bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of Nonlinear Waves on Offshore Wind Turbines and Associated Fatigue Load Assessment
Authors: Marino E. , Lugni C. , Manuel L. , Nguyen H. , Borri C.
Published: September 2014

By using a global simulation framework that employs a domain-decomposition strategy for computational efficiency, this study investigates the effects of fully nonlinear (FNL) waves on the fatigue loads exerted on the support structure (monopile) of a fixed-bottom offshore wind turbine. A comparison is made with more conventional linear wave hydrodynamics. The FNL numerical wave solver is invoked only on specific sub-domains where nonlinearities are detected; thus, only locally in space and time, a linear wave solution is replaced by the FNL results as input to the Morison equation used for the hydrodynamic loads. The accuracy and efficiency of this strategy allows long timedomain simulations where strongly nonlinear free-surface phenomena, like imminent breaking waves, are accounted for in the prediction of structural loads. The unsteady nonlinear free-surface problem governing the propagation of gravity waves is formulated using potential theory and a higher-order boundary element method (HOBEM) is used to discretize Laplace’s equation. The FNL solver is employed and associated hydrodynamic loads are predicted in conjunction with aerodynamic loads on the rotor of a 5-MW wind turbine using the NREL open-source software, FAST. We assess fatigue loads by means of both time- and frequency-domain methods. This study shows that the use of linear theory-based hydrodynamics can lead to significant underestimation of fatigue loads and damage.
Resource Scalability at Wave Energy Test Sites
Authors: Cahill Brendan
Published: September 2014

Harnessing the power of ocean waves offers enormous potential as a source of renewable energy. To date the technologies for capturing this resource, collectively known as wave energy converters (WECs), have yet to reach commercial viability and continued research and development efforts are required to move wave energy to the industrial scale. Integral to this process is ensuring that technologies progress along a staged development pathway; proving WEC concepts using small scale physical models in controlled settings such as laboratory wave tanks before eventually advancing to testing sub-prototype and full scale devices in real sea conditions.

The primary objective of this research is to improve the understanding of how best to address the scaling of wave resource measurements and wave energy device power production when analyzing the results of sea-trials. This paper draws on measured data from three test sites; Galway Bay in Ireland, the Pacific Marine Energy Test Centre off the coast of Oregon, and Lake Washington, and assesses how accurately they recreate, at reduced scale, the conditions that commercial WEC installations are likely to encounter at exposed deployment locations. Appropriate techniques for extrapolating these results to predict the performance of commercial WECs at energy-rich locations on the west coasts of Ireland and the US are also demonstrated and discussed.

The output from this research will be a set of protocols for addressing wave energy resource scalability to help guide device developers through this important stage of technology progression. Improved knowledge regarding resource scalability will allow for more streamlined progression of WEC concepts from wave tanks to sea-trials, and eventually to full-scale ocean deployment. It will also result in a reduced uncertainty about device power output and survivability, which are key drivers in determining the economic viability of projects.
Experimental Evaluation of the Ultimate Bending Moment of a Thin Box Girder
Authors: Gordo José Manuel , Guedes Soares C.
Published: September 2014

The results of a four points bending test on a box girder are presented. The experiment is part of series of tests with similar configuration but different thickness and span between frames. The present work refers to the slenderest plate box girder with a plate’s thickness of 2 mm but with a short span between frames. The experiment includes initial loading cycles allowing for residual stresses relief. The moment curvature relationship is established for a large range of curvature. The ultimate bending moment of the box is evaluated and compared with the first yield moment and the plastic moment allowing the evaluation of the efficiency of the structure. The post buckling behavior and collapse mode are characterized. Comparison of the experiment with a progressive collapse method is made taking into consideration the effect of residual stresses on envelop of the moment curvature curve of the structure.
Determination of Design Metocean Conditions by Response Based Analysis
Authors: Drobyshevski Y. , Whelan J. R. , Wadhwa H. , Anokhin V.
Published: September 2014

Response Based Analysis (RBA) aims at prediction of the long term distributions of critical responses such as motions, accelerations, wave loads, which have significant impact on the design of a floating system. As compared with the conventional analysis, which predicts the responses of the facility to the N-year return period metocean conditions, RBA provides directly the N-year return period responses by analysing the statistics of their long term time histories. Another outcome of RBA is the Design Metocean Conditions (DMCs) which are combinations of sea state, wind and current causing the corresponding N-year response. The knowledge of the DMCs enables the more detail time domain analysis and model tests to be performed for a set of critical combinations of metocean parameters. It also enables all the associated responses to be determined.

