bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Tsunami Hazard Map for Supporting Evacuation Guidance in Tsunami
Authors: Masuda Koichi , Ikoma Tomoki , Aida Yasuhiro , Hoshino Satoshi , Takayama Jumpei
Published: October 2015

We developed a tsunami hazard map for supporting evacuation guidance which is intended for government use. The evacuation behavior simulator achieved in making changes in every moment with an analysis that unifies evacuation behavior simulation and tsunami propagation simulation, as this enables the calculation of the difficult evacuation zones. This paper offers a practice case study for Shimizu ward, Shimizu city, Shizuoka prefecture, in Japan. The difficult evacuation zone was around Yokosuna-nishi-machi in the northwest part of the study site. The simulation conditions included walking speed and evacuation direction, which was verified for this difficult evacuation zone. This is effective for evacuation toward inland, especially elevated ground which doesn’t become inundated by tsunami. In this paper, the results of simulations were reflected in a hazard map. Then we propose the hazard map as intended for the government, for supporting evacuation guidance in a tsunami.
Sensitivity of Rogue Wave Prediction to the Oceanic Stratification
Authors: Guo Qiuchen , Alam M.-Reza
Published: October 2015

Oceanic rogue waves are short-lived very large amplitude waves (a giant crest typically followed or preceded by a deep trough) that appear and disappear suddenly in the ocean causing damage to ships and offshore structures. Assuming that the state of the ocean at the present time is perfectly known, then the upcoming rogue waves can be predicted via numerically solving the equations that govern the evolution of the waves. State of the art radar technology can now provide accurate wave height measurements over large spatial domains and when combined with advanced wave-field reconstruction techniques together render deterministic details of the current state of the ocean (i.e. surface elevation and velocity field) at any given moment of time with a very high accuracy. The ocean density is, however, stratified (mainly due to the salinity and temperature differences). This density stratification, with today’s technology, is very difficult to measure accurately. As a result, in most predictive schemes these density variations are neglected. While the overall effect of the stratification on the average state of the ocean may not be significant, here we show that these density variations can strongly affect the prediction of oceanic rogue wave. Specifically, we consider a broadband oceanic spectrum in a two-layer density stratified fluid and study, via extensive statistical analysis, the effects of the strength of the stratification (difference between densities) and the depth of the thermocline on the prediction of upcoming rogue waves.
Modeling of a Permanent Magnet Linear Generator for Wave-Energy Conversion
Authors: Tom Nathan , Son Daewoong , Belissen Valentin , Yeung Ronald W.
Published: October 2015

This paper begins with a brief review of the equation of motion for a generic floating body with modification to incorporate the influence of a power-take-off (PTO) unit. Since the damping coefficient is considered the dominant contribution to the PTO reaction force, the optimum non time-varying values are presented for all frequencies, recovering the well-known impedance-matching principle at the resonance condition of the coupled system. The construction of a laboratory-scale permanent magnet linear generator (PMLG), developed at the University of California at Berkeley, is discussed along with the basic electromagnetic equations used to model its performance. Modeling of the PMLG begins with a lumped magnetic circuit analysis, which provides an analytical solution to predict the magnetic flux available for power conversion. The voltage generated across each phase of the stator, induced by the motion of the armature, provides an estimate for the electromagnetic damping as a function of the applied resistive load. The performance of the PMLG and the validation of the proposed analytical model is completed by a set of dry-bench tests. Results from the bench test showed good agreement with the described electromechanical model, thus providing an analytical solution that can assist in further optimization of the PMLG.
Optimizing the Performance of a Dual Coaxial-Cylinder Wave-Energy Extractor
Authors: Son Daewoong , Belissen Valentin , Yeung Ronald W.
Published: October 2015

This study evaluates two significant design modifications of a dual coaxial-cylinder system as a wave-energy extractor reported in Son and Yeung (2014, OMAE2014-#24582). First, a new and stronger power take-off (PTO) unit for a permanent magnet linear generator (PMLG) was built, along with an appropriate supporting structure, so as to match optimality conditions in terms of impedance matching and mechanical to electrical conversion efficiency. Based on a series of (dry-)bench tests, the properties of the PTO were obtained and the optimal operating conditions were determined. Second, the flat-bottom shape of the outer toroidal floater was modified according to “The Berkeley Wedge design” (Madhi et al, 2014, “The Berkeley Wedge: an asymmetrical energy-capturing floating breakwater of high performance,” Journal of Marine Systems and Ocean Technology, vol. 9(1), pp. 5–16). The new bottom shape led to reduction of the floater damping by almost 70%, which yielded a 3-fold increase in the floater motion response. Experiments in a wave-tank validated the response behavior of the dual-cylinder system with the use of the new PTO. The Berkeley-Wedge shape allowed more than 3 times more energy be extracted compared to the flat-bottom geometry, while the new generator also improved the energy conversion efficiency. As a result, the overall system efficiency of the device was enhanced remarkably five times over that of the previous design.
Optimization of Hydraulic Efficiency of a Free Surface Semicircular Breakwater Using Wave Screens
Authors: Teh Hee Min , Venugopal Vengatesan
Published: October 2015

