSV infection is presented. ISG15 overexpression and small interfering RNA (siRNA)-silencing experiments, along with ISG15 knockout (ISG15−/−) cells, revealed an anti-RSV effect of the molecule. Conjugation inhibition assays demonstrated that ISG15 exerts its antiviral activity via protein ISGylation. This antiviral activity requires high levels of ISG15 to be present in the cells before RSV infection. Finally, ISG15 is also upregulated in human respiratory pseudostratified epithelia and in nasopharyngeal washes from infants infected with RSV, pointing to a possible antiviral role of the moleculein vivo. These results advance our understanding of the innate immune response elicited by RSV and open new possibilities to control infections by the virus.

IMPORTANCEAt present, no vaccine or effective treatment for human respiratory syncytial virus (RSV) is available. This study shows that interferon-stimulated gene 15 (ISG15) lowers RSV growth through protein ISGylation. In addition, ISG15 accumulation highly correlates with the RSV load in nasopharyngeal washes from children, indicating that ISG15 may also have an antiviral rolein vivo. These results improve our understanding of the innate immune response to RSV and identify ISG15 as a potential target for virus control.
TRIM5α Degradation via Autophagy Is Not Required for Retroviral Restriction
Authors: Imam Sabrina , Talley Sarah , Nelson Rachel S. , Dharan Adarsh , O'Connor Christopher , Hope Thomas J. , Campbell Edward M.
Published: January 2016

TRIM5α is an interferon-inducible retroviral restriction factor that prevents infection by inducing the abortive disassembly of capsid cores recognized by its C-terminal PRY/SPRY domain. The mechanism by which TRIM5α mediates the disassembly of viral cores is poorly understood. Previous studies demonstrated that proteasome inhibitors abrogate the ability of TRIM5α to induce premature core disassembly and prevent reverse transcription; however, viral infection is still inhibited, indicating that the proteasome is partially involved in the restriction process. Alternatively, we and others have observed that TRIM5α associates with proteins involved in autophagic degradation pathways, and one recent study found that autophagic degradation is required for the restriction of retroviruses by TRIM5α. Here, we show that TRIM5α is basally degraded via autophagy in the absence of restriction-sensitive virus. We observe that the autophagy markers LC3b and lysosome-associated membrane protein 2A (LAMP2A) localize to a subset of TRIM5α cytoplasmic bodies, and inhibition of lysosomal degradation with bafilomycin A1 increases this association. To test the requirement for macroautophagy in restriction, we examined the ability of TRIM5α to restrict retroviral infection in cells depleted of the autophagic mediators ATG5, Beclin1, and p62. In all cases, restriction of retroviruses by human TRIM5α, rhesus macaque TRIM5α, and owl monkey TRIM-Cyp remained potent in cells depleted of these autophagic effectors by small interfering RNA (siRNA) knockdown or clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing. Collectively, these results are consistent with observations that the turnover of TRIM5α proteins is sensitive to autophagy inhibition; however, the data presented here do not support observations that the inhibition of autophagy abrogates retroviral restriction by TRIM5 proteins.

IMPORTANCE
Restriction factors are a class of proteins that inhibit viral replication. Following fusion of a retrovirus with a host cell membrane, the retroviral capsid is released into the cytoplasm of the target cell. TRIM5α inhibits retroviral infection by promoting the abortive disassembly of incoming retroviral capsid cores; as a result, the retroviral genome is unable to traffic to the nucleus, and the viral life cycle is extinguished. In the process of restriction, TRIM5α itself is degraded by the proteasome. However, in the present study, we have shown that in the absence of a restriction-sensitive virus, TRIM5α is degraded by both proteasomal and autophagic degradation pathways. Notably, we observed that restriction of retroviruses by TRIM5α does not require autophagic machinery. These data indicate that the effector functions of TRIM5α can be separated from its degradation and may have further implications for understanding the mechanisms of other TRIM family members.
Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods
Authors: Hochstein Rebecca A. , Amenabar Maximiliano J. , Munson-McGee Jacob H. , Boyd Eric S. , Young Mark J.
Published: January 2016

The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea,Bacteria, andEukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus,Acidianustailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related toAcidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescencein situhybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts.