The RBA framework is generally well addressed in the literature, but the DMC identification methods are not necessarily clearly established. The objective of this paper is to present the theoretical background, numerical method and an example for the determination of the N-year return period responses and the associated DMCs for a floating facility. The method includes prediction of the N-year response, identification of the metocean combinations within the available time history which produce this response, determination of the required percentile of the short term response to match the N-year response, and the search for the most probable DMC within the joint probability density of the metocean parameters. Features of the method are discussed and results are presented for several critical responses of a weather vaning vessel.
Implementing New Nonlinear Term in Third Generation Wave Models
Authors: Gramstad Odin , Babanin Alexander
Published: September 2014

The non-linear interaction term is one of the three key source functions in every third-generation spectral wave model. An update of physics of this term is discussed.

The standard statistical/phase-averaged description of the nonlinear transfer of energy in the wave spectrum (wave-turbulence) is based on Hasselmann’s kinetic equation [1]. In the derivation of the kinetic equation (KE) it is assumed that the evolution takes place on the slow O(ε−4) time scale, where ε is the wave steepness. This excludes the effects of near-resonant quartet interactions that may lead to spectral evolution on the ‘fast’ O(ε−2) time scale.

Generalizations of the KE (GKE) that enable description of spectral evolution on the O(ε−2) time scale [2–4] are discussed. The GKE, first solved numerically in [4], is implemented as a source term in the third generation wave model WAVEWATCH-III. The new source term (GKE) is tested and compared to the other nonlinear-interaction source terms in WAVEWATCH-III; the full KE (WRT method) and the approximate DIA method. It is shown that the GKE gives similar results to the KE in the case of a relatively broad banded and directional spread spectrum, while it shows somewhat larger difference in the case of a more narrow banded spectrum with narrower directional distribution.

We suggest that the GKE may be a suitable replacement to the KE in situations where ‘fast’ spectral evolution takes place.
Predicting the Gain From Deliquification Measures for European Wells
Authors: Nennie E. D. , de Boer J. P. , Schiferli W.
Published: September 2014

Various Dutch operators have identified a need for increased application of deliquification measures in their North Sea wells. To help meet this need a Joint Industry Project (JIP) was set up to identify knowledge and experience gained in the United States on gas well deliquification and transfer this to European wells. In the first phase of the project a broad overview of the techniques used to deliquify gas wells suffering from liquid loading was made together with a set of available guidelines predicting the range of application.

Having identified potential techniques, a selection tool was developed which suggests the most suitable deliquification technique for a given well. The selection tool can predict the gains in production and ultimate recovery resulting from applying a range of techniques.

The selection tool is based on Tubing Performance Curve (TPC) analysis combined with Inflow Performance Relationship (IPR) analysis; performance therefore depends on the pressure drop over the wellbore (as modelled in the TPC) and on reservoir characteristics. For each of these techniques, a model was available or developed to simplify their operating principles to a TPC.

Results from this tool can aid in deciding which deliquification technique to implement, as it gives a clear overview of the production gain that can be expected for the different techniques [8].
Fatigue Damage Evaluation in Ferromagnetic Steel by Mechanical and Piezomagnetic Measurements
Authors: Bao Sheng , Lou Hangfei
Published: September 2014

The objective of this research is to explore correlations between mechanical and piezomagnetic hysteresis of ferromagnetic steel samples with progressive changes that take place during the fatigue process. A series of strain controlled fatigue tests were carried out to study the piezomagnetic fields surrounding steel specimens in a quantitative way by measuring magnetic field variations resulting from the cyclic application of stress. It was observed that the piezomagnetic hysteresis traces change systematically with the progression of fatigue. The evolution of piezomagnetic hysteresis, when plotted as a function of the number of loading cycles, demonstrates the three principal stages of fatigue: initial accommodation, accretion of damage and terminal failure. The results derived from the piezomagnetic hysteresis traces are consistent with those obtained from mechanical hysteresis studies. However, when approaching failure, the piezomagnetic traces show more conspicuous changes than the corresponding mechanical stress-strain curves.
Effect of Supercritical CO2 on PVDF
Authors: Laurentino Daniele A. , Silva Marlon D. C. , Costa Celio A. , Pessoa Fernando L. P. , Costa Marysilvia F.
Published: September 2014

The pre-salt fields have a high content of carbon dioxide (CO2) that can be in the supercritical state due to reservoir conditions of temperature and pressure. This high concentration of carbon dioxide has a direct impact on the strategies used in the exploration and exploitation of the reservoir, including the selection of materials and equipment used in the wells. Risers are parts of flexible lines made up of several layers and are very important equipment in offshore operations. Flexible lines are widely used in various operations to extract and transport fluids in the wells, as well as one of the solutions to the challenges of the pre-salt. Poly (vinylidene fluoride) (PVDF) is a polymer used in the manufacture of the sealing layer of the risers. In this paper, PVDF samples were exposed to supercritical CO2 and analyzed for volume, density and mechanical properties and compared to unexposed PVDF.
Hydrodynamic Forces Acting on Objects in a Moonpool
Authors: Aspelund Leiv , Pettersen Bjørnar , Visscher Jan , Idsøe Næss Tor-Bjørn
Published: September 2014

Traditionally, it has often been assumed that the flow conditions in a moonpool are only moderately altered when an object is introduced therein. Moreover, the hydrodynamic forces acting on the object has typically been estimated by Morison’s equation for small volume structures, using the fluid kinematics of the empty moonpool as a basis and applying correction factors for the confined flow conditions, as for an object in a tube or a channel.