A free surface semicircular breakwater (SCB) with rectangular perforations has been developed to serve as a wave defence structure. Hydrodynamic performance of the breakwaters of various perforations has been thoroughly investigated through wave measurements in a wave flume under random waves. The SCBs were experimentally confirmed to be good anti-reflection wave structures; however, the level of wave transmission at the leeside of the SCBs was rather high particularly when immersed in limited depth and confronted by waves of longer period. This study aims at optimizing the hydraulic characteristics of the SCB by extending its draft by means of wave screens. Three test configurations have been identified in this study, namely (1) the SCB with front screen, (2) the SCB with rear screen, and (3) the SCB with double screens. For each wave screen, three porosities (i.e. 25, 40 and 50%) have been considered in the experiments. The models of shallow immersion depths have been tested in random waves of different characteristics in a wave flume. Wave transformation at different locations upstream and downstream of the test models has been recorded by wave probes. The hydraulic performance of the breakwater are quantified by the coefficients of wave transmission, reflection and energy dissipation, and the wave climate in the vicinity of the breakwater are presented in the form of a ratio relative to the incident wave height. The optimum design of SCB supplemented by truncated wave screen(s) is proposed at the end of the study.
Concrete-Ice Abrasion Mechanism
Authors: Tyutrin Roman S. , Pomnikov Egor E. , Baenkhaev Andrey K.
Published: October 2015

There are not many data related to the mechanism of concrete-ice abrasion published. Some of researches try to find similarities in concrete-ice abrasion mechanism with various wear mechanisms from tribology, others propose their own theory. In general, ice abrasion of concrete has some similarities, noticed by researches, with wear mechanisms of other materials for example same splitting on several stages (surface, transition, stable), or relation between friction and abrasion rate. Most of the equations use hardness or fracture toughness as the characteristic of the material. These parameters were tested both for ice and concrete in general. But may these results be applicable for micro scale modelling? This article gives an overview of several possible mechanisms and describes their main points. As well as author’s hypothesis of the mechanism is proposed.
Dynamic Model of a Mobile Offshore Drilling Unit in Deep Water Environments for Drilling Simulation
Authors: Arvani Farid , Rideout D. Geoff , Butt Stephen D.
Published: October 2015

In this study, a dynamic model of a Mobile Offshore Drilling Unit (MODU) is described that simulates drilling scenarios, imposed by the environmental factors in offshore drilling. The Response Amplitude Operators (RAOs) of an industry-recognized semi-submersible MODU are modeled for all six degrees of freedom. A stochastic modeling of waves in the North Sea is used and heave disturbance induced by elevation motion of sea surface is modeled using the JONSWAP spectrum. A bond graph model of a MODU predicts axial vibration, torsional vibration, and coupling between axial and torsional vibration due to bit-rock interaction. Axial and torsional submodels use a lumped-segment approach. The model can predict the expected coupling between Weight On Bit (WOB), bit speed, and bit-rock interface conditions. A series of sensitivity analyses were performed to investigate the significance of MODU motion on WOB fluctuations.
Numerical and Experimental Analysis of Added Resistance of Ships in Waves
Authors: el Moctar Ould , Sigmund Sebastian , Schellin Thomas E.
Published: October 2015

A RANS-based field method numerically predicted added resistance in regular head waves for a 14000 TEU containership (Duisburg Test Case) and a medium-size cruise ship. We concentrated our investigations on short waves. For different frequencies, we decomposed added resistance into diffraction and radiation force components, whereby diffraction forces were obtained by restraining the ship in waves and radiation forces, by prescribing the motions of the ship in calm water. In short waves, the diffraction part of total resistance was dominant as almost no ship motions were induced. In long waves, the sum of diffraction and radiation forces exceeded total resistance, i.e., the interaction of these two force components, which caused the reduction of total resistance, had to be accounted for. Predictions were compared with model test measurements. Particular emphasis was placed on the following aspects: discretization errors, frictional resistance as part of total added resistance in waves, diffraction and radiation components of added resistance in waves, and the influence of surge motion on added resistance. Investigations comprised two steps, namely, a preliminary simulation to determine calm-water resistance and a second simulation to compute total resistance in waves, always using the same grids. Added resistance was obtained by subtracting calm-water resistance from total averaged wave resistance. When frictional resistance dominated calm-water resistance, which holds for nearly all conventional ships at moderate Froude numbers, high grid densities were required in the neighborhood surrounding the hull.
Effect of Reeling on Sulfide Stress Corrosion Cracking of Welded API5LX65 Line Pipe
Authors: Thodla Ramgopal , Gordon Robin , Gui Feng
Published: October 2015

The effect of reeling on sulfide stress cracking (SSC) resistance of welded line pipe was investigated in two different environments, a modified NACE B environment and a fitness for service environment (pH = 5/pH2S = 0.46psia). Micro hardness maps were performed to characterize the welds both in the as fabricated condition as well as in the strained and aged condition. The hardness values in all of the conditions, was less than 250VHN (in compliance with NACE requirements). Triplicate specimens were tested in the as fabricated, strained and aged intrados and extrados in both the environments. SSC resistance in a severely sour environment (pH = 3.5/1psia H2S) was affected by reeling with cracking observed in both the intrados and extrados samples. No cracking was observed in the as-fabricated welds. However, in a moderately sour environment (pH = 5/0.46psia H2S) reeling did not have a detrimental effect on the SSC performance. No evidence of cracking on the as-fabricated, intrados, and extrados welds. In moderate sour service reeling doesn’t appear to have a detrimental effect on the SSC behavior.
Development of an Environmental and Ship Motion Forecasting System
Authors: Connell Benjamin S. H. , Rudzinsky Jason P. , Brundick Christopher S. , Milewski William M. , Kusters John G. , Farquharson Gordon
Published: October 2015

