bluuebunny/crossref_metadata_2025 huggingface dataset:
Time Domain Simulation of Vortex-Induced Vibrations Based on Phase-Coupled Oscillator Synchronization
Authors: Thorsen Mats J. , Sævik Svein , Larsen Carl M.
Published: October 2015

Since 2012, there has been ongoing development of a simplified hydrodynamic force model at the Norwegian University of Science and Technology which enables time domain simulation of vortex-induced vibrations (VIV). Time domain simulation has a number of advantages compared to frequency domain. More specifically, having a time domain formulation of the hydrodynamic force which is efficient and reliable, will allow designers to include any relevant non-linear effects in their simulations, thereby increasing the level of realism and confidence in the results. The present model computes the dynamic cross-flow and in-line fluid force on a circular cross-section based on the incoming local flow velocity and the motion of the cylinder section. The most important difference between this and other existing models is the way synchronization between the vortex shedding and cylinder motion is taken into account. In contrast to the traditional VIV prediction tools, the vortex shedding frequency is in this model free to vary within a specified range, and changes according to the instantaneous phase difference between the cylinder velocity and the vortex shedding process itself. Hence, the oscillating lift and drag forces continuously update their frequencies, trying to lock on to the frequency of vibration. Combined with a simple hydrodynamic damping model and a constant added mass, it has previously been shown that highly realistic results can be obtained. In this paper, the theoretical background is reviewed, and the capabilities of the model are tested against new cases. These are: i) High mode VIV of tension-dominated riser in sheared flow, and ii) Low mode VIV of a pipeline with high bending stiffness. Both cross-flow and in-line vibrations are considered, and comparison with experimental observations is given. Based on the results, strengths and weaknesses of the model is discussed, and an outline of future developments is given.
An Investigation of Riser Fairing Instability
Authors: Kristiansen Trygve , Braaten Henning , Lie Halvor , Baarholm Rolf , Skaugset Kjetil
Published: October 2015

An analysis of galloping of two different types of riser fairings is presented. The first is named “long fairing” (LF) and the other “Short Crab Claw” (Short CC). The first one has a traditionally winged formed shape with a cord-to-diameter ratio of 2.43. The other one is more truncated in shape, and has cord-to-diameter ratio of only 1.4.

Results from two related experimental set-ups are included in the work; one 2D experiment with towing tests of fairings that are free to translate and rotate to investigate instability regions, and one 2D experiment with fixed fairings to obtain drag, moment and lift curves. The present analysis is based on two-degrees of freedom, linearized equations of motion, and predicts a range of velocities where instability occurs. Below and above this region, the fairing is stable. Damping complicates the analysis. An empirical damping model is included and discussed. The two fairing types inhibit appreciably different instability characteristics. In particular, the Short CC fairing has a narrower instability region than the long fairing, and is therefore less prone to instabilities.
Efficient Thrust Allocation for DP Systems Using a Biased Least Squares Criterion
Authors: Kaasen Karl E.
Published: October 2015

The principle of dynamic positioning with thrusters is described and the problem of thrust allocation discussed. To allocate the demand for surge and sway forces and yaw moment from the DP controller to a greater number of thruster variables requires some extra mathematical conditions to make the problem uniquely solvable. Often the extra conditions are obtained by formulating a criterion for optimal thruster usage, typically an allocation that is power-minimal. Such problems usually cannot be solved without resorting to numerical search methods, which can be unattractive when the available time is scarce, which is the case when DP with allocation is used in model testing or when a large number of long stochastic simulations need to be carried out. For such cases, simple weighted least squares allocation with linear equality constraints is an attractive alternative. This method is very close to being power minimal provided the weights are chosen correctly. To handle cases of thruster saturation a method is proposed, which uses bias thrust and a certain matrix of nullspace vectors. A similar principle is proposed for presetting of favourable angles for azimuth thrusters to reduce the effect of the slow azimuth response.
An Anti-Recoil Control Design Using the New Riser Hybrid Tensioning System in Deepwater Drilling
Authors: Wu Yin
Published: October 2015

A new riser anti-recoil control design is presented in this research paper using the novel riser hybrid tensioning system by combining a fast acting electrically powered riser tensioning system with existing conventional hydro-pneumatic tensioners. This work is the further development of a control system for the previous work presented in the framework proposal of riser hybrid tensioning system.

This innovation that we bring forward here is all designed to increase operating envelope of the vessel. A system model integrating both electrical and hydro-pneumatic tensioners and the riser string is built for anti-recoil control purpose. The main goal of this control design is a safer and more predictable position control of the riser string. A LQG control design technique is applied here. A feedback controller with Kalman estimator of the system state space variables is designed and implemented. The Matlab simulation helped to demonstrate the concept feasibility of this anti-recoil control strategy and to further verify that a more robust and accurate control performance could be achieved by this riser hybrid tensioning system.