IMPORTANCEVirus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus,Acidianustailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life.
Bacterial Transcription as a Target for Antibacterial Drug Development
Authors: Ma Cong , Yang Xiao , Lewis Peter J.
Published: January 2016

Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
Endoscopic resection of a giant fibrovascular polyp of the oesophagus with the assistance of ultrasonic shears
Authors: Lobo Niyati , Hall Andrew , Weir Justin , Mace Alasdair
Published: January 2016

Giant fibrovascular polyps of the oesophagus are rare benign tumours originating from the upper oesophagus. A 58-year-old woman presented with a 6-week history of a sore throat, odynophagia and progressive dysphagia, managing only a soft diet. CT of the neck and thorax, and barium swallow, both demonstrated a giant fibrovascular polyp measuring approximately 7 cm in length arising from the proximal oesophagus. The patient underwent endoscopic resection of the polyp with the assistance of ultrasonic shears. We present the case of a giant fibrovascular polyp and describe our novel technique for successful endoscopic resection using ultrasonic shears.
Bovine ischaemic teat necrosis: a further potential role for digital dermatitis treponemes
Authors: Clegg S. R. , Carter S. D. , Stewart J. P. , Amin D. M. , Blowey R. W. , Evans N. J.
Published: January 2016

A recent outbreak of ischaemic teat necrosis (ITN) on mainland UK has resulted in large economic losses for dairy farmers. Typical cases start as an area of dry, thickened and encrusted skin on the medial aspect of the base of the teat, where the teat joins the udder, often with a fetid odour. The erosion spreads down the teat, often causing intense irritation, which in turn leads to more severely affected animals removing the entire teat. Due to the severity of ITN and the substantial economic costs to the industry, analyses were undertaken to ascertain if an infectious agent might be involved in the pathology. The study has considered a role for digital dermatitis (DD) treponemes in the aetiopathogenesis of ITN because, as well as being the prime bacteria associated with infectious lameness, they have been associated with a number of emerging skin diseases of cattle, including udder lesions. A high association between presence of DD‐associated treponemes and incidence of ITN (19/22), compared with absence in the control population is reported. Furthermore, sequencing of the 16S rRNA gene of treponeme isolates supports the hypothesis that the identified treponemes are similar or identical to those isolated from classical foot DD lesions in cattle (and sheep). Further studies are required to allow effective targeted prevention measures and/or treatments to be developed.
A stationary solution of the Navier–Stokes equations in a perturbed layer domain in ℝ3
Authors: Kobayashi Teppei
Published: January 2016

Many mathematicians treat stationary problems of the Navier–Stokes equations in various unbounded domains with compact and noncompact boundaries (e.g. exterior domains, half spaces, aperture domains). In this paper we prove that for a perturbed layer domain there exists a stationary solution of the Navier–Stokes equations approaching the Poiseuille flow with the restricted condition.
Computational fluid dynamics for modeling the turbulent natural convection in a double air-channel solar chimney system
Authors: Zavala-Guillén I. , Xamán J. , Álvarez G. , Arce J. , Hernández-Pérez I. , Gijón-Rivera M.
Published: January 2016

This study reports the modeling of the turbulent natural convection in a double air-channel solar chimney (SC-DC) and its comparison with a single air-channel solar chimney (SC-C). Prediction of the mass flow and the thermal behavior of the SC-DC were obtained under three different climates of Mexico during one summer day. The climates correspond to: tropical savannah (Mérida), arid desert (Hermosillo) and temperate with warm summer (Mexico City). A code based on the Finite Volume Method was developed and a [Formula: see text] turbulence model has been used to model air turbulence in the solar chimney (SC). The code was validated against experimental data. The results indicate that during the day the SC-DC extracts about 50% more mass flow than the SC-C. When the SC-DC is located in Mérida, Hermosillo and Mexico City, the air-changes extracted along the day were 60, 63 and 52, respectively. The air temperature at the outlet of the chimney increased up to 33%, 38% and 61% with respect to the temperature it has at the inlet for Mérida, Hermosillo and Mexico City, respectively.
Chaotic Medical Image Encryption Algorithm Based on Bit-Plane Decomposition
Authors: Dai Yin , Wang Huanzhen , Wang Yuyi
Published: January 2016

Due to the rapid rise of telemedicine, a lot of patients’ information will be transmitted through the Internet. However, the patients’ information is related to personal privacy, therefore, patients’ information needs to be encrypted when transmited and stored. Medical image encryption is a part of it. Due to the informative fine features of medical images, a common image encryption algorithm is no longer applied. Common encryption algorithm has a single theory based on chaos image encryption algorithm, other encryption algorithms are based on information entropy. However, the images processed with these cipher text encryption algorithm are cyclical, the outline is clear and the anti-tamper capability is not strong. In view of the bit being the smallest measure unit of pixel, in order to overcome the weakness from above algorithm, and take the advantage of the chaotic system, this paper will present a chaotic medical image encryption algorithm based on bit-plane decomposition. The paper combines the image encryption and chaotic system to improve the security. This way, it can increase the security of key space and image effectively. The histogram, pixel correlation, number of pixels change rate (NPCR) and other experimental results show that the algorithm satisfies the desired effect.
Research on Copy-Move Image Forgery Detection Using Features of Discrete Polar Complex Exponential Transform
Authors: Gan Yanfen , Zhong Junliu
Published: January 2016