To investigate the validity of the traditional approach, an experimental study on the forces acting on objects in a moonpool was performed at NTNU/MARINTEK in Trondheim, Norway in 2013. The experiments were done using a simplified 2-dimensional moonpool model which was given a forced heave motion. Two objects, both with square cross sections but of different sizes, were put inside the moonpool one at the time. The resulting wave elevations inside the moonpool and the forces acting on the objects were recorded and analyzed. To get a deeper understanding of the flow characteristics in the moonpool, PIV measurements were used to obtain the fluid velocity fields.

The experiments revealed that even moderately sized objects (relative to the size of the moonpool) change the fluid motions in the moonpool to a large extent; the overall wave elevation amplitude is strongly reduced and the resonance period is altered. A consequence of this is that there is a large discrepancy between the hydrodynamic forces acting on the objects measured in the experiments and the forces calculated using the traditional approach. The PIV results showed the formation of vortices at the inlet of the moonpool and at the edges of the objects, which is the main source of non-linear damping of the wave elevation inside a moonpool.
Prediction of Ship Responses in Large Amplitude Waves Using a Body Nonlinear Time Domain Method With 2nd Order Froude-Krylov Pressure
Authors: Rajendran Suresh , Fonseca Nuno , Guedes Soares C.
Published: September 2014

The paper analyzes the effect of 2nd order waves on the vertical ship responses in extreme seas. The numerical simulations are carried out using a body nonlinear time domain code based on strip theory. The radiation, diffraction, Froude-krylov and hydrostatic forces are calculated for the exact wetted surface area of the ship for each time step. A practical engineering approach is followed to calculate the body nonlinear radiation and diffraction forces. First order Froude Krylov pressures are replaced with a second order model for the present study. The 2nd order Froude-Krylov pressures are integrated upto the exact wetted surface area for each time instant. The ship responses in regular waves with varying steepness are analyzed. Finally, the vertical ship responses are compared with the responses in design waves measured in the wave tank.
Experimental Study of Strucural Responses of a Ship With Multi-Segments and Variable Cross-Section Beams
Authors: Ding Jun , Tian Chao , Wang Xueliang , Cheng Xiaoming , Yang Peng
Published: September 2014

The motion and structural response to wave loading are studied experimentally for a large ship modeled with multiple segments and beams of variable cross-sections. As opposed to the traditional method with small number of segments and beams of uniform cross-section, the multi-segmented model with beams of variable cross-sections can more accurately simulate some of the hull properties that will otherwise be neglected.

In this paper, the design method for the multi-segmented model is presented, and the model test results for the multi-segmented model with variable cross-section beams are compared with the traditional uniform beams and less segmented model for calm water, regular and irregular wave conditions. The influences of the segment number, variable cross-section, vessel speed and wave height are investigated using the load forecasting methods based on the rigid body and hydroelastic theories. It has been found that using variable cross-section beams can simulate hull stiffness of each section more accurately, and with the increase of the segment number in the ship model, the high frequency characteristics of the bending response are better reflected. Furthermore, the calculation results agree well with the experimental data, and the hydroelastic theory is found to be able to predict the higher frequencies of the hull structural responses. At the same time, with the increase of the vessel speed and wave height, the bending moment and wave height show an obvious nonlinear relationship.

The methods and results presented in this paper have a certain guiding significance for the tank model tests and design of large ship structures.
Lower Limb Joint Angular Position and Muscle Activity During Elliptical Exercise in Healthy Young Men
Authors: Paquette Max R. , Zucker-Levin Audrey , DeVita Paul , Hoekstra Joseph , Pearsall David
Published: September 2014