This control technique increases the testability of the riser anti-recoil system; reduce potential damage and increase operator’s confidence. The new proposed data logging system improves the detectability of the anti-recoil system. And the position control, when the riser string “soft hang-off” on the tensioners, opens the possibility to extend the operability to other applications.
Real-Time Prediction of Ship Interaction Forces Using Simplified Models
Authors: Silva Gustavo O. , Tannuri Eduardo A. , Ruggeri Felipe
Published: October 2015

Real-Time Ship Maneuvering Simulation Models is becoming more common and necessary in some feasibility analysis of ports and horizontal design. Due to the complexity of the hydrodynamic effects, a fairly realistic modeling is difficult to obtain, so that this type of simulation becomes limited in some cases. Large ships face difficulties to access ports once the shallow water and bank effects become significant. Since these factors are essential in some maneuverability studies, they must be modeled to Real-Time Simulations. In order to increase the application range of this kind of simulation, this paper presents simplified models to estimate additional hydrodynamic forces related to ship-to-ship and ship-to-bank interactions. Based on some physical input data which can be easily obtained during a Real-Time simulation, such as vessel speed and relative distances between a ship and another solid body, applying a set of measured points from the vessel to check the respective environment geometric shapes, identifying the bank conditions and other nearby vessels at a given instant. Thus, we are able to determine a realistic hydrodynamic effect. Due to the difficulty to create an accurate model, the prediction of the hydrodynamic forces was obtained from experimentally validated numerical methods such as the Boundary Elements Method (BEM), using the Rankine Panel Method. This validation consists in a comparative study among other works in this area to ensure a reliable response. The model calibration was performed using dimensionless coefficients and the BEM results are applied to the Real-Time simulation for a vessel type studied. In this study, a modeling of ship-to-ship will be presented modeled to interact in a Real-Time simulator, as a way to improve the real-time simulation and it will show that this method provides more realistic results to studies related to ship-to-ship interaction.
Time Domain Assessment of Nonlinear Coupled Ship Motions and Sloshing in Free Surface Tanks
Authors: Cercos-Pita Jose Luis , Bulian Gabriele , Souto-Iglesias Antonio
Published: October 2015

Ships at sea almost invariably carry liquids onboard, and liquids are contained in appropriate tanks. Being able to take into account the effects of liquids onboard when predicting ship motions is, therefore, of utmost importance for the safe operation of a vessel. In certain conditions, such predictions also require taking into account nonlinearities in both ship motions and in the internal flow, and linear approaches are not sufficient. Within this context, the present paper describes a simulation approach where a blended 6-DOF nonlinear ship motions prediction solver handling the external fluid-ship interaction, is coupled with a Smoothed-Particle-Hydrodynamics (SPH) solver for simulating the internal flow tank dynamics. The solvers are described and an example application is reported.
On the Occurrence of Higher Harmonics in the VIV Response
Authors: Wu Jie , Yin Decao , Lie Halvor , Larsen Carl M. , Baarholm Rolf J. , Jhingran Vikas , Liapis Stergios
Published: October 2015

Vortex Induced Vibrations (VIV) can lead to fast accumulation of fatigue damage and increased drag loads on slender marine structures. A cylinder subjected to VIV can vibrate in both in-line (IL) and cross-flow (CF) directions. The CF response is dominated by the primary shedding frequency and the IL response frequency is often two times of the primary CF frequency. In addition, higher harmonics can also be present. The third order harmonics are more pronounced when the motion orbit of the cylinder is close to “figure 8″ shape and cylinder is moving against the flow at its largest transverse motion. Recent studies with flexible beam VIV tests have shown that higher harmonics can have significant contribution to the fatigue damage in addition to the loads at the primary shedding frequency. However, there is a lack of understanding of when and where higher harmonic loads occur. The fatigue damage due to the higher harmonics is not considered in the present VIV prediction tools.

In the present paper, the test data of selected cases subjected to linearly sheared flow profile from two test programs, the Shell high mode VIV test[11] and the Hanøytangen test[5] have been studied. The factors that may influence the occurrence of the higher harmonics, such as the bending stiffness, reduced velocity and orbits stability, have been studied. The importance of higher harmonics in VIV fatigue has also been investigated. Finally, a method to include higher harmonics in the fatigue calculation is presented.
Artificial Neural Networks for Reducing Computational Effort in Active Truncated Model Testing of Mooring Lines
Authors: Christiansen Niels Hørbye , Voie Per Erlend Torbergsen , Høgsberg Jan
Published: October 2015