With the aid of sophisticated photo-editing software, such as Photoshop, copy-move image forgery operation has been widely applied and has become a major concern in the field of information security in the modern society. A lot of work on detecting this kind of forgery has gained great achievements, but the detection results of geometrical transformations of copy-move regions are not so satisfactory. In this paper, a new method based on the Polar Complex Exponential Transform is proposed. This method addresses issues in image geometric moment, focusing on constructing rotation invariant moment and extracting features of the rotation invariant moment. In order to reduce rounding errors of the transform from the Polar coordinate system to the Cartesian coordinate system, a new transformation method is presented and discussed in detail at the same time. The new method constructs a [Formula: see text] shrunk template to transform the Cartesian coordinate system back to the Polar coordinate system. It can reduce transform errors to a much greater degree. Forgery detection, such as copy-move image forgery detection, is a difficult procedure, but experiments prove our method is a great improvement in detecting and identifying forgery images affected by the rotated transform.
Parameter-Level Data Flow Modeling Oriented to Product Design Process
Authors: Li Shen , Shao Xiao Dong , Zhang Zhi Hua , Ge Xiao Bo
Published: January 2016

In this paper, a method of data flow modeling for a product design process oriented to data parameter is proposed. The data parameters are defined, which are classified as the basic data parameters and complex data parameters. The mechanism of the mapping relationship between different forms of documents and some basic data parameters, and a data transmission based on parameters, are constructed. Aiming at the characteristics of the iterative design process, the parameters version mechanism including node modification and iteration information is proposed. The data parameters transmission relationships are represented by a parameters network model (PNM) based on a directed graph. Finally, through the table of data parameters mapping onto the workflow node and PNM, the data ports and data links in the data flow model are generated automatically by the program. Validation in the 15-meter-diameter S/Ka frequency band antenna design process of the “Reflector, Back frame and Center part design” data flow model shows that the method can effectively shorten the time of data flow modeling and improve the data transmission efficiency.
FABRICATION AND WEAR BEHAVIOR ANALYSIS ON AlCrFeNi HIGH ENTROPY ALLOY COATING UNDER DRY SLIDING AND OIL LUBRICATION TEST CONDITIONS
Authors: TANG YIPIN , WANG SHOUREN , SUN BIN , WANG YAN , QIAO YANG
Published: January 2016

In this paper, AlCrFeNi high entropy alloy coating was fabricated on the surface of Q235 steel using hot pressing sintering process. The coating has the controlled thickness size and excellent mechanical properties. Scanning electron microscopy (SEM), XRD and hardness testing method were used to study the morphology, phase structure and hardness of high entropy alloys coating. The lattice distortion plays a significant role in increasing the hardness. Coating formation mechanism caused by the element diffusion under the hot pressing effect is also discussed in the paper. Simultaneously, the dry sliding and oil lubrication wear tests, wear morphology observation and wear mechanism discussion were completed. As the result shows, AlCrFeNi high entropy alloys coating exhibits superior wear resistance either at dry sliding or oil lubrication tests owing to its hard high entropy solid solution structure.
Dynamics for the damped Boussinesq equation with delay
Authors: Zhao Lu , Yang Meihua , Zhang Chengjian
Published: January 2016

This paper is concerned with the dynamical behavior of the damped Boussinesq equation containing a delay forcing term. It shows that, under suitable dissipative conditions, such a system possesses a pullback attractor and a uniform forward attractor in [Formula: see text].
On the Lyapunov spectrum of relative transfer operators
Authors: Bessa Mário , Stadlbauer Manuel
Published: January 2016

We analyze the Lyapunov spectrum of the relative Ruelle operator associated with a skew product whose base is an ergodic automorphism and whose fibers are full shifts. We prove that these operators can be approximated in the [Formula: see text]-topology by positive matrices with an associated dominated splitting.
Multiple mixing from weak hyperbolicity by the Hopf argument
Authors: Coudène Yves , Hasselblatt Boris , Troubetzkoy Serge
Published: January 2016

We show that using only weak hyperbolicity (no smoothness, compactness or exponential rates) the Hopf argument produces multiple mixing in an elementary way. While this recovers classical results with far simpler proofs, the point is the broader applicability implied by the weak hypotheses. Some of the results can also be viewed as establishing “mixing implies multiple mixing” outside the classical hyperbolic context.
A DFT study on the mechanism of reaction between 2, 4-diisocyanatotolune and cellulose
Authors: Cao Jiping , Liu Yali , Shi Aijuan , Yuan Yuan , Wang Mingliang
Published: January 2016