The purpose of this study was to compare lower extremity joint angular position and muscle activity during elliptical exercise using different foot positions and also during exercise on a lateral elliptical trainer. Sixteen men exercised on a lateral elliptical and on a standard elliptical trainer using straight foot position, increased toe-out angle, and a wide step. Motion capture and electromyography systems were used to obtain 3D lower extremity joint kinematics and muscle activity, respectively. The lateral trainer produced greater sagittal and frontal plane knee range of motion (ROM), greater peak knee flexion and extension, and higher vastus medialis activation compared with other conditions (P < .05). Toe-out and wide step produced the greatest and smallest peak knee adduction angles, respectively (P < .05). The lateral trainer produced greater sagittal and frontal plane hip ROM and greater peak hip extension and flexion compared with all other conditions (P < .05). Toe-out angle produced the largest peak hip external rotation angle and lowest gluteus muscle activation (P < .05). Findings from this study indicate that standard elliptical exercise with wide step may place the knee joint in a desirable frontal plane angular position to reduce medial knee loads, and that lateral elliptical exercise could help improve quadriceps strength but could also lead to larger knee contact forces.
Beware of T Cells That Don't Know How to Stop
Authors: Mueller Kristen L.
Published: September 2014

A mutation in a single copy of the
CTLA4
gene in people is associated with immune dysfunction.
No Bones About It
Authors: Nusinovich Yevgeniya
Published: September 2014

Heterotopic ossification induced by injuries and burns is mediated by signaling through the SMAD pathway and can be targeted with topical apyrase.
Animal Behavior Follows Rewards
Authors: McCartney Melissa
Published: September 2014

Dopamine promotes spine structural plasticity during a narrow time window in mouse neuron distal dendrites.
Therapeutic Hope for Metastatic Breast Cancer
Authors: Ferrarelli Leslie K.
Published: September 2014

Inhibiting the kinase p38α may suppress the growth of new metastatic lesions and reduce the growth of established metastatic lesions in breast cancer patients.
A Male and Female Gametocyte Functional Viability Assay To Identify Biologically Relevant Malaria Transmission-Blocking Drugs
Authors: Ruecker A. , Mathias D. K. , Straschil U. , Churcher T. S. , Dinglasan R. R. , Leroy D. , Sinden R. E. , Delves M. J.
Published: September 2014

Malaria elimination will require interventions that prevent parasite transmission from the human host to the mosquito. Experimentally, this is usually determined by the expensive and laborious
Plasmodium falciparum
standard membrane feeding assay (PfSMFA), which has limited utility for high-throughput drug screening. In response, we developed the
P. falciparum
dual gamete formation assay (PfDGFA), which faithfully simulates the initial stages of the PfSMFA
in vitro
. It utilizes a dual readout that individually and simultaneously reports on the functional viability of male and female mature stage V gametocytes. To validate, we screen the Medicines for Malaria Venture (MMV) Malaria Box library with the PfDGFA. Unique to this assay, we find compounds that target male gametocytes only and also compounds with reversible and irreversible activity. Most importantly, we show that compound activity in the PfDGFA accurately predicts activity in PfSMFAs, which validates and supports its adoption into the transmission-stage screening pipeline.
Detection of Variants of the pRAS3, pAB5S9, and pSN254 Plasmids in Aeromonas salmonicida subsp. salmonicida: Multidrug Resistance, Interspecies Exchanges, and Plasmid Reshaping
Authors: Vincent Antony T. , Trudel Mélanie V. , Paquet Valérie E. , Boyle Brian , Tanaka Katherine H. , Dallaire-Dufresne Stéphanie , Daher Rana K. , Frenette Michel , Derome Nicolas , Charette Steve J.
Published: September 2014

The ubiquitous water-borne Gram-negative bacterium
Aeromonas salmonicida
subsp.
salmonicida
is the causative agent of furunculosis, a worldwide disease in fish farms. Plasmids carrying antibiotic resistance genes have already been described for this bacterium. The aim of the present study was to identify and characterize additional multidrug resistance plasmids in
A. salmonicida
subsp.
salmonicida
. We sequenced the plasmids present in two multiple antibiotic-resistant isolates using high-throughput technologies. We also investigated 19 other isolates with various multidrug resistance profiles by genotyping PCR and assessed their resistance to tetracycline. We identified variants of the pAB5S9 and pSN254 plasmids that carry several antibiotic resistance genes and that have been previously reported in bacteria other than
A. salmonicida
subsp.
salmonicida
, which suggests a high level of interspecies exchange. Genotyping analyses and the antibiotic resistance profiles of the 19 other isolates support the idea that multiple versions of pAB5S9 and pSN254 exist in
A. salmonicida
subsp.
salmonicida
. We also identified variants of the pRAS3 plasmid. The present study revealed that
A. salmonicida
subsp.
salmonicida
harbors a wide variety of plasmids, which suggests that this ubiquitous bacterium may contribute to the spread of antibiotic resistance genes in the environment.
Discovery of Novel Antigiardiasis Drug Candidates
Authors: Kulakova Liudmila , Galkin Andrey , Chen Catherine Z. , Southall Noel , Marugan Juan J. , Zheng Wei , Herzberg Osnat
Published: September 2014