As oil and gas exploration moves to deeper waters the need for methods to conduct reliable model experiments increases. It is difficult obtain useful data by putting a scaled model of an entire mooring line systems into an ocean basin test facility. A way to conduct more realistic experiments is by active truncated models. In these models only the very top part of the system is represented by a physical model whereas the behavior of the part below the truncation is calculated by numerical models and accounted for in the physical model by active actuators applying relevant forces to the physical model. Hence, in principal it is possible to achieve reliable experimental data for much larger water depths than what the actual depth of the test basin would suggest. However, since the computations must be faster than real time, as the numerical simulations and the physical experiment run simultaneously, this method is very demanding in terms of numerical efficiency and computational power. Therefore, this method has not yet proved to be feasible. It has recently been shown how a hybridmethod combining classical numerical models and artificial neural networks (ANN) can provide a dramatic reduction in computational effort when performing time domain simulation of mooring lines. The hybrid method uses a classical numerical model to generate simulation data, which are then subsequently used to train the ANN. After successful training the ANN is able to take over the simulation at a speed two orders of magnitude faster than conventional numerical methods. The AAN ability to learn and predict the nonlinear relation between a given input and the corresponding output makes the hybrid method tailor made for the active actuators used in the truncated experiments. All the ANN training can be done prior to the experiment and with a properly trained ANN it is no problem to obtain accurate simulations much faster than real time — without any need for large computational capacity. The present study demonstrates how this hybrid method can be applied to the active truncated experiments yielding a system where the demand for numerical efficiency and computational power is no longer an issue.
Understanding Hybrid Subsea Foundation Design
Authors: Hossain M. Kabir , Shi Han , Abdalla Basel , Spari Markella K.
Published: October 2015

Hybrid subsea foundations (HSF) are combined foundation systems of mudmats and piles. The primary motivation of combining these two foundation types is to provide greater resistance to large horizontal loads in addition to vertical loads, for which use of mudmats alone will require it to be of impractically large size. The contribution from the piles in the lateral capacity helps to limit the size of the mudmat, which is critical in subsea environment. In a brownfield situation, this is sometimes a hard limit with only limited space available to place a new mudmat in the existing field layout. Also, in some cases, the HSF may prove to be a more economical option for resisting large horizontal loads compared to, for example, to suction piles. While the authors are aware of some scattered project-specific design and use of subsea mudmat-pile hybrid foundations by individual contractors and operators, there is no industry-wide publicly known best practice currently available. These designs of HSF appear to be generally based on simplified analytical approach that require superimposition of conventional shallow and deep foundation capacity calculation methods, hence violates the static and kinematic compatibility requirements fundamental for a sound and robust prediction procedure.

This paper attempts to provide some insight into the behavior of mudmat-pile foundations as a hybrid integrated system numerically using finite element modeling and analysis (FEA). The interactions between the mudmat and the piles in an HSF are complex and hence a FEA-based approach is considered most suitable. The FEA model in this study included the mudmat, the corner piles, the pile-mudmat connections and the seabed soil. Sensitivity of the HSF capacity to the size of the piles (length and diameter), the connection type of the piles to the mudmat, and the number of piles are selectively investigated and the results presented. Based on these results some pertinent observations relevant to design of HSFs are also given.

While the study is of limited scope, it offers important insights into the effects of the primary design variables on HSF’s capacities. Therefore, the authors hope the information herein will be of benefit to practicing subsea engineers who might have to face choices to consider mudmat-pile hybrid foundations as a real option for their projects.
Progressive Failure of Offshore Slopes due to Construction in Upslope Areas
Authors: Dey Rajib , Hawlader Bipul , Wang Chen
Published: October 2015

Human activities such as construction loading in upslope areas could be a potential triggering factor for many offshore landslides such as the 1979 Nice landslide. Post-slide investigations show that the existence of marine sensitive clay layers might be one of the potential causes of many large-scale submarine landslides. In this paper, a finite element (FE) modeling technique is developed to analyze the failure of a slope in undrained condition. Nonlinear strain softening behaviour of undrained shear strength of marine sensitive clays is incorporated in the FE analysis. Strain localization in narrow zones (i.e. shear bands) could be successfully simulated. The formation of shear bands and their propagation could explain some potential failure mechanisms. The FE results show that large-scale catastrophic failure of submarine slopes might have occurred due to shear band propagation through strain softening clay layers, which cannot be explained using the traditional limit equilibrium methods for slope stability analysis. Effects of different factors, such as thickness of the marine clay layer and its sensitivity, on stability of submarine slope are also examined.
Failure Analysis of the Tripping Operation and its Impact on Well Control
Authors: Abimbola Majeed , Khan Faisal , Garaniya Vikram , Butt Stephen
Published: October 2015

As the cost of drilling and completion of offshore well is soaring, efforts are required for better well planning. Safety is to be given the highest priority over all other aspects of well planning. Among different element of drilling, well control is one of the most critical components for the safety of the operation, employees and the environment. Primary well control is ensured by keeping the hydrostatic pressure of the mud above the pore pressure across an open hole section. A loss of well control implies an influx of formation fluid into the wellbore which can culminate to a blowout if uncontrollable. Among the factors that contribute to a blowout are: stuck pipe, casing failure, swabbing, cementing, equipment failure and drilling into other well. Swabbing often occurs during tripping out of an open hole. In this study, investigations of the effects of tripping operation on primary well control are conducted. Failure scenarios of tripping operations in conventional overbalanced drilling and managed pressure drilling are studied using fault tree analysis. These scenarios are subsequently mapped into Bayesian Networks to overcome fault tree modelling limitations such s dependability assessment and common cause failure. The analysis of the BN models identified RCD failure, BHP reduction due to insufficient mud density and lost circulation, DAPC integrated control system, DAPC choke manifold, DAPC back pressure pump, and human error as critical elements in the loss of well control through tripping out operation.
How to Determine the Principal Dimensions of FPSO Vessel
Authors: Akandu Ezebuchi , Incecik Atilla , Barltrop Nigel
Published: October 2015