The reaction mechanisms between 2, 4-Diisocyanatotolune (2, 4-TDI) and cellulose have been investigated using the density functional theory at the B3LYP/6-31[Formula: see text]G (d, p) level. The calculations show that the direct addition of 2, 4-TDI and cellulose possesses an unrealistically high barrier of 32–34[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. With a neighboring [Formula: see text]-d-glucose serving as a proton transporter by forming a flexible six-membered ring transition state, the energy barrier of the reaction is significantly reduced to 16–18 kcal[Formula: see text]mol[Formula: see text], which is in a good accordance with the experimental activation energy of 13.9–16.7[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is indicated that the reaction between 2, 4-TDI and cellulose is auto-catalyzed with a neighboring [Formula: see text]-d-glucose acting as a reactive catalyst.
On Jackson-type inequalities associated with separable Haar wavelets
Authors: Andrianov P. , Skopina M.
Published: January 2016

Uniform approximation of multivariate periodic functions by Haar polynomials is studied. A general sharp Jackson type inequality and its refinement for certain types of numbers [Formula: see text] are discussed. An interesting phenomenon appears for some numbers [Formula: see text]: a sharp estimate is not unique.
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes
Authors: DeJesus Michael A. , Ioerger Thomas R.
Published: January 2016

Sequencing of transposon-mutant libraries using next-generation sequencing (TnSeq) has become a popular method for determining which genes and non-coding regions are essential for growth under various conditions in bacteria. For methods that rely on quantitative comparison of counts of reads at transposon insertion sites, proper normalization of TnSeq datasets is vitally important. Real TnSeq datasets are often noisy and exhibit a significant skew that can be dominated by high counts at a small number of sites (often for non-biological reasons). If two datasets that are not appropriately normalized are compared, it might cause the artifactual appearance of Differentially Essential (DE) genes in a statistical test, constituting type I errors (false positives). In this paper, we propose a novel method for normalization of TnSeq datasets that corrects for the skew of read-count distributions by fitting them to a Beta-Geometric distribution. We show that this read-count correction procedure reduces the number of false positives when comparing replicate datasets grown under the same conditions (for which no genuine differences in essentiality are expected). We compare these results to results obtained with other normalization procedures, and show that it results in greater reduction in the number of false positives. In addition we investigate the effects of normalization on the detection of DE genes.
Jacobi stability for dynamical systems of two-dimensional second-order differential equations and application to overhead crane system
Authors: Yajima Takahiro , Yamasaki Kazuhito
Published: January 2016

Geometric structures of dynamical systems are investigated based on a differential geometric method (Jacobi stability of KCC-theory). This study focuses on differences of Jacobi stability of two-dimensional second-order differential equation from that of one-dimensional second-order differential equation. One of different properties from a one-dimensional case is the Jacobi unstable condition given by eigenvalues of deviation curvature with different signs. Then, this geometric theory is applied to an overhead crane system as a two-dimensional dynamical system. It is shown a relationship between the Hopf bifurcation of linearized overhead crane and the Jacobi stability. Especially, the Jacobi stable trajectory is found for stable and unstable spirals of the two-dimensional linearized system. In case of the linearized overhead crane system, the Jacobi stable spiral approaches to the equilibrium point faster than the Jacobi unstable spiral. This means that the Jacobi stability is related to the resilience of deviated trajectory in the transient state. Moreover, for the nonlinear overhead crane system, the Jacobi stability for limit cycle changes stable and unstable over time.
A generalization of a method of Mordell to ternary quadratic forms
Authors: Blackwell Sarah , Durham Gabriel , Thompson Katherine , Treece Tiffany
Published: January 2016

Mordell in 1958 gave a new proof of the three squares theorem. We generalize those techniques to characterize the integers represented by the remaining six “Ramanujan–Dickson ternaries” as well as three other ternary forms.
Monitoring the penetration and accumulation of gold nanoparticles in rat skin ex vivo using surface-enhanced Raman scattering spectroscopy
Authors: Xiong Honglian , Guo Zhouyi , Zhong Huiqing , Ji Yanhong
Published: January 2016

Contamination by accidental cutaneous contact with the commercial products and the air pollutants raised a considerable health and safety issue. This study aimed to trace the dynamics of the 20 nm gold nanoparticle (GNP) penetration and accumulation in rat skin tissues using a surface-enhanced Raman scattering (SERS) technique. After the topical application of GNPs on rat skin surface, the SERS spectra were recorded for every 15 [Formula: see text]m to an overall depth of 75 [Formula: see text]m from skin surface for 150 min. The processes of GNP penetration in rat skin were accompanied by aggregation of GNPs, which affected SERS spectra. The results revealed that 20 nm GNPs can penetrate through stratum corneum layer, viable epidermis layer, and then into dermis layer. This study demonstrated for the first time the potential of SERS spectroscopy to monitor the penetration and accumulation of GNPs in rat skin.
Approximation algorithm for uniform quay crane scheduling at container ports
Authors: Liu Ming , Zheng Feifeng , Xu Yinfeng , Chu Chengbin
Published: January 2016