Giardiasis is a severe intestinal parasitic disease caused by
Giardia lamblia
, which inflicts many people in poor regions and is the most common parasitic infection in the United States. Current standard care drugs are associated with undesirable side effects, treatment failures, and an increasing incidence of drug resistance. As follow-up to a high-throughput screening of an approved drug library, which identified compounds lethal to
G. lamblia
trophozoites, we have determined the minimum lethal concentrations of 28 drugs and advanced 10 of them to
in vivo
studies in mice. The results were compared to treatment with the standard care drug, metronidazole, in order to identify drugs with equal or better anti-
Giardia
activities. Three drugs, fumagillin, carbadox, and tioxidazole, were identified. These compounds were also potent against metronidazole-resistant human
G. lamblia
isolates (assemblages A and B), as determined in
in vitro
assays. Of these three compounds, fumagillin is currently an orphan drug used within the European Union to treat microsporidiosis in immunocompromised individuals, whereas carbadox and tioxidazole are used in veterinary medicine. A dose-dependent study of fumagillin in a giardiasis mouse model revealed that the effective dose of fumagillin was ∼100-fold lower than the metronidazole dose. Therefore, fumagillin may be advanced to further studies as an alternative treatment for giardiasis when metronidazole fails.
Potency and Resistance Analysis of Hepatitis C Virus NS5B Polymerase Inhibitor BMS-791325 on All Major Genotypes
Authors: Liu Mengping , Tuttle Maria , Gao Min , Lemm Julie A.
Published: September 2014

BMS-791325 is a hepatitis C virus (HCV) inhibitor binding to the thumb domain of the NS5B RNA-dependent RNA polymerase. BMS-791325 is well characterized in genotype 1 (GT1) and exhibits good inhibitory activity (50% effective concentration [EC
50
], <10 nM) against hybrid replicons containing patient NS5B sequences from GT3a, -4a, and -5a while potency against GT2 is significantly reduced (J. A. Lemm et al., Antimicrob. Agents Chemother. 58:3485–3495, 2014, doi:
http://dx.doi.org/10.1128/AAC.02495-13
). BMS-791325 potency against GT6a hybrid replicons is more variable, with two of three hybrid clones having EC
50
s similar to that for GT1 while a third patient clone was ∼10 times less susceptible to BMS-791325. To characterize the resistance profile of BMS-791325 beyond GT1, curing studies were performed across GT1a and -3a to -6a and demonstrated that GT1a has the highest resistance barrier versus BMS-791325 while GT6a has the lowest. Selection of GT3 to -6 NS5B chimeric replicon cells at different concentrations of BMS-791325 revealed substitutions in the thumb domain of NS5B at residues 494 and 495 that conferred different levels of resistance to BMS-791325 but remained susceptible to NS5A or NS3 protease inhibitors. In addition, we demonstrate that the reduced potency of BMS-791325 against one GT6a patient is due to an A494 polymorphism present in ∼21% of sequences in the European HCV database. The results from this report suggest that BMS-791325 is a candidate for combination treatment of HCV GT3 to -6 chronic infections, and the resistance profiles identified will provide useful information for future clinical development.
Evaluation of Clonality and Carbapenem Resistance Mechanisms among Acinetobacter baumannii-Acinetobacter calcoaceticus Complex and Enterobacteriaceae Isolates Collected in European and Mediterranean Countries and Detection of Two Novel β-Lactamases, GES-22 and VIM-35
Authors: Castanheira Mariana , Costello Sarah E. , Woosley Leah N. , Deshpande Lalitagauri M. , Davies Todd A. , Jones Ronald N.
Published: September 2014