Military sea basing operations include mooring ships together offshore and transferring cargo and equipment between them. A newly developed Environmental and Ship Motion Forecasting (ESMF) System will facilitate these operations by providing predictions of ship motions in waves. Coherent forecasts of the ship motions are provided through remote sensing of the ambient waves and using these waves as input to a predictive ship motion simulation. Key technologies developed in support of the ESMF system include: a custom-built wave sensing radar; a least squares inverse wave retrieval algorithm; a ship motion model for performing rapid seakeeping simulations; and a robust peer-to-peer system architecture. The ESMF system was tested extensively in a demonstration aboard the R/V Melville with very good results, often achieving correlations of forecast-to-realized signals of better than 80% over 30 minute intervals.
Vapor deposition on doublet airfoil substrates: Control of coating thickness and microstructure
Authors: Rodgers Theron M. , Zhao Hengbei , Wadley Haydn N. G.
Published: October 2015

Gas jet assisted vapor deposition processes for depositing coatings are conducted at higher pressures than conventional physical vapor deposition methods, and have shown promise for coating complex shaped substrates including those with non-line-of-sight (NLS) regions on their surface. These regions typically receive vapor atoms at a lower rate and with a wider incident angular distribution than substrate regions in line-of-sight (LS) of the vapor source. To investigate the coating of such substrates, the thickness and microstructure variation along the inner (curved) surfaces of a model doublet airfoil containing both LS and NLS regions has been investigated. Results from atomistic simulations and experiments confirm that the coating's thickness is thinner in flux-shadowed regions than in other regions for all the coating processes investigated. They also indicated that the coatings columnar microstructure and pore volume fraction vary with surface location through the LS to NLS transition zone. A substrate rotation strategy for optimizing the thickness over the entire doublet airfoil surface was investigated, and led to the identification of a process that resulted in only small variation of coating thickness, columnar growth angle, and pore volume fraction on all doublet airfoil surfaces.
Impedance measurement techniques for one-port and two-port networks
Authors: Bai Mingsian R. , Lo Yi-Yang , Chen You Siang
Published: October 2015

A microphone array impedance matrix measurement technique is presented for linear and passive acoustic two-port networks. Two impedance tubes fitted with three non-uniformly spaced microphones are required in the measurement. The non-uniform spacing is intended to avoid ill-posedness problems in calculating two plane-wave components traveling in opposite directions. Based on the one-port measurement, acoustic two-port networks modeled with the source and the load connected are examined. Three experimental procedures, the two-load measurement method (TLMM), the reciprocal-constrained method (RCM), and the reciprocity-symmetry-constrained method (RSCM), are developed to measure the acoustic impedance matrix. Experiments are conducted for several acoustic two-port systems to verify the proposed techniques. The results demonstrate the efficacy of the three experimental procedures when applied to symmetrical and reciprocal systems. For asymmetrical systems, the TLMM and RCM are preferred over the RSCM for measuring the impedance matrix. On top of that, the non-uniform array in conjunction with TLMM is extended to a general electroacoustic two-port system, which can be regarded as a unique contribution of the present work.
Aging effect on Mandarin Chinese vowel and tone identification
Authors: Yang Xiaohu , Wang Yuxia , Xu Lilong , Zhang Hui , Xu Can , Liu Chang
Published: October 2015

Mandarin Chinese speech sounds (vowels × tones) were presented to younger and older Chinese-native speakers with normal hearing. For the identification of vowel-plus-tone, vowel-only, and tone-only, younger listeners significantly outperformed older listeners. The tone 3 identification scores correlated significantly with the age of older listeners. Moreover, for older listeners, the identification rate of vowel-plus-tone was significantly lower than that of vowel-only and tone-only, whereas for younger listeners, there was no difference among the three identification scores. Therefore, aging negatively affected Mandarin vowel and tone perception, especially when listeners needed to process both phonemic and tonal information.
A Surrogate Technique for Investigating Deterministic Dynamics in Discrete Human Movement
Authors: Taylor Paul G. , Small Michael , Lee Kwee-Yum , Landeo Raul , O’Meara Damien M. , Millett Emma L.
Published: October 2015

Entropy is an effective tool for investigation of human movement variability. However, before applying entropy, it can be beneficial to employ analyses to confirm that observed data are not solely the result of stochastic processes. This can be achieved by contrasting observed data with that produced using surrogate methods. Unlike continuous movement, no appropriate method has been applied to discrete human movement. This article proposes a novel surrogate method for discrete movement data, outlining the processes for determining its critical values. The proposed technique reliably generated surrogates for discrete joint angle time series, destroying fine-scale dynamics of the observed signal, while maintaining macro structural characteristics. Comparison of entropy estimates indicated observed signals had greater regularity than surrogates and were not only the result of stochastic but also deterministic processes. The proposed surrogate method is both a valid and reliable technique to investigate determinism in other discrete human movement time series.
Ultrasound-mediated gastrointestinal drug delivery
Authors: Schoellhammer Carl M. , Schroeder Avi , Maa Ruby , Lauwers Gregory Yves , Swiston Albert , Zervas Michael , Barman Ross , DiCiccio Angela M. , Brugge William R. , Anderson Daniel G. , Blankschtein Daniel , Langer Robert , Traverso Giovanni
Published: October 2015