The evaluation of the principal dimensions of the Floating Production, Storage and Offloading (FPSO) system is one of the most critical tasks at the initial design stage of the vessel. It is therefore important to get this right from the onset. This paper presents a simple method of determining the optimal principal dimensions of FPSO vessels of any specified oil storage capacity. An interactive programme, the Principal Dimensions Programme (PDP) has therefore been designed to accurately evaluate them based on the required cubic number (L × B × D) and the needed oil storage capacity (as the modern segregated vessels are volume-limited). The prediction of these dimensions has been given to ensure a safe operation and optimal performance of the vessels with regards to their motion responses in deep sea waves.
Computational and Experimental Assessment of Turbulence Stimulation on Flow Induced Motion of Circular Cylinder
Authors: Kinaci Omer Kemal , Lakka Sami , Sun Hai , Bernitsas Michael M.
Published: October 2015

In the Marine Renewable Energy Laboratory (MRELab) of the University of Michigan, Flow Induced Motion (FIM) is studied as a means to convert marine hydrokinetic energy to electricity using the VIVACE energy harvester [1–4]. Turbulence stimulation in the form of sand-strips, referred to as Passive Turbulence Control (PTC), were added to oscillating cylinders in 2008 [5]. PTC enabled VIVACE to harness hydrokinetic energy from currents/tides over the entire range of FIM including VIV and galloping. In 2011, the MRELab produced experimentally the PTC-to-FIM Map defining the induced cylinder motion based on the location of PTC [6]. In 2013, the robustness of the map was tested and dominant zones were identified [7]. Even though the PTC-to-FIM Map has become a powerful tool in inducing specific motions of circular cylinders, several parameters remain unexplored. Experiments, though the ultimate verification tool, are time consuming and hard to provide all needed information. A computational tool that could predict the FIM of a cylinder correctly would be invaluable to study the full parametric design space. A major side-benefit of PTC was the fact that PTC enabled computational fluid dynamic (CFD) simulations to generate results in good agreement with experiments by forcing the location of the separation point [8]. This valuable tool, along with experiments, is used in this paper to investigate PTC design parameters such as width and thickness and their impact on flow features with the intent of maximizing FIM and, thus, hydrokinetic energy conversion.
Full Scale Fairing Qualification Tests
Authors: Constantinides Yiannis , Liapis Stergios , Spencer Don , Islam Mohammed , Skaugset Kjetil , Batra Apurva , Baarholm Rolf
Published: October 2015

Production risers as well as drilling risers are often subjected to Vortex-induced vibrations (VIV) when exposed to ocean currents. VIV have been observed in the field and can cause fatigue failure and excessive drag on the riser. In order to suppress VIV and reduce drag, fairings are often used. This paper presents hydrodynamic qualification tests for two types of fairings: the short crab claw (SCC) and a tapered dual fin design. The short crab claw fairing design is a novel design that was developed by the Norwegian Deepwater Programme (NDP). As will be detailed in this paper, the SCC design offers very low drag, completely suppresses VIV and reduces riser interference.

In 2012, a model test campaign was undertaken to understand and qualify the hydrodynamic performance of fairings at prototype conditions. The program consisted of testing the three fairing geometries and a strake to understand the stand-alone performance in VIV and the performance in interference. This was accomplished by utilizing a single pipe setup for the standalone test and a two-pipe setup for the interference tests. The paper reports the results of the program and draws conclusions on the hydrodynamic performance of the VIV suppression devices tested.

Overall, all VIV suppression devices tested were able to suppress VIV with the SCC fairing being the most effective. In all cases tested, the downstream fairings / strakes were very effective in suppressing VIV in an interference scenario where a fairing was placed upstream. Contrary to the well-documented case of two strakes in tandem, in this case the upstream fairings did not reduce the effectiveness of the downstream fairings/strakes.
Biology of Allothrombium shirazicum Zhang (Acari: Trombidiidae) in Garmsar, Semnan province, Iran
Authors: SABOORI ALIREZA , KAMALI KARIM
Published: October 2015

Allothrombium shirazicum is a common natural enemy ofAphis punicae and other arthropods in Iran. It is univoltine in Iran. The eggs hatch in spring, nymphs emerge in summer and adults appear in autumn. Larvae are ectoparasites of A. punicae whereas deutonymphs and adults are free-living predators of small arthropods and their eggs. Both adults and eggs overwinter. Adults hibernate in the soil and different shelters and eggs hibernate in the soil. At the end of winter, overwitered female lay eggs in the soil. These eggs and overwintered eggs hatch in spring.
Multipinhole SPECT helical scan parameters and imaging volume
Authors: Yao Rutao , Deng Xiao , Wei Qingyang , Dai Tiantian , Ma Tianyu , Lecomte Roger
Published: October 2015

Purpose:

The authors developed SPECT imaging capability on an animal PET scanner using a multiple‐pinhole collimator and step‐and‐shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance.