We evaluated doripenem-resistant
Acinetobacter baumannii
-
Acinetobacter calcoaceticus
complex (ACB;
n
= 411) and
Enterobacteriaceae
(
n
= 92) isolates collected from patients from 14 European and Mediterranean countries during 2009 to 2011 for the presence of carbapenemase-encoding genes and clonality. Following susceptibility testing, carbapenem-resistant (doripenem MIC, >2 μg/ml) isolates were screened for carbapenemases. New β-lactamase genes were expressed in a common background and susceptibility was tested. Class 1 integrons were sequenced. Clonality was evaluated by pulsed-field gel electrophoresis and multilocus sequence typing (Pasteur scheme). Relative expression of β-lactam intrinsic resistance mechanisms was determined for carbapenemase-negative
Enterobacteriaceae
. ACB and
Enterobacteriaceae
displayed 58.9 and 0.9% doripenem resistance, respectively.
bla
OXA-23
,
bla
OXA-58
, and
bla
OXA-24/OXA-40
were detected among 277, 77, and 29 ACB, respectively (in 8, 6, and 5 countries). Ten Turkish isolates carried
bla
GES-11
or
bla
GES-22
. GES-22 (G243A and M169L mutations in GES-1) had an extended-spectrum β-lactamase profile. A total of 33 clusters of ≥2 ACB isolates were observed, and 227 isolates belonged to sequence type 2/international clone II. Other international clones were limited to Turkey and Israel. Doripenem-resistant
Enterobacteriaceae
increased significantly (0.7 to 1.6%), and 15
bla
KPC-2
- and 22
bla
KPC-3
-carrying isolates, mostly belonging to clonal complexes 11 and 258, were observed.
Enterobacteriaceae
isolates producing OXA-48 (
n
= 16; in Turkey and Italy), VIM-1 (
n
= 10; in Greece, Poland, and Spain), VIM-26 (
n
= 1; in Greece), and IMP-19, VIM-4, and the novel VIM-35 (
n
= 1 each from Poland) were detected. VIM-35 had one substitution compared to VIM-1 (A235T) and a similar susceptibility profile. One or more resistance mechanisms were identified in 4/6 carbapenemase-negative
Enterobacteriaceae
. This broad evaluation confirms results from country-specific surveys and shows a highly diverse population of carbapenemase-producing ACB and
Enterobacteriaceae
in Europe and Mediterranean countries.
The Endothelin System Has a Significant Role in the Pathogenesis and Progression of Mycobacterium tuberculosis Infection
Authors: Correa Andre F. , Bailão Alexandre M. , Bastos Izabela M. D. , Orme Ian M. , Soares Célia M. A. , Kipnis Andre , Santana Jaime M. , Junqueira-Kipnis Ana Paula
Published: September 2014

Tuberculosis (TB) remains a major global health problem, and although multiple studies have addressed the relationship betweenMycobacterium tuberculosisand the host on an immunological level, few studies have addressed the impact of host physiological responses. Proteases produced by bacteria have been associated with important alterations in the host tissues, and a limited number of these enzymes have been characterized in mycobacterial species.M. tuberculosisproduces a protease called Zmp1, which appears to be associated with virulence and has a putative action as an endothelin-converting enzyme. Endothelins are a family of vasoactive peptides, of which 3 distinct isoforms exist, and endothelin 1 (ET-1) is the most abundant and the best-characterized isoform. The aim of this work was to characterize the Zmp1 protease and evaluate its role in pathogenicity. Here, we have shown thatM. tuberculosisproduces and secretes an enzyme with ET-1 cleavage activity. These data demonstrate a possible role of Zmp1 for mycobacterium-host interactions and highlights its potential as a drug target. Moreover, the results suggest that endothelin pathways have a role in the pathogenesis ofM. tuberculosisinfections, and ETA or ETB receptor signaling can modulate the host response to the infection. We hypothesize that a balance between Zmp1 control of ET-1 levels and ETA/ETB signaling can allowM. tuberculosisadaptation and survival in the lung tissues.
Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli
Authors: Thomason Maureen K. , Bischler Thorsten , Eisenbart Sara K. , Förstner Konrad U. , Zhang Aixia , Herbig Alexander , Nieselt Kay , Sharma Cynthia M. , Storz Gisela
Published: September 2014

While the model organism
Escherichia coli
has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the
E. coli
transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type
E. coli
and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the
rnc
and
rne
mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in
E. coli
and is easily accessible, together with the cDNA coverage plots, in an online genome browser.
A Genetic Screen in Myxococcus xanthus Identifies Mutants That Uncouple Outer Membrane Exchange from a Downstream Cellular Response
Authors: Dey Arup , Wall Daniel
Published: September 2014

Upon physical contact with sibling cells, myxobacteria transiently fuse their outer membranes (OMs) and exchange OM proteins and lipids. From previous work, TraA and TraB were identified to be essential factors for OM exchange (OME) in donor and recipient cells. To define the genetic complexity of OME, we carried out a comprehensive forward genetic screen. The screen was based on the observation that
Myxococcus xanthus
nonmotile cells, by a Tra-dependent mechanism, block swarm expansion of motile cells when mixed. Thus, mutants defective in OME or a downstream responsive pathway were readily identified as escape flares from mixed inocula seeded on agar. This screen was surprisingly powerful, as we found >50 mutants defective in OME. Importantly, all of the mutations mapped to the
traAB
operon, suggesting that there may be few, if any, proteins besides TraA and TraB directly required for OME. We also found a second and phenotypically different class of mutants that exhibited wild-type OME but were defective in a responsive pathway. This pathway is postulated to control inner membrane homeostasis by covalently attaching amino acids to phospholipids. The identified proteins are homologous to the
Staphylococcus aureus
MprF protein, which is involved in membrane adaptation and antibiotic resistance. Interestingly, we also found that a small number of nonmotile cells were sufficient to block the swarming behavior of a large gliding-proficient population. This result suggests that an OME-derived signal could be amplified from a few nonmotile producers to act on many responder cells.
Microbial community in anoxic–oxic–settling–anaerobic sludge reduction process revealed by 454 pyrosequencing analysis
Authors: Ning Xinqiang , Qiao Wenwen , Zhang Lei , Gao Xu
Published: September 2014