Ultrasound enables rapid and local delivery of drugs to the gastrointestinal tract for treatment of inflammatory diseases, such as ulcerative colitis.
Identification of broadly conserved cross-species protective
Leishmania
antigen and its responding CD4
+
T cells
Authors: Mou Zhirong , Li Jintao , Boussoffara Thouraya , Kishi Hiroyuki , Hamana Hiroshi , Ezzati Peyman , Hu Chuanmin , Yi Weijing , Liu Dong , Khadem Forough , Okwor Ifeoma , Jia Ping , Shitaoka Kiyomi , Wang Shufeng , Ndao Momar , Petersen Christine , Chen Jianping , Rafati Sima , Louzir Hechmi , Muraguchi Atsushi , Wilkins John A. , Uzonna Jude E.
Published: October 2015

A
Leishmania
protein vaccine elicited immune responses and mediated strong cross-species protection.
PET imaging of tumor glycolysis downstream of hexokinase through noninvasive measurement of pyruvate kinase M2
Authors: Witney Timothy H. , James Michelle L. , Shen Bin , Chang Edwin , Pohling Christoph , Arksey Natasha , Hoehne Aileen , Shuhendler Adam , Park Jun-Hyung , Bodapati Deepika , Weber Judith , Gowrishankar Gayatri , Rao Jianghong , Chin Frederick T. , Gambhir Sanjiv Sam
Published: October 2015

A PET imaging reagent targeting PKM2 allows noninvasive assessment of glycolysis in glioblastoma multiforme, distinguishing it from normal brain tissue.
B cells assume the command
Authors: Waisman Ari , Korn Thomas
Published: October 2015

A proinflammatory B cell cytokine activates autoimmunity, and B cell depletion treats multiple sclerosis (Li
et al.,
this issue).
Gene therapy hide and seek
Authors: Dalkara Deniz
Published: October 2015

AAV capsid epitopes conserved across multiple serotypes stimulate immune responses to gene therapy vectors.
A key to gut health in a few microns of mucus
Authors: Faith Jeremiah J.
Published: October 2015

Quantitative imaging facilitates assessment of gut mucus and reveals a protective influence of certain dietary carbohydrates on mucus layer thickness.
Molecular Epidemiology of Streptococcus uberis Clinical Mastitis in Dairy Herds: Strain Heterogeneity and Transmission
Authors: Davies P. L. , Leigh J. A. , Bradley A. J. , Archer S. C. , Emes R. D. , Green M. J.
Published: October 2015

Multilocus sequence typing was successfully completed on 494 isolates of
Streptococcus uberis
from clinical mastitis cases in a study of 52 commercial dairy herds over a 12-month period. In total, 195 sequence types (STs) were identified.
S. uberis
mastitis cases that occurred in different cows within the same herd and were attributed to a common ST were classified as potential transmission events (PTEs). Clinical cases attributed to 35 of the 195 STs identified in this study were classified PTE. PTEs were identified in 63% of the herds. PTE-associated cases, which include the first recorded occurrence of that ST in that herd (index case) and all persistent infections with that PTE ST, represented 40% of all the clinical mastitis cases and occurred in 63% of the herds. PTE-associated cases accounted for >50% of all
S. uberis
clinical mastitis cases in 33% of the herds. Nine STs (ST-5, -6, -20, -22, -24, -35, -233, -361, and -512), eight of which were grouped within a clonal complex (sharing at least four alleles), were statistically overrepresented (OVR STs). The findings indicate that 38% of all clinical mastitis cases and 63% of the PTEs attributed to
S. uberis
in dairy herds may be caused by the nine most prevalent strains. The findings suggest that a small subset of STs is disproportionally important in the epidemiology of
S. uberis
mastitis in the United Kingdom, with cow-to-cow transmission of
S. uberis
potentially occurring in the majority of herds in the United Kingdom, and may be the most important route of infection in many herds.
Accuracy of Conventional PCR Targeting the 16S rRNA Gene with the Ot-16sRF1 and Ot-16sRR1 Primers for Diagnosis of Scrub Typhus: a Case-Control Study
Authors: Kim Choon-Mee , Cho Min Keun , Kim Dong-Min , Yun Na-Ra , Kim Seok Won , Jang Sook Jin , Ahn Young-Joon , Lim Donghoon
Published: October 2015

We retrospectively evaluated the accuracy of conventional PCR targeting the 16S rRNA gene (16S C-PCR) using the Ot-16sRF1/Ot-16sRR1 primers for diagnosing scrub typhus. The diagnosis of
Orientia tsutsugamushi
infection by 16S C-PCR presented an increased sensitivity of 87.0% and specificity of 100% compared with those obtained with other targets and is thus a simple and clinically useful method with good diagnostic accuracy.
Molecular Identification of Zoonotic Tissue-Invasive Tapeworm Larvae Other than Taenia solium in Suspected Human Cysticercosis Cases
Authors: Tappe Dennis , Berkholz Jörg , Mahlke Uwe , Lobeck Hartmut , Nagel Thomas , Haeupler Alexandra , Muntau Birgit , Racz Paul , Poppert Sven
Published: October 2015