Methods:

The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluated by two figures‐of‐merit: the sampling completeness percentage (SCP) and the root‐mean‐square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere‐grid phantom.

Results:

The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV.

Conclusions:

The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.
Demonstration of the Airy disk using photography and simple light sources
Authors: Trantham Kenneth , Reece Timothy J.
Published: October 2015

A procedure for observing diffraction from a circular aperture using photography equipment and commonly available light sources is presented. Commonly called the Airy pattern, such a diffraction pattern is characterized by a central bright spot, with concentric bright and dark rings. The images obtained in this procedure are suitable for discussing and demonstrating Rayleigh's criterion in introductory physics classes. It is shown that the patterns observed change as expected with wavelength and aperture.
The envelope of ballistic trajectories and elliptic orbits
Authors: Butikov Eugene I.
Published: October 2015

Simple geometric derivations are given for the shape of the “safety domain” boundary for the family of Keplerian orbits of equal energy in a central gravitational field and for projectile trajectories in a uniform field. Examples of practical uses of the envelope of the family of orbits are discussed and illustrated by computer simulations. This material is appropriate for physics teachers and undergraduate students studying classical mechanics and orbital motions.
Hurricane Balls: A rigid-body-motion project for undergraduates
Authors: Jackson David P. , Mertens David , Pearson Brett J.
Published: October 2015

We discuss a project on rigid-body motion that is appropriate for students in an upper-division course in classical mechanics. We analyze the motion of Hurricane Balls, two spheres that are welded (or glued) together so they act as a single object that can be spun like a top. The steady-state motion consists of purely rotational motion about the center of mass, such that only one ball is in contact with the table as it rolls without slipping. We give a qualitative explanation for why one ball rises into the air, and we theoretically analyze the system using multiple approaches. We also perform a high-speed video analysis to obtain experimental data on how the orientation depends on the spin rate, and find agreement within a few percent of the theory.
Oestreicher and elastography
Authors: Carstensen Edwin L. , Parker Kevin J.
Published: October 2015

A sphere moving back and forth in tissue generates the kinds of complex displacement fields that are used in elastography. The analytical solution of Hans Oestreicher for this phenomenon [(1951). J. Acoust. Soc. Am. 23, 704–714] gives an understanding of the transverse and longitudinal, fast and slow waves that are generated. The results suggest several ways to determine the absorption coefficients of tissues, which together with phase velocity permit the computation of both the real shear modulus and the shear viscosity as functions of frequency.
U.S. targets matter-antimatter frontier
Authors: Cho Adrian
Published: October 2015

Search for rare nuclear decay would test whether the neutrino is its own antiparticle.
Shining a light on sexual harassment in astronomy
Authors: Clery Daniel
Published: October 2015

Astronomer Joan Schmelz talks about what needs to change in the wake of the Marcy case.
Measurement and laser control of attosecond charge migration in ionized iodoacetylene
Authors: Kraus P. M. , Mignolet B. , Baykusheva D. , Rupenyan A. , Horný L. , Penka E. F. , Grassi G. , Tolstikhin O. I. , Schneider J. , Jensen F. , Madsen L. B. , Bandrauk A. D. , Remacle F. , Wörner H. J.
Published: October 2015

Electronic movement flashing into view

Numerous chemical processes begin with ionization: the ejection of an electron from a molecule. What happens in the immediate aftermath of that event? Kraus
et al.
explored this question in iodoacetylene by detecting and analyzing the spectrum of emitted high harmonics (see the Perspective by Ueda). They traced the migration of the residual positively charged hole along the molecular axis on a time scale faster than a quadrillionth of a second. They thereby characterized the capacity of a laser field to steer the hole's motion in appropriately oriented molecules.

Science
, this issue p.
790
; see also p.
740
Nlrp6 regulates intestinal antiviral innate immunity
Authors: Wang Penghua , Zhu Shu , Yang Long , Cui Shuang , Pan Wen , Jackson Ruaidhri , Zheng Yunjiang , Rongvaux Anthony , Sun Qiangming , Yang Guang , Gao Shandian , Lin Rongtuan , You Fuping , Flavell Richard , Fikrig Erol
Published: October 2015

Nlrp6 keeps gut infections in check

Most viruses infect only certain cells of the body. Enteric viruses, such as norovirus and rotavirus, specifically infect the gut. Wang
et al.
now show that the response to such viruses is tissue-specific, too. Antiviral immunity to enteric but not systemic viral infections in mice required Nlrp6, a member of the NOD-like receptor family of proteins that play important roles in host defense. Together with the RNA helicase protein Dhx15, Nlrp6 bound viral RNA and elicited downstream antiviral immune responses necessary for viral clearance. These included the production of type I and type III interferons and the expression of interferon-stimulated genes.