Modification of the anoxic–oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic–oxic–settling–anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased.
The Relation Between Diamond Tiling and Hexagonal Tiling
Authors: Grosser Tobias , Verdoolaege Sven , Cohen Albert , Sadayappan P.
Published: September 2014

Iterative stencil computations are important in scientific computing and more also in the embedded and mobile domain. Recent publications have shown that tiling schemes that ensure concurrent start provide efficient ways to execute these kernels. Diamond tiling and hybrid-hexagonal tiling are two tiling schemes that enable concurrent start. Both have different advantages: diamond tiling has been integrated in a general purpose optimization framework and uses a cost function to choose among tiling hyperplanes, whereas the greater flexibility with tile sizes for hybrid-hexagonal tiling has been exploited for effective generation of GPU code.

In this paper we undertake a comparative study of these two tiling approaches and propose a hybrid approach that combines them. We analyze the effects of tile size and wavefront choices on tile-level parallelism, and formulate constraints for optimal diamond tile shapes. We then extend, for the case of two dimensions, the diamond tiling formulation into a hexagonal tiling one, which offers both the flexibility of hexagonal tiling and the generality of the original diamond tiling implementation. We also show how to compute tile sizes that maximize the compute-to-communication ratio, and apply this result to compare the best achievable ratio and the associated synchronization overhead for diamond and hexagonal tiling.
Code Refinement of Stencil Codes
Authors: Köster Marcel , Leißa Roland , Hack Sebastian , Membarth Richard , Slusallek Philipp
Published: September 2014

A straightforward implementation of an algorithm in a general-purpose programming language does usually not deliver peak performance: Compilers often fail to automatically tune the code for certain hardware peculiarities like memory hierarchy or vector execution units. Manually tuning the code is firstly error-prone as well as time-consuming and secondly taints the code by exposing those peculiarities to the implementation. A popular method to avoid these problems is to implement the algorithm in a Domain-Specific Language (DSL). A DSL compiler can then automatically tune the code for the target platform.

In this article we show how to embed a DSL for stencil codes in another language. In contrast to prior approaches we only use a single language for this task which offers explicit control over code refinement. This is used to specialize stencils for particular scenarios. Our results show that our specialized programs achieve competitive performance compared to hand-tuned CUDA programs while maintaining a convenient coding experience.
Group Scheduling with Two Competing Agents on a Single Machine
Authors: Li Shi-Sheng , Chen Ren-Xia
Published: September 2014

We consider the scheduling problem in which two agents, each with a set of jobs, compete to perform their respective jobs on a single machine under a group technology (GT) environment. The jobs of agents are classified into groups according to their production similarities in advance, all jobs of the same group are required to be processed contiguously on the machine. A sequence-independent setup time precedes the processing of each group. We propose a polynomial time solution for the problem of minimizing the maximum regular cost of one agent, subject to an upper bound on the maximum regular cost of the second agent. We also show that the problem of minimizing the total completion time of the first agent, subject to an upper bound on the maximum lateness of the second agent is strongly [Formula: see text]-hard. The case where all groups of the first agent have the same number of jobs is shown to be polynomially solvable.
Performance of the ALICE experiment at the CERN LHC
Authors:   The ALICE Collaboration
Published: September 2014

ALICE is the heavy-ion experiment at the CERN Large Hadron Collider. The experiment continuously took data during the first physics campaign of the machine from fall 2009 until early 2013, using proton and lead-ion beams. In this paper we describe the running environment and the data handling procedures, and discuss the performance of the ALICE detectors and analysis methods for various physics observables.
Cost-Based Stackelberg Potential Game for Cognitive Radio Ad Hoc Network
Authors: Minhas Qurratulain , Mahmood Hasan
Published: September 2014