At a container port, container vessels are served by quay cranes for loading and unloading containers. Each vessel is typically split into bays from head to tail where containers are stored. Parallel quay cranes can process different bays simultaneously, and their processing efficiency significantly affects the turn-around time of a container vessel. Sharing a single traveling rail, the quay cranes cannot crossover each other, and this phenomenon is referred as the non-crossing constraint. In addition, the quay cranes may have different processing speeds due to gradual equipment updates. Inspired by updating activities of cranes in modern container terminals, this paper studies a scheduling problem with two uniform quay cranes, aiming at minimizing the turn-around time of a vessel, i.e., the makespan. We mainly develop an integrated approximation algorithm which is [Formula: see text]-approximation, where the two quay cranes are of processing speeds 1 and [Formula: see text], respectively.
Magnified Damping Under Rashba Spin–Orbit Coupling
Authors: Tan Seng Ghee , Jalil Mansoor B. A.
Published: January 2016

The spin–orbit coupling spin torque consists of the field-like [S. G. Tan et al., arXiv:0705.3502 (2007).] and the damping-like terms [H. Kurebayashi et al., Nat. Nanotechnol. 9, 211 (2014).] that have been widely studied for applications in magnetic memory. We focus, in this paper, not on the spin–orbit effect producing the above spin torques, but on its magnifying the damping constant of all field-like spin torques. As first-order precession leads to second-order damping, the Rashba constant is naturally co-opted, producing a magnified field-like damping effect. The Landau–Liftshitz–Gilbert equations are written separately for the local magnetization and the itinerant spin, allowing the progression of magnetization to be self-consistently locked to the spin.
Late Antique marble trade: new insights obtained from stone artefacts from the San Severo complex (Ravenna, Italy)
Authors: Tůmová Helena , Augenti Andrea , Kuchařová Aneta , Cirelli Enrico , Přikryl Richard
Published: January 2016

Ravenna represented an important administrative, commercial and cultural centre in the fifth and sixth centuries. The present study explored the commercial mechanisms of Ravenna in Late Antiquity from the point of view of the marble trade, as well as the trade in other architectural elements. A portion of the research is based on the macroscopic and quantitative study of stone materials (around 1000 fragments) from the Late Antique and medieval complex of San Severo in Classe (Ravenna, Italy). The results indicated that the predominant commercial relationships of Ravenna with respect to stone artefacts (marbles, limestones, porphyry, breccia, granites) were orientated mainly towards the regions of Asia Minor, with some trade also occurring in minor quantities with North Africa, Greece, Italy, and France.

Three representative marble samples were analysed to make determinations of their provenance. The methods used were based upon a combination of petrographic image analysis, polarizing and cathodoluminescence microscopy of thin sections, and stable isotope geochemistry of carbonates. The Proconnesos and, eventually, other Turkish provenance of the selected samples is considered.
Constraints on melt distribution from seismology: a case study in Ethiopia
Authors: Hammond J. O. S. , Kendall J.-M.
Published: January 2016

Low seismic velocities and/or strong seismic anisotropy are often interpreted as being caused by partial melt. To better understand this, we used numerical modelling, varying the shape and amount of melt, to show how seismic phases are affected by melt. We observed that seismic waves are more sensitive to the shape than to the amount of melt. Rayleigh wave velocities were almost always reduced in the presence of melt, while Pn/wide-angle P-wave refraction and Love wave velocities showed low velocity anomalies for vertically aligned melt, but little anomaly for horizontally aligned melt. These data can therefore be used to determine the alignment of melt. Shear wave splitting/receiver functions showed strong anisotropy and can be used to constrain the strike of vertically aligned partial melt. We showed that melt in the mantle beneath Ethiopia is probably stored in low aspect ratio disc-like inclusions, suggesting that the melt is not in textural equilibrium. We estimated that 2–7% of the vertically aligned melt is stored beneath the Main Ethiopian Rift, >6% of the horizontally and vertically aligned melt is stored beneath the Red Sea Rift and 1–6% of the horizontally aligned melt is stored beneath the Danakil microplate. This supports the idea of strong shear-derived segregation of melt in the narrow Main Ethiopian Rift compared with that observed beneath Afar.
Static Network Reliability Estimation under the Marshall-Olkin Copula
Authors: Botev Zdravko I. , L'Ecuyer Pierre , Simard Richard , Tuffin Bruno
Published: January 2016