Rarely, zoonotic
Taenia
species other than
Taenia solium
cause human cysticercosis. The larval stages are morphologically often indistinguishable. We therefore investigated 12 samples of suspected human cysticercosis cases at the molecular level and surprisingly identified one
Taenia crassiceps
and one
Taenia serialis
(coenurosis) infection, which were caused by tapeworm larvae normally infecting rodents and sheep via eggs released from foxes and dogs.
First Detection of TR34 L98H and TR46 Y121F T289A Cyp51 Mutations in Aspergillus fumigatus Isolates in the United States
Authors: Wiederhold Nathan P. , Gil Veronica Garcia , Gutierrez Felipe , Lindner Jonathan R. , Albataineh Mohammad T. , McCarthy Dora I. , Sanders Carmita , Fan Hongxin , Fothergill Annette W. , Sutton Deanna A.
Published: October 2015

Azole resistance in
Aspergillus fumigatus
is an increasing problem. The TR34 L98H and TR46 Y121F T289A mutations that can occur in patients without previous azole exposure have been reported in Europe, Asia, the Middle East, Africa, and Australia. Here, we report the detection of both the TR34 L98H and TR46 Y121F T289A mutations in confirmed
A. fumigatus
isolates collected in institutions in the United States. These mutations, other mutations known to cause azole resistance, and azole MICs are reported here.
Viral DNA-Dependent Induction of Innate Immune Response to Hepatitis B Virus in Immortalized Mouse Hepatocytes
Authors: Cui Xiuji , Clark Daniel N. , Liu Kuancheng , Xu Xiao-Dong , Guo Ju-Tao , Hu Jianming
Published: October 2015

Hepatitis B virus (HBV) infects hundreds of millions of people worldwide and causes acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma. HBV is an enveloped virus with a relaxed circular (RC) DNA genome. In the nuclei of infected human hepatocytes, conversion of RC DNA from the incoming virion or cytoplasmic mature nucleocapsid (NC) to the covalently closed circular (CCC) DNA, which serves as the template for producing all viral transcripts, is essential to establish and sustain viral replication. A prerequisite for CCC DNA formation is the uncoating (disassembly) of NCs to expose their RC DNA content for conversion to CCC DNA. We report here that in an immortalized mouse hepatocyte cell line, AML12HBV10, in which RC DNA exposure is enhanced, the exposed viral DNA could trigger an innate immune response that was able to modulate viral gene expression and replication. When viral gene expression and replication were low, the innate response initially stimulated these processes but subsequently acted to shut off viral gene expression and replication after they reached peak levels. Inhibition of viral DNA synthesis or cellular DNA sensing and innate immune signaling diminished the innate response. These results indicate that HBV DNA, when exposed in the host cell cytoplasm, can function to trigger an innate immune response that, in turn, modulates viral gene expression and replication.

IMPORTANCE
Chronic infection by hepatitis B virus (HBV) afflicts hundreds of millions worldwide and is sustained by the episomal covalently closed circular (CCC) DNA in the nuclei of infected hepatocytes. Release of viral genomic DNA from cytoplasmic nucleocapsids (NCs) (NC disassembly or uncoating) is a prerequisite for its conversion to CCC DNA, which can also potentially expose the viral DNA to host DNA sensors and trigger an innate immune response. We have found that in an immortalized mouse hepatocyte cell line in which efficient CCC DNA formation was associated with enhanced exposure of nucleocapsid-associated DNA, the exposed viral DNA indeed triggered host cytoplasmic DNA sensing and an innate immune response that was able to modulate HBV gene expression and replication. Thus, HBV can, under select conditions, be recognized by the host innate immune response through exposed viral DNA, which may be exploited therapeutically to clear viral persistence.
Growth and Pathogenic Potential of Naturally Selected Reassortants after Coinfection with Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Viruses
Authors: Song Min-Suk , Baek Yun Hee , Pascua Philippe Noriel Q. , Kwon Hyeok-il , Kim Eun-Ha , Park Su-Jin , Kim Se Mi , Kim Young-Il , Choi Won-Suk , Kim Eung-Gook , Kim Chul-Joong , Choi Young Ki
Published: October 2015

Coinfection of ferrets with H5N1 and pH1N1 viruses resulted in two predominate genotypes in the lungs containing surface genes of highly pathogenic avian influenza H5N1 virus in the backbone of pandemic H1N1 2009 (pH1N1). Compared to parental strains, these reassortants exhibited increased growth and virulence
in vitro
and in mice but failed to be transmitted indirectly to naive contact ferrets. Thus, this demonstrates a possible natural reassortment following coinfection as well as the pathogenicity of the potential reassortants.
Low-Level Expression of the E1B 20-Kilodalton Protein by Adenovirus 14p1 Enhances Viral Immunopathogenesis
Authors: Radke Jay R. , Yong Sherri L. , Cook James L.
Published: October 2015