In cognitive radio ad hoc networks, the opportunistic access of vacant wireless channel opens a new frontier for efficient spectrum utilization as in many situations, a wide range of spectrum is not even partially utilized by the license owners (primary users, PUs). While the idea seems to be lucrative for spectrum hungry users without licenses, a natural competition between potential stake holders arises, which needs to be regulated in order to efficiently utilize available resources and avoid chaos. With the introduction of unlicensed users in licensed bands, the operations and interests of PUs need to be protected, hence the spectrum owners are given an advantage and control over the multiple access policy (a leader-follower scenario). In this work, we address the problems in spectrum access and channel selection equilibrium in a leader (PU)-follower (secondary user, SU) setup. In contrast to previous game formulations that lack efficient power and pricing schemes, we present a cooperative Stackelberg potential game for cognitive players. A dynamic cost function is articulated to induce awareness in players to mitigate the effects of selfish choices in spectrum access while at the same time steer the distributed network towards achieving Nash equilibrium. The proposed scheme is mutually beneficial for all players and focuses on improving the network performance and power efficiency. We design the network potential function such that the nodes have performance based incentives to cooperate and achieve a Nash equilibrium solution for efficient channel acquisition and capacity. Simulation results show fast convergence in channel selection strategies and increase in capacity for the entire network.
Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites
Authors: Fang Chun , Noguchi Tamotsu , Yamana Hayato
Published: September 2014

Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.
High Dose of Lamivudine and Resistance in Patients with Chronic Hepatitis B
Authors: Wani Hamid Ullah , Al Kaabi Saad , Sharma Manik , Singh Rajvir , John Anil , Derbala Moutaz , Al-Mohannadi Muneera J.
Published: September 2014

Background. Lamivudine is the most affordable drug used for chronic hepatitis B and has a high safety profile. With the daily dose of 100 mg there is progressive appearance of resistance to lamivudine therapy. In our study we used 150 mg of lamivudine daily as a standard dose which warrants further exploration for the efficacy of the drug. Aims of the Study. To assess the efficacy of lamivudine 150 mg daily on resistance in patients with chronic hepatitis B. Methods. This retrospective study consists of 53 patients with chronic hepatitis B treated with 150 mg of lamivudine daily. The biochemical and virological response to the treatment were recorded at a 1-year and 2-, 3-, 4-, and 5-year period and time of emergence of resistance to the treatment was noted. Results. The mean age of the patients was 54 years with 80% being males. The resistance to lamivudine 150 mg daily at 1 year and 2, 3, and 5 years was 12.5%, 22.5%, 37.5%, and 60%, respectively, which is much less compared to the standard dose of 100 mg of lamivudine. Conclusions. Lamivudine is safe and a higher dose of 150 mg daily delays the resistance in patients with chronic hepatitis B.
Chemokines Referee Inflammation within the Central Nervous System during Infection and Disease
Authors: Durrant Douglas M. , Williams Jessica L. , Daniels Brian P. , Klein Robyn S.
Published: September 2014

The discovery that chemokines and their receptors are expressed by a variety of cell types within the normal adult central nervous system (CNS) has led to an expansion of their repertoire as molecular interfaces between the immune and nervous systems. Thus, CNS chemokines are now divided into those molecules that regulate inflammatory cell migration into the CNS and those that initiate CNS repair from inflammation-mediated tissue damage. Work in our laboratory throughout the past decade has sought to elucidate how chemokines coordinate leukocyte entry and interactions at CNS endothelial barriers, under both homeostatic and inflammatory conditions, and how they promote repair within the CNS parenchyma. These studies have identified several chemokines, including CXCL12 and CXCL10, as critical regulators of leukocyte migration from perivascular locations. CXCL12 additionally plays an essential role in promoting remyelination of injured white matter. In both scenarios we have shown that chemokines serve as molecular links between inflammatory mediators and other effector molecules involved in neuroprotective processes.
Systemic Sclerosis and Silicone Breast Implant: A Case Report and Review of the Literature
Authors: Psarras Antonios , Gkougkourelas Ioannis , Tselios Konstantinos , Sarantopoulos Alexandros , Boura Panagiota
Published: September 2014

Environmentally induced systemic sclerosis is a well-recognized condition, which is correlated with exposure to various chemical compounds or drugs. However, development of scleroderma-like disease after exposure to silicone has always been a controversial issue and, over time, it has triggered spirited debate whether there is a certain association or not. Herein, we report the case of a 35-year-old female who developed Raynaud’s phenomenon and, finally, systemic sclerosis shortly after silicone breast implantation surgery.
Accelerated Testing with Multiple Failure Modes under Several Temperature Conditions
Authors: Yu Zongyue , Ren Zhiqian , Tao Junyong , Chen Xun
Published: September 2014

A complicated device may have multiple failure modes, and some of the failure modes are sensitive to low temperatures. To assess the reliability of a product with multiple failure modes, this paper presents an accelerated testing in which both of the high temperatures and the low temperatures are applied. Firstly, an acceleration model based on the Arrhenius model but accounting for the influence of both the high temperatures and low temperatures is proposed. Accordingly, an accelerated testing plan including both the high temperatures and low temperatures is designed, and a statistical analysis method is developed. The reliability function of the product with multiple failure modes under variable working conditions is given by the proposed statistical analysis method. Finally, a numerical example is studied to illustrate the proposed accelerated testing. The results show that the proposed accelerated testing is rather efficient.