In a static network reliability model, one typically assumes that the failures of the components of the network are independent. This simplifying assumption makes it possible to estimate the network reliability efficiently via specialized Monte Carlo algorithms. Hence, a natural question to consider is whether this independence assumption can be relaxed while still attaining an elegant and tractable model that permits an efficient Monte Carlo algorithm for unreliability estimation. In this article, we provide one possible answer by considering a static network reliability model with dependent link failures, based on a Marshall-Olkin copula, which models the dependence via shocks that take down subsets of components at exponential times, and propose a collection of adapted versions of permutation Monte Carlo (PMC, a conditional Monte Carlo method), its refinement called the
turnip method
, and generalized splitting (GS) methods to estimate very small unreliabilities accurately under this model. The PMC and turnip estimators have bounded relative error when the network topology is fixed while the link failure probabilities converge to 0, whereas GS does not have this property. But when the size of the network (or the number of shocks) increases, PMC and turnip eventually fail, whereas GS works nicely (empirically) for very large networks, with over 5,000 shocks in our examples.
Connectivity Reestablishment in Self-Organizing Sensor Networks with Dumb Nodes
Authors: Kar Pushpendu , Roy Arijit , Misra Sudip
Published: January 2016

In this work, we propose a scheme, named
CoRAD
, for the reestablishment of lost connectivity using sensor nodes with adjustable communication range in stationary wireless sensor networks (WSNs), when “dumb” behavior occurs some of the nodes. Due to the occurrence of such behavior, there may be temporary loss of connectivity between among the nodes. Such a phenomenon is different from the commonly known node isolation problem in stationary WSNs. The mere activation of intermediate sleep nodes cannot guarantee reestablishment of connectivity, because there may not exist neighbor nodes of the isolated nodes. On the contrary, the increase in communication range of a single sensor node may make it die quickly. Including this, a sensor node has maximum limit of increase in communication range that may not be sufficient to reestablish connectivity. Therefore, considering all these factors for self-organization of the network and isolated node re-connection, we propose a price-based scheme, which addresses the issue by activating intermediate sleep nodes or by adjusting the communication range of some of the other nodes in the network. The scheme also deactivates the additional activated nodes and reduces the increased communication range when the dumb nodes resume their normal behavior, upon the return of favorable environmental conditions. To implement the proposed scheme,
CoRAD
it is required to construct the network using GPS-enabled adjustable communication range sensor nodes. Through simulation we compare our proposed scheme with the existing topology management schemes -- LETC and A1 -- in the same scenario by considering the number of activated nodes, message overhead, and energy consumption. We find that the proposed scheme shows improved performance compared to the existing topology management schemes.
Understanding Programming Expertise
Authors: Crk Igor , Kluthe Timothy , Stefik Andreas
Published: January 2016

Recent decades have seen a resurgence of interest in electroencephalography (EEG), as neuroscience develops new models of cognition and refines old ones, associating them with detectable indicators of brain activity. This article presents a more direct measure of programmer expertise, derived from noninvasive observation of the brain’s electrical activity. This article provides a foundational approach for investigating the role of expertise in programming language comprehension, showing that this electrical activity in the brain can indicate (1) prior programming experience by class level (current state of progression through an undergraduate computer science program), and (2) self-reported experience levels.
Tight Bounds for the Price of Anarchy of Simultaneous First-Price Auctions
Authors: Christodoulou George , Kovács Annamária , Sgouritsa Alkmini , Tang Bo
Published: January 2016

We study the price of anarchy (PoA) of simultaneous first-price auctions (FPAs) for buyers with submodular and subadditive valuations. The current best upper bounds for the Bayesian price of anarchy (BPoA) of these auctions are
e
/(
e
− 1) [Syrgkanis and Tardos 2013] and 2 [Feldman et al. 2013], respectively. We provide matching lower bounds for both cases
even
for the case of full information and for mixed Nash equilibria via an explicit construction. We present an alternative proof of the upper bound of
e
/(
e
− 1) for FPAs with fractionally subadditive valuations that reveals the worst-case price distribution, which is used as a building block for the matching lower bound construction.

We generalize our results to a general class of item bidding auctions that we call bid-dependent auctions (including FPAs and all-pay auctions) where the winner is always the highest bidder and each bidder’s payment depends only on his own bid.