Science
, this issue p.
826
Mechanosensitive channel MSL8 regulates osmotic forces during pollen hydration and germination
Authors: Hamilton Eric S. , Jensen Gregory S. , Maksaev Grigory , Katims Andrew , Sherp Ashley M. , Haswell Elizabeth S.
Published: October 2015

Metered rehydration in pollen grains

When a desiccated pollen grain lands on fertile territory, it rehydrates on the way to activating its growth and metabolic processes. Studying the small plant
Arabidopsis
, Hamilton
et al.
have identified a mechanosensory ion channel that responds to the distention of the plasma membrane as the pollen grain rehydrates. With this channel damaged or absent, the pollen grains germinated overenthusiastically but then showed a tendency to burst.

Science
, this issue p.
438
Toward a rapid and reversible male pill
Authors: Castaneda Julio , Matzuk Martin M.
Published: October 2015

Sperm-specific calcineurin is a novel fertility and contraceptive target

[Also see Report by

Miyata
et al.

]
Genome Sequence of “
Candidatus
Thioglobus autotrophica” Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria
Authors: Shah Vega , Morris Robert M.
Published: October 2015

Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we announce the complete genome sequence of “
Candidatus
Thioglobus autotrophica” strain EF1, the first cultured chemoautotrophic representative from the SUP05 clade.
Draft Genome Sequence of Thiostrepton-Producing Streptomyces azureus ATCC 14921
Authors: Sakihara Kengo , Maeda Jumpei , Tashiro Kosuke , Fujino Yasuhiro , Kuhara Satoru , Ohshima Toshihisa , Ogata Seiya , Doi Katsumi
Published: October 2015

Streptomyces azureus
ATCC 14921 belongs to the
Streptomyces cyaneus
cluster and is known to be a thiostrepton producer. Here, we report a draft genome sequence for this strain, consisting of 350 contigs containing a total of 8,790,525 bp, 8,164 predicted coding sequences, and a G+C content of 70.9%.
Complete Genome Sequence of Spiroplasma kunkelii Strain CR2-3x, Causal Agent of Corn Stunt Disease in
Zea mays
L
Authors: Davis Robert E. , Shao Jonathan , Dally Ellen L. , Zhao Yan , Gasparich Gail E. , Gaynor Brady J. , Athey John C. , Harrison Nigel A. , Donofrio Nicole
Published: October 2015

Spiroplasma kunkelii
causes corn stunt disease of
Zea mays
L. in the Americas. Here, we report the nucleotide sequence of the 1,463,926-bp circular chromosome and four plasmids of strain CR2-3x. This information will facilitate studies of
Spiroplasma
pathogenicity and evolutionary adaptations to transkingdom parasitism in plants and insect vectors.
Draft Genome Sequence of Bradyrhizobium japonicum Is-1, Which Is Incompatible with
Rj
2
Genotype Soybeans
Authors: Sakata Tomoyuki , Kanesaki Yu , Yoshikawa Hirofumi , Tsurumaru Hirohito , Yamakawa Takeo
Published: October 2015

We report the draft genome sequence of
Bradyrhizobium japonicum
Is-1, which is incompatible with
Rj
2
genotype soybeans. The estimated genome size of this strain is 8.9 Mb. Genome sequence information of this strain will help to identify a causal gene for this incompatibility.
Complete Genome Sequence of
Southern tomato virus
Identified in China Using Next-Generation Sequencing
Authors: Padmanabhan Chellappan , Zheng Yi , Li Rugang , Sun Shu-E , Zhang Deyong , Liu Yong , Fei Zhangjun , Ling Kai-Shu
Published: October 2015

The complete genome sequence of
Southern tomato virus
(STV), a double-stranded RNA virus that affects tomato in China, was determined using small RNA deep sequencing. This Chinese isolate shares 99% sequence identity to other isolates from Mexico, France, Spain, and the United States. This is the first report of STV infecting tomatoes in Asia.
Complete Genome Sequence of Spiroplasma cantharicola CC-1
T
(DSM 21588), a Bacterium Isolated from Soldier Beetle (
Cantharis carolinus
)
Authors: Lo Wen-Sui , Liu Po-Yu , Kuo Chih-Horng
Published: October 2015

Spiroplasma cantharicola
CC-1
T
(DSM 21588) was isolated from the gut of a soldier beetle (
Cantharis carolinus
) collected in Maryland, USA. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology.
Draft Genome Sequence of
Achromobacter
sp. Strain DMS1, Capable of Degrading Polyaromatic Hydrocarbons Isolated from the Industrially Perturbed Environment of Amlakhadi Canal, India
Authors: Amin Shivani , Shah Binal , Jain Kunal , Patel Anand , Patel Namrata , Joshi Chaitanya G. , Madamwar Datta
Published: October 2015