Adenovirus 14p1 (Ad14p1) is an emergent variant of Ad serotype 14 (Ad14) that has caused increased severity of respiratory illnesses during globally distributed outbreaks, including cases of acute respiratory distress syndrome and death. We found that human cell infection with Ad14p1 results in markedly decreased expression of the E1B 20-kilodalton (20K) protein compared to that with infection with wild-type (wt) Ad14. This reduced Ad14p1 E1B 20K expression caused a loss-of-function phenotype of Ad-infected cell corpses that, in contrast to cells infected with wt Ad14, either failed to repress or increased NF-κB-dependent, proinflammatory cytokine responses of responder human alveolar macrophages. A small-animal model of Ad14-induced lung infection was used to test the translational relevance of these
in vitro
observations. Intratracheal infection of Syrian hamsters with Ad14p1 caused a marked, patchy bronchopneumonia, whereas hamster infection with wt Ad14 caused minimal peribronchial inflammation. These results suggest that this difference in E1B 20K gene expression during Ad14p1 infection and its modulating effect on the interactions between Ad14-infected cells and the host innate immune response could explain the increased immunopathogenic potential and associated increase in clinical illness in some people infected with the Ad14p1 outbreak strain.

IMPORTANCE
We previously reported that Ad-infected human cells exhibit E1B 19K-dependent repression of virally induced, NF-κB-dependent macrophage cytokine responses (J. R. Radke, F. Grigera, D. S. Ucker, and J. L. Cook, J Virol 88:2658–2669, 2014,
http://dx.doi.org/10.1128/JVI.02372-13
). The more virulent, emergent strain of Ad14, Ad14p1, causes increased cytopathology
in vitro
, which suggested a possible E1B 20K defect. Whether there is a linkage between these observations was unknown. We show that there is markedly reduced expression of E1B 20K in Ad14p1-infected human cells and that this causes an increased proinflammatory cytokine response of human alveolar macrophages and more severe inflammatory lung disease in infected hamsters. This is the first evidence of a clinical relevance of differential expression of the small Ad E1B gene product. The results suggest that there is a low, critical threshold of E1B 19/20K expression that is needed for viral replication and infection transmission but that a higher level of E1B 19/20K expression is required for the usual repression and control of the Ad-triggered host innate immune response.
A Single Maturation Cleavage Site in Adenovirus Impacts Cell Entry and Capsid Assembly
Authors: Moyer Crystal L. , Besser Eli S. , Nemerow Glen R.
Published: October 2015

Proteolytic maturation drives the conversion of stable, immature virus particles to a mature, metastable state primed for cell infection. In the case of human adenovirus, this proteolytic cleavage is mediated by the virally encoded protease AVP. Protein VI, an internal capsid cement protein and substrate for AVP, is cleaved at two sites, one of which is near the N terminus of the protein. In mature capsids, the 33 residues at the N terminus of protein VI (pVIn) are sequestered inside the cavity formed by peripentonal hexon trimers at the 5-fold vertex. Here, we describe a glycine-to-alanine mutation in the N-terminal cleavage site of protein VI that profoundly impacts proteolytic processing, the generation of infectious particles, and cell entry. The phenotypic effects associated with this mutant provide a mechanistic framework for understanding the multifunctional nature of protein VI. Based on our findings, we propose that the primary function of the pVIn peptide is to mediate interactions between protein VI and hexon during virus replication, driving hexon nuclear accumulation and particle assembly. Once particles are assembled, AVP-mediated cleavage facilitates the release of the membrane lytic region at the amino terminus of mature VI, allowing it to lyse the endosome during cell infection. These findings highlight the importance of a single maturation cleavage site for both infectious particle production and cell entry and emphasize the exquisite spatiotemporal regulation governing adenovirus assembly and disassembly.

IMPORTANCE
Postassembly virus maturation is a cornerstone principle in virology. However, a mechanistic understanding of how icosahedral viruses utilize this process to transform immature capsids into infection-competent particles is largely lacking. Adenovirus maturation involves proteolytic processing of seven precursor proteins. There is currently no information for the role of each independent cleavage event in the generation of infectious virions. To address this, we investigated the proteolytic maturation of one adenovirus precursor molecule, protein VI. Structurally, protein VI cements the outer capsid shell and links it to the viral core. Functionally, protein VI is involved in endosome disruption, subcellular trafficking, transcription activation, and virus assembly. Our studies demonstrate that the multifunctional nature of protein VI is largely linked to its maturation. Through mutational analysis, we show that disrupting the N-terminal cleavage of preprotein VI has major deleterious effects on the assembly of infectious virions and their subsequent ability to infect host cells.
Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses
Authors: Shi Mang , Lin Xian-Dan , Vasilakis Nikos , Tian Jun-Hua , Li Ci-Xiu , Chen Liang-Jun , Eastwood Gillian , Diao Xiu-Nian , Chen Ming-Hui , Chen Xiao , Qin Xin-Cheng , Widen Steven G. , Wood Thomas G. , Tesh Robert B. , Xu Jianguo , Holmes Edward C. , Zhang Yong-Zhen
Published: October 2015

Viruses of the familyFlaviviridaeare important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to theFlaviviridaein a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the knownFlaviviridae(“flavi-like” viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with theFlaviviridaein the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of theFlaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that theFlaviviridaeinfect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated.