Finally, we apply our techniques to discriminatory price multiunit auctions. We complement the results of de Keijzer et al. [2013] for the case of subadditive valuations by providing a matching lower bound of 2. For the case of submodular valuations, we provide a lower bound of 1.109. For the same class of valuations, we were able to reproduce the upper bound of
e
/(
e
− 1) using our nonsmooth approach.
The role of STIM and ORAI proteins in phagocytic immune cells
Authors: Demaurex Nicolas , Nunes Paula
Published: January 2016

Phagocytic cells, such as neutrophils, macrophages, and dendritic cells, migrate to sites of infection or damage and are integral to innate immunity through two main mechanisms. The first is to directly neutralize foreign agents and damaged or infected cells by secreting toxic substances or ingesting them through phagocytosis. The second is to alert the adaptive immune system through the secretion of cytokines and the presentation of the ingested materials as antigens, inducing T cell maturation into helper, cytotoxic, or regulatory phenotypes. While calcium signaling has been implicated in numerous phagocyte functions, including differentiation, maturation, migration, secretion, and phagocytosis, the molecular components that mediate these Ca2+ signals have been elusive. The discovery of the STIM and ORAI proteins has allowed researchers to begin clarifying the mechanisms and physiological impact of store-operated Ca2+ entry, the major pathway for generating calcium signals in innate immune cells. Here, we review evidence from cell lines and mouse models linking STIM and ORAI proteins to the control of specific innate immune functions of neutrophils, macrophages, and dendritic cells.
Novel application of complementary imaging techniques to examine in vivo glucose metabolism in the kidney
Authors: Hato Takashi , Friedman Allon N. , Mang Henry , Plotkin Zoya , Dube Shataakshi , Hutchins Gary D. , Territo Paul R. , McCarthy Brian P. , Riley Amanda A. , Pichumani Kumar , Malloy Craig R. , Harris Robert A. , Dagher Pierre C. , Sutton Timothy A.
Published: January 2016

The metabolic status of the kidney is a determinant of injury susceptibility and a measure of progression for many disease processes; however, noninvasive modalities to assess kidney metabolism are lacking. In this study, we employed positron emission tomography (PET) and intravital multiphoton microscopy (MPM) to assess cortical and proximal tubule glucose tracer uptake, respectively, following experimental perturbations of kidney metabolism. Applying dynamic image acquisition PET with 2-18fluoro-2-deoxyglucose (18F-FDG) and tracer kinetic modeling, we found that an intracellular compartment in the cortex of the kidney could be distinguished from the blood and urine compartments in animals. Given emerging literature that the tumor suppressor protein p53 is an important regulator of cellular metabolism, we demonstrated that PET imaging was able to discern a threefold increase in cortical 18F-FDG uptake following the pharmacological inhibition of p53 in animals. Intravital MPM with the fluorescent glucose analog 2-[ N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxyglucose (2-NBDG) provided increased resolution and corroborated these findings at the level of the proximal tubule. Extending our observation of p53 inhibition on proximal tubule glucose tracer uptake, we demonstrated by intravital MPM that pharmacological inhibition of p53 diminishes mitochondrial potential difference. We provide additional evidence that inhibition of p53 alters key metabolic enzymes regulating glycolysis and increases intermediates of glycolysis. In summary, we provide evidence that PET is a valuable tool for examining kidney metabolism in preclinical and clinical studies, intravital MPM is a powerful adjunct to PET in preclinical studies of metabolism, and p53 inhibition alters basal kidney metabolism.
The neural dynamics of somatosensory processing and adaptation across childhood: a high-density electrical mapping study
Authors: Uppal Neha , Foxe John J. , Butler John S. , Acluche Frantzy , Molholm Sophie
Published: January 2016

Young children are often hyperreactive to somatosensory inputs hardly noticed by adults, as exemplified by irritation to seams or labels in clothing. The neurodevelopmental mechanisms underlying changes in sensory reactivity are not well understood. Based on the idea that neurodevelopmental changes in somatosensory processing and/or changes in sensory adaptation might underlie developmental differences in somatosensory reactivity, high-density electroencephalography was used to examine how the nervous system responds and adapts to repeated vibrotactile stimulation over childhood. Participants aged 6–18 yr old were presented with 50-ms vibrotactile stimuli to the right wrist over the median nerve at 5 blocked interstimulus intervals (ranging from ∼7 to ∼1 stimulus per second). Somatosensory evoked potentials (SEPs) revealed three major phases of activation within the first 200 ms, with scalp topographies suggestive of neural generators in contralateral somatosensory cortex. Although overall SEPs were highly similar for younger, middle, and older age groups (6.1–9.8, 10.0–12.9, and 13.0–17.8 yr old), there were significant age-related amplitude differences in initial and later phases of the SEP. In contrast, robust adaptation effects for fast vs. slow presentation rates were observed that did not differ as a function of age. A greater amplitude response in the later portion of the SEP was observed for the youngest group and may be related to developmental changes in responsivity to somatosensory stimuli. These data suggest the protracted development of the somatosensory system over childhood, whereas adaptation, as assayed in this study, is largely in place by ∼7 yr of age.
KV1 channels identified in rodent myelinated axons, linked to Cx29 in innermost myelin: support for electrically active myelin in mammalian saltatory conduction
Authors: Rash John E. , Vanderpool Kimberly G. , Yasumura Thomas , Hickman Jordan , Beatty Jonathan T. , Nagy James I.
Published: January 2016