Here, we report the draft genome sequence of
Achromobacter
sp. strain DMS1, which is 4.9 Mbp and has 3,727 coding sequences (CDSs), and is capable of degrading xenobiotic compounds and harboring genes for aromatic hydrocarbon metabolism. Its genome will unravel the basic mechanism involved in bioremediation of anthropogens.
Induction of Kaposi's Sarcoma-Associated Herpesvirus-Encoded Viral Interleukin-6 by X-Box Binding Protein 1
Authors: Hu Duosha , Wang Victoria , Yang Min , Abdullah Shahed , Davis David A. , Uldrick Thomas S. , Polizzotto Mark N. , Veeranna Ravindra P. , Pittaluga Stefania , Tosato Giovanna , Yarchoan Robert
Published: October 2015

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and a subset of multicentric Castleman disease (MCD). The KSHV life cycle has two principal gene repertoires, latent and lytic. KSHV viral interleukin-6 (vIL-6), an analog of human IL-6, is usually lytic; production of vIL-6 by involved plasmablasts is a central feature of KSHV-MCD. vIL-6 also plays a role in PEL and KS. We show that a number of plasmablasts from lymph nodes of patients with KSHV-MCD express vIL-6 but not ORF45, a KSHV lytic gene. We further show that vIL-6 is directly induced by the spliced (active) X-box binding protein-1 (XBP-1s), a transcription factor activated by endoplasmic reticulum (ER) stress and differentiation of B cells in lymph nodes. The promoter region of vIL-6 contains several potential XBP-response elements (XREs), and two of these elements in particular mediate the effect of XBP-1s. Mutation of these elements abrogates the response to XBP-1s but not to the KSHV replication and transcription activator (RTA). Also, XBP-1s binds to the vIL-6 promoter in the region of these XREs. Exposure of PEL cells to a chemical inducer of XBP-1s can induce vIL-6. Patient-derived PEL tumor cells that produce vIL-6 frequently coexpress XBP-1, and immunofluorescence staining of involved KSHV-MCD lymph nodes reveals that most plasmablasts expressing vIL-6 also coexpress XBP-1. These results provide evidence that XBP-1s is a direct activator of KSHV vIL-6 and that this is an important step in the pathogenesis of KSHV-MCD and PEL.

IMPORTANCE
Kaposi sarcoma herpesvirus (KSHV)-associated multicentric Castleman disease (KSHV-MCD) is characterized by severe inflammatory symptoms caused by an excess of cytokines, particularly KSHV-encoded viral interleukin-6 (vIL-6) produced by lymph node plasmablasts. vIL-6 is usually a lytic gene. We show that a number of KSHV-MCD lymph node plasmablasts express vIL-6 but do not have full lytic KSHV replication. Differentiating lymph node B cells express spliced (active) X-box binding protein-1 (XBP-1s). We show that XBP-1s binds to the promoter of vIL-6 and can directly induce production of vIL-6 through X-box protein response elements on the vIL-6 promoter region. We further show that chemical inducers of XBP-1s can upregulate production of vIL-6. Finally, we show that most vIL-6-producing plasmablasts from lymph nodes of KSHV-MCD patients coexpress XBP-1s. These results demonstrate that XBP-1s can directly induce vIL-6 and provide evidence that this is a key step in the pathogenesis of KSHV-MCD and other KSHV-induced diseases.
Development and Characterization of a Guinea Pig-Adapted Sudan Virus
Authors: Wong Gary , He Shihua , Wei Haiyan , Kroeker Andrea , Audet Jonathan , Leung Anders , Cutts Todd , Graham Jill , Kobasa Darwyn , Embury-Hyatt Carissa , Kobinger Gary P. , Qiu Xiangguo
Published: October 2015

Infections with Sudan virus (SUDV), a member of the genus
Ebolavirus
, result in a severe hemorrhagic fever with a fatal outcome in over 50% of human cases. The paucity of prophylactics and therapeutics against SUDV is attributed to the lack of a small-animal model to screen promising compounds. By repeatedly passaging SUDV within the livers and spleens of guinea pigs
in vivo
, a guinea pig-adapted SUDV variant (SUDV-GA) uniformly lethal to these animals, with a 50% lethal dose (LD
50
) of 5.3 × 10
−2
50% tissue culture infective doses (TCID
50
), was developed. Animals infected with SUDV-GA developed high viremia and died between 9 and 14 days postinfection. Several hallmarks of SUDV infection, including lymphadenopathy, increased liver enzyme activities, and coagulation abnormalities, were observed. Virological analyses and gross pathology, histopathology, and immunohistochemistry findings indicate that SUDV-GA replicates in the livers and spleens of infected animals similarly to SUDV infections in nonhuman primates. These developments will accelerate the development of specific medical countermeasures in preparation for a future disease outbreak due to SUDV.