IMPORTANCEThe familyFlaviviridaeof RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of theFlaviviridaehas largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of theFlaviviridaeand related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.
Identification of a Novel Viral Protein Expressed from the PB2 Segment of Influenza A Virus
Authors: Yamayoshi Seiya , Watanabe Mariko , Goto Hideo , Kawaoka Yoshihiro
Published: October 2015

Over the past 2 decades, several novel influenza virus proteins have been identified that modulate viral infections
in vitro
and/or
in vivo
. The PB2 segment, which is one of the longest influenza A virus segments, is known to encode only one viral protein, PB2. In the present study, we used reverse transcription-PCR (RT-PCR) targeting viral mRNAs transcribed from the PB2 segment to look for novel viral proteins encoded by spliced mRNAs. We identified a new viral protein, PB2-S1, encoded by a novel spliced mRNA in which the region corresponding to nucleotides 1513 to 1894 of the PB2 mRNA is deleted. PB2-S1 was detected in virus-infected cells and in cells transfected with a protein expression plasmid encoding PB2. PB2-S1 localized to mitochondria, inhibited the RIG-I-dependent interferon signaling pathway, and interfered with viral polymerase activity (dependent on its PB1-binding capability). The nucleotide sequences around the splicing donor and acceptor sites for PB2-S1 were highly conserved among pre-2009 human H1N1 viruses but not among human H1N1pdm and H3N2 viruses. PB2-S1-deficient viruses, however, showed growth kinetics in MDCK cells and virulence in mice similar to those of wild-type virus. The biological significance of PB2-S1 to the replication and pathogenicity of seasonal H1N1 influenza A viruses warrants further investigation.

IMPORTANCE
Transcriptome analysis of cells infected with influenza A virus has improved our understanding of the host response to viral infection, because such analysis yields considerable information about both
in vitro
and
in vivo
viral infections. However, little attention has been paid to transcriptomes derived from the viral genome. Here we focused on the splicing of mRNA expressed from the PB2 segment and identified a spliced viral mRNA encoding a novel viral protein. This result suggests that other, as yet unidentified viral proteins encoded by spliced mRNAs could be expressed in virus-infected cells. A viral transcriptome including the viral spliceosome should be evaluated to gain new insights into influenza virus infection.
Baculovirus Inhibitor-of-Apoptosis Op-IAP3 Blocks Apoptosis by Interaction with and Stabilization of a Host Insect Cellular IAP
Authors: Byers Nathaniel M. , Vandergaast Rianna L. , Friesen Paul D.
Published: October 2015

Baculovirus-encoded inhibitor of apoptosis (IAP) proteins likely evolved from their host cell IAP homologs, which function as critical regulators of cell death. Despite their striking relatedness to cellular IAPs, including the conservation of two baculovirus IAP repeat (BIR) domains and a C-terminal RING, viral IAPs use an unresolved mechanism to suppress apoptosis in insects. To define this mechanism, we investigated Op-IAP3, the prototypical IAP from baculovirus OpMNPV. We found that Op-IAP3 forms a stable complex with SfIAP, the native, short-lived IAP of host insect
Spodoptera frugiperda
. Long-lived Op-IAP3 prevented virus-induced SfIAP degradation, which normally causes caspase activation and apoptosis. In uninfected cells, Op-IAP3 also increased SfIAP steady-state levels and extended SfIAP's half-life. Conversely, SfIAP stabilization was lost or reversed in the presence of mutated Op-IAP3 that was engineered for reduced stability. Thus, Op-IAP3 stabilizes SfIAP and preserves its antiapoptotic function. In contrast to SfIAP, Op-IAP3 failed to bind or inhibit native
Spodoptera
caspases. Furthermore, BIR mutations that abrogate binding of well-conserved IAP antagonists did not affect Op-IAP3's capacity to prevent virus-induced apoptosis. Remarkably, Op-IAP3 also failed to prevent apoptosis when endogenous SfIAP was ablated by RNA silencing. Thus, Op-IAP3 requires SfIAP as a cofactor. Our findings suggest a new model wherein Op-IAP3 interacts directly with SfIAP to maintain its intracellular level, thereby suppressing virus-induced apoptosis indirectly. Consistent with this model, Op-IAP3 has evolved an intrinsic stability that may serve to repress signal-induced turnover and autoubiquitination when bound to its targeted cellular IAP.

IMPORTANCE
The IAPs were first discovered in baculoviruses because of their potency for preventing apoptosis. However, the antiapoptotic mechanism of viral IAPs in host insects has been elusive. We show here that the prototypical viral IAP, Op-IAP3, blocks apoptosis indirectly by associating with unstable, autoubiquitinating host IAP in such a way that cellular IAP levels and antiapoptotic activities are maintained. This mechanism explains Op-IAP3's requirement for native cellular IAP as a cofactor and the dispensability of caspase inhibition. Viral IAP-mediated preservation of the host IAP homolog capitalizes on normal IAP-IAP interactions and is likely the result of viral IAP evolution in which degron-mediated destabilization and ubiquitination potential have been reduced. This mechanism illustrates another novel means by which DNA viruses incorporate host death regulators that are modified for resistance to host regulatory controls for the purpose of suppressing host cell apoptosis and acquiring replication advantages.
Intricate Roles of Mammalian Sirtuins in Defense against Viral Pathogens
Authors: Budayeva Hanna G. , Rowland Elizabeth A. , Cristea Ileana M.
Published: October 2015