Saltatory conduction in mammalian myelinated axons was thought to be well understood before recent discoveries revealed unexpected subcellular distributions and molecular identities of the K+-conductance pathways that provide for rapid axonal repolarization. In this study, we visualize, identify, localize, quantify, and ultrastructurally characterize axonal KV1.1/KV1.2 channels in sciatic nerves of rodents. With the use of light microscopic immunocytochemistry and freeze-fracture replica immunogold labeling electron microscopy, KV1.1/KV1.2 channels are localized to three anatomically and compositionally distinct domains in the internodal axolemmas of large myelinated axons, where they form densely packed “rosettes” of 9-nm intramembrane particles. These axolemmal KV1.1/KV1.2 rosettes are precisely aligned with and ultrastructurally coupled to connexin29 (Cx29) channels, also in matching rosettes, in the surrounding juxtaparanodal myelin collars and along the inner mesaxon. As >98% of transmembrane proteins large enough to represent ion channels in these specialized domains, ∼500,000 KV1.1/KV1.2 channels define the paired juxtaparanodal regions as exclusive membrane domains for the voltage-gated K+conductance that underlies rapid axonal repolarization in mammals. The 1:1 molecular linkage of KV1 channels to Cx29 channels in the apposed juxtaparanodal collars, plus their linkage to an additional 250,000–400,000 Cx29 channels along each inner mesaxon in every large-diameter myelinated axon examined, supports previously proposed K+conductance directly from juxtaparanodal axoplasm into juxtaparanodal myeloplasm in mammalian axons. With neither Cx29 protein nor myelin rosettes detectable in frog myelinated axons, these data showing axon-to-myelin linkage by abundant KV1/Cx29 channels in rodent axons support renewed consideration of an electrically active role for myelin in increasing both saltatory conduction velocity and maximum propagation frequency in mammalian myelinated axons.
A Semi-Markov Decision Model for Recognizing the Destination of a Maneuvering Agent in Real Time Strategy Games
Authors: Yin Quanjun , Yue Shiguang , Zha Yabing , Jiao Peng
Published: January 2016

Recognizing destinations of a maneuvering agent is important in real time strategy games. Because finding path in an uncertain environment is essentially a sequential decision problem, we can model the maneuvering process by the Markov decision process (MDP). However, the MDP does not define an action duration. In this paper, we propose a novel semi-Markov decision model (SMDM). In the SMDM, the destination is regarded as a hidden state, which affects selection of an action; the action is affiliated with a duration variable, which indicates whether the action is completed. We also exploit a Rao-Blackwellised particle filter (RBPF) for inference under the dynamic Bayesian network structure of the SMDM. In experiments, we simulate agents’ maneuvering in a combat field and employ agents’ traces to evaluate the performance of our method. The results show that the SMDM outperforms another extension of the MDP in terms of precision, recall, andF-measure. Destinations are recognized efficiently by our method no matter whether they are changed or not. Additionally, the RBPF infer destinations with smaller variance and less time than the SPF. The average failure rates of the RBPF are lower when the number of particles is not enough.
New Ti-Alloys and Surface Modifications to Improve the Mechanical Properties and the Biological Response to Orthopedic and Dental Implants: A Review
Authors: Kirmanidou Yvoni , Sidira Margarita , Drosou Maria-Eleni , Bennani Vincent , Bakopoulou Athina , Tsouknidas Alexander , Michailidis Nikolaos , Michalakis Konstantinos
Published: January 2016

Titanium implants are widely used in the orthopedic and dentistry fields for many decades, for joint arthroplasties, spinal and maxillofacial reconstructions, and dental prostheses. However, despite the quite satisfactory survival rates failures still exist. New Ti-alloys and surface treatments have been developed, in an attempt to overcome those failures. This review provides information about new Ti-alloys that provide better mechanical properties to the implants, such as superelasticity, mechanical strength, and corrosion resistance. Furthermore, in vitro and in vivo studies, which investigate the biocompatibility and cytotoxicity of these new biomaterials, are introduced. In addition, data regarding the bioactivity of new surface treatments and surface topographies on Ti-implants is provided. The aim of this paper is to discuss the current trends, advantages, and disadvantages of new titanium-based biomaterials, fabricated to enhance the quality of life of many patients around the world.