IMPORTANCE
A disease outbreak due to Ebola virus (EBOV), suspected to have emerged during December 2013 in Guinea, with over 11,000 dead and 28,000 infected, is finally winding down. Experimental EBOV vaccines and treatments were administered to patients under compassionate circumstances with promising results, and availability of an approved countermeasure appears to be close. However, the same range of experimental candidates against a potential disease outbreak caused by other members of the genus
Ebolavirus
, such as Sudan virus (SUDV), is not readily available. One bottleneck contributing to this situation is the lack of a small-animal model to screen promising drugs in an efficient and economical manner. To address this, we have generated a SUDV variant (SUDV-GA) that is uniformly lethal to guinea pigs. Animals infected with SUDV-GA develop disease similar to that of SUDV-infected humans and monkeys. We believe that this model will significantly accelerate the development of life-saving measures against SUDV infections.
The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
Authors: Hannigan Geoffrey D. , Meisel Jacquelyn S. , Tyldsley Amanda S. , Zheng Qi , Hodkinson Brendan P. , SanMiguel Adam J. , Minot Samuel , Bushman Frederic D. , Grice Elizabeth A.
Published: October 2015

Viruses make up a major component of the human microbiota but are poorly understood in the skin, our primary barrier to the external environment. Viral communities have the potential to modulate states of cutaneous health and disease. Bacteriophages are known to influence the structure and function of microbial communities through predation and genetic exchange. Human viruses are associated with skin cancers and a multitude of cutaneous manifestations. Despite these important roles, little is known regarding the human skin virome and its interactions with the host microbiome. Here we evaluated the human cutaneous double-stranded DNA virome by metagenomic sequencing of DNA from purified virus-like particles (VLPs). In parallel, we employed metagenomic sequencing of the total skin microbiome to assess covariation and infer interactions with the virome. Samples were collected from 16 subjects at eight body sites over 1 month. In addition to the microenviroment, which is known to partition the bacterial and fungal microbiota, natural skin occlusion was strongly associated with skin virome community composition. Viral contigs were enriched for genes indicative of a temperate phage replication style and also maintained genes encoding potential antibiotic resistance and virulence factors. CRISPR spacers identified in the bacterial DNA sequences provided a record of phage predation and suggest a mechanism to explain spatial partitioning of skin phage communities. Finally, we modeled the structure of bacterial and phage communities together to reveal a complex microbial environment with aCorynebacteriumhub. These results reveal the previously underappreciated diversity, encoded functions, and viral-microbial dynamic unique to the human skin virome.

IMPORTANCETo date, most cutaneous microbiome studies have focused on bacterial and fungal communities. Skin viral communities and their relationships with their hosts remain poorly understood despite their potential to modulate states of cutaneous health and disease. Previous studies employing whole-metagenome sequencing without purification for virus-like particles (VLPs) have provided some insight into the viral component of the skin microbiome but have not completely characterized these communities or analyzed interactions with the host microbiome. Here we present an optimized virus purification technique and corresponding analysis tools for gaining novel insights into the skin virome, including viral “dark matter,” and its potential interactions with the host microbiome. The work presented here establishes a baseline of the healthy human skin virome and is a necessary foundation for future studies examining viral perturbations in skin health and disease.
Two rare cases of head and neck tuberculosis
Authors: Basal Yesim , Ermişler Barış , Eryilmaz Aylin , Ertuğrul Bülent
Published: October 2015

Tuberculosis is an infectious disease, which is the leading cause of mortality and morbidity and is still a serious health concern. The fact that extra pulmonary tuberculosis does not have specific examination and radiographic findings and that clinical findings vary depending on the organ in which it is detected cause diagnostic difficulties. The head and neck region is an uncommon site for tuberculosis and tuberculosis can localise in many different places of the head and neck region. In this article, the authors present a case of nasopharyngeal tuberculosis, which clinically mimics nasopharyngeal carcinoma and rare cutaneous tuberculosis of the pinna. A wide knowledge of head and neck tuberculosis, including the disease in the differential diagnosis and carrying out microbiological examinations are necessary for accurate diagnosis.
Genomic characterisation of two cancers of unknown primary cases supports a kidney cancer origin
Authors: Wei Elizabeth Y , Chen Ying-Bei , Hsieh James J
Published: October 2015

Cancer of unknown primary (CUP) comprises of 3–5% of new cancer diagnoses in the USA. Diagnostic work up typically includes CT of the chest, abdomen and pelvis, and histopathological review of tissue specimens. These measures are neither sensitive nor specific in determining tissue of origin (ToO) of primary tumours and, therefore, are unable to guide therapy. We present two cases of CUP for which we utilised ultra-deep genomic sequencing to identify the candidate ToO and to propose treatment. Patient 1 presented with metastases involving the lung, lymph nodes and bone. Patient 2 presented with an acute pathological fracture of the T7 vertebral body and metastases involving the bone, lymph nodes and soft tissue. No primary renal mass was found. Sequencing revealed SETD2 and NF2 mutations, and heterozygous loss of the short arm of chromosome 3 (3p). Mutations in conjunction with clinicopathological features strongly support a diagnosis of renal cell carcinoma. Both patients initially responded to mTORC1 inhibition therapy.