For a number of years, sirtuin enzymes have been appreciated as effective “sensors” of the cellular environment to rapidly transmit information to diverse cellular pathways. Much effort was placed into exploring their roles in human cancers and aging. However, a growing body of literature brings these enzymes to the spotlight in the field of virology. Here, we discuss sirtuin functions in the context of viral infection, which provide regulatory points for therapeutic intervention against pathogens.
Convergence of Alarmone and Cell Cycle Signaling from
Trans
-Encoded Sensory Domains
Authors: Sanselicio Stefano , Viollier Patrick H.
Published: October 2015

Despite the myriad of different sensory domains encoded in bacterial genomes, only a few are known to control the cell cycle. Here, suppressor genetics was used to unveil the regulatory interplay between the PAS (Per-Arnt-Sim) domain protein MopJ and the uncharacterized GAF (cyclic GMP-phosphodiesterase–adenylyl cyclase–FhlA) domain protein PtsP, which resembles an alternative component of the phosphoenolpyruvate (PEP) transferase system. Both of these systems indirectly target the
Caulobacter crescentus
cell cycle master regulator CtrA, but in different ways. While MopJ acts on CtrA via the cell cycle kinases DivJ and DivL, which control the removal of CtrA at the G
1
-S transition, our data show that PtsP signals through the conserved alarmone (p)ppGpp, which prevents CtrA cycling under nutritional stress and in stationary phase. We found that PtsP interacts genetically and physically with the (p)ppGpp synthase/hydrolase SpoT and that it modulates several promoters that are directly activated by the cell cycle transcriptional regulator GcrA. Thus, parallel systems integrate nutritional and systemic signals within the cell cycle transcriptional network, converging on the essential alphaproteobacterial regulator CtrA while also affecting global cell cycle transcription in other ways.

IMPORTANCE
Many alphaproteobacteria divide asymmetrically, and their cell cycle progression is carefully regulated. How these bacteria control the cell cycle in response to nutrient limitation is not well understood. Here, we identify a multicomponent signaling pathway that acts on the cell cycle when nutrients become scarce in stationary phase. We show that efficient accumulation of the master cell cycle regulator CtrA in stationary-phase
Caulobacter crescentus
cells requires the previously identified stationary-phase/cell cycle regulator MopJ as well as the phosphoenolpyruvate protein phosphotransferase PtsP, which acts via the conserved (p)ppGpp synthase SpoT. We identify cell cycle-regulated promoters that are affected by this pathway, providing an explanation of how (p)ppGpp-signaling might couple starvation to control cell cycle progression in
Caulobacter
spp. and likely other
Alphaproteobacteria
. This pathway has the potential to integrate carbon fluctuation into cell cycle control, since in phosphotransferase systems it is the glycolytic product phosphenolpyruvate (PEP) rather than ATP that is used as the phosphor donor for phosphorylation.
Binding of Alphaherpesvirus Glycoprotein H to Surface α4β1-Integrins Activates Calcium-Signaling Pathways and Induces Phosphatidylserine Exposure on the Plasma Membrane
Authors: Azab Walid , Gramatica Andrea , Herrmann Andreas , Osterrieder Nikolaus
Published: October 2015

Intracellular signaling connected to integrin activation is known to induce cytoplasmic Ca2+release, which in turn mediates a number of downstream signals. The cellular entry pathways of two closely related alphaherpesviruses, equine herpesviruses 1 and 4 (EHV-1 and EHV-4), are differentially regulated with respect to the requirement of interaction of glycoprotein H (gH) with α4β1-integrins. We show here that binding of EHV-1, but not EHV-4, to target cells resulted in a rapid and significant increase in cytosolic Ca2+levels. EHV-1 expressing EHV-4 gH (gH4) in lieu of authentic gH1 failed to induce Ca2+release, while EHV-4 with gH1 triggered significant Ca2+release. Blocking the interaction between gH1 and α4β1-integrins, inhibiting phospholipase C (PLC) activation, or blocking binding of inositol 1,4,5-triphosphate (IP3) to its receptor on the endoplasmic reticulum (ER) abrogated Ca2+release. Interestingly, phosphatidylserine (PS) was exposed on the plasma membrane in response to cytosolic calcium increase after EHV-1 binding through a scramblase-dependent mechanism. Inhibition of both Ca2+release from the ER and scramblase activation blocked PS scrambling and redirected virus entry to the endocytic pathway, indicating that PS may play a role in facilitating virus entry directly at the plasma membrane.

IMPORTANCEHerpesviruses are a large family of enveloped viruses that infect a wide range of hosts, causing a variety of diseases. These viruses have developed a number of strategies for successful entry into different cell types. We and others have shown that alphaherpesviruses, including EHV-1 and herpes simplex virus 1 (HSV-1), can route their entry pathway and do so by manipulation of cell signaling cascades to ensure viral genome delivery to nuclei. We show here that the interaction between EHV-1 gH and cellular α4β1-integrins is necessary to induce emptying of ER calcium stores, which induces phosphatidylserine exposure on the plasma membrane through a scramblase-dependent mechanism. This change in lipid asymmetry facilitates virus entry and might help fusion of the viral envelope at the plasma membrane. These findings will help to advance our understanding of herpesvirus entry mechanism and may facilitate the development of novel drugs that can be implemented for prevention of infection and disease.