bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent Advances in Pipeline Free Span Design: A New Revision of DNV-RP-F105
Authors: Vedeld Knut , Sollund Håvar , Fyrileiv Olav
Published: October 2016

Pipeline free span design has evolved from basic avoidance criteria in the DNV ’76 rules [1], to fatigue and ultimate limit state considerations in Guideline no. 14 [2]. Modern multimode, multi-span free span design is predominantly performed according to DNV-RP-F105 [3].

In 2006, the latest revision of DNV-RP-F105 [3] was written as a direct result of extensive research, performed due to significant free span challenges in the Ormen Lange pipeline project. DNV-RP-F105 was at the time, and still is, the only pipeline design code giving contemporary design guidance for vortex induced vibrations (VIV) and direct wave loading design for pipelines in free spans.

The last revision of DNV-RP-F105 included a few, but highly important advances, particularly the consideration for multi-mode and multi-span pipeline dynamic response behavior. In the 10 years that have followed, no breakthroughs of similar magnitude have been achieved for pipeline free spans, but a large number of incremental improvements to existing calculation methods, and some novel advances in less critical aspects of VIV understanding have been made. As a result, DNV-RP-F105 has recently been revised to account for these advances, which include improved frequency-domain analyses of wave-induced fatigue, a new response model for cross-flow VIV in low Keulegan-Carpenter (KC) regimes in pure waves, new analytical methods for dynamic response calculations of short spans in harsh conditions, and extensive guidance on how to apply the recommended practice for assessment of fatigue and extreme environmental load effects on curved structural members such as spools, jumpers and manifold flexloops.

This paper gives an overview of most of the important changes and updates to the new revision of DNV-RP-F105. Case studies are used to demonstrate the importance and effects of the changes made, and to some extent how the revision of DNV-RP-F105 can enhance its applicability and ease of use.
Crack Extension Effects on Welding Residual Stress in Fitness for Service Assessment of Crack-Like Defect in Weld
Authors: Hong Jeong K.
Published: October 2016

The current industry code and standard fitness-for-service assessment (ICS FFSA) procedures ignore the release of the welding residual stress (WRS) in defect assessment of a crack growing in a WRS field. Doing so can result in overly restrictive results in the ICS FFSA of an engineering component. The current ICS FFSA procedures have produced compendiums of WRS distributions and stress intensity factor (SIF) solutions that are characterized by the joint geometry and welding parameters. It is also known that these distributions are based on extensive numerical analyses and provide upper bound estimates; therefore, these types of solutions do not necessarily satisfy the self-equilibrating state.

In this investigation, through-wall WRS distributions from the literature data, including measurements and finite element analysis (FEA) results for girth welded pipes, are compared to the representative ICS FFSA WRS procedures.

Also, the WRS and SIF solutions using the proposed procedure are compared to those using the ICS FFSA procedures employing 2D and 3D models.

From the investigation, it is observed that the ICS FFSA procedures show discrepancies for certain conditions and the levels of conservatism are dependent on the model geometry, boundary constraint condition, crack size, and crack shape.

For some cases, the estimations provided from the ICS FFSA procedures are not conservative compared to the reference solutions from literatures and FEA simulations.

As a continuous study of the previous investigation [OMAE 2015-41319], the objective of the present paper is to motivate the industry to improve ICS FFSA procedures by clarifying the ambiguous technical issues of crack-like defect assessment in weld regions.
Numerical Study on Flap Style Rudder Hydrodynamic Characteristics With Different Connections
Authors: Dong Zhenwei , Xiao Zhijian , Gong Shiqi , Zhang Zhiguo , Feng Dakui
Published: October 2016

The flow field characteristics of 2-D flap style rudders with and without gap are analyzed through 4 models. To explore the influence of different filling styles, one flap rudder with gap and three flap rudders without gap are simulated from 0 to 30 degrees angle of attack with k-omega SST turbulence model.

Validation is done by comparing the results with EFD data from reference and the mesh independence verification is also made. Then lift and drag coefficients are compared among four models. Pressure, velocity distributions are given to explain the difference on hydrodynamic characteristics among them. Unsteady computation method is used to investigate the fluctuation characteristics of drag coefficients at large angle of attack. Stream lines are shown to better understand the vortex system on the suction surface.
Balancing Power Absorption and Fatigue Loads in Irregular Waves for an Oscillating Surge Wave Energy Converter
Authors: Tom Nathan M. , Yu Yi-Hsiang , Wright Alan D. , Lawson Michael
Published: October 2016

The aim of this paper is to describe how to control the power-to-load ratio of a novel wave energy converter (WEC) in irregular waves. The novel WEC that is being developed at the National Renewable Energy Laboratory combines an oscillating surge wave energy converter (OSWEC) with control surfaces as part of the structure; however, this work only considers one fixed geometric configuration. This work extends the optimal control problem so as to not solely maximize the time-averaged power, but to also consider the power-take-off (PTO) torque and foundation forces that arise because of WEC motion. The objective function of the controller will include competing terms that force the controller to balance power capture with structural loading. Separate penalty weights were placed on the surge-foundation force and PTO torque magnitude, which allows the controller to be tuned to emphasize either power absorption or load shedding. Results of this study found that, with proper selection of penalty weights, gains in time-averaged power would exceed the gains in structural loading while minimizing the reactive power requirement.
Balancing Power Absorption and Structural Loading for an Asymmetric Heave Wave-Energy Converter in Regular Waves
Authors: Tom Nathan M. , Madhi Farshad , Yeung Ronald W.
Published: October 2016

The aim of this paper is to maximize the power-to-load ratio of the Berkeley Wedge: a one-degree-of-freedom, asymmetrical, energy-capturing, floating breakwater of high performance that is relatively free of viscosity effects. Linear hydrodynamic theory was used to calculate bounds on the expected time-averaged power (TAP) and corresponding surge restraining force, pitch restraining torque, and power take-off (PTO) control force when assuming that the heave motion of the wave energy converter remains sinusoidal. This particular device was documented to be an almost-perfect absorber if one-degree-of-freedom motion is maintained. The success of such or similar future wave energy converter technologies would require the development of control strategies that can adapt device performance to maximize energy generation in operational conditions while mitigating hydrodynamic loads in extreme waves to reduce the structural mass and overall cost. This paper formulates the optimal control problem to incorporate metrics that provide a measure of the surge restraining force, pitch restraining torque, and PTO control force. The optimizer must now handle an objective function with competing terms in an attempt to maximize power capture while minimizing structural and actuator loads. A penalty weight is placed on the surge restraining force, pitch restraining torque, and PTO actuation force, thereby allowing the control focus to be placed either on power absorption or load mitigation. Thus, in achieving these goals, a per-unit gain in TAP would not lead to a greater per-unit demand in structural strength, hence yielding a favorable benefit-to-cost ratio. Demonstrative results in the form of TAP, reactive TAP, and the amplitudes of the surge restraining force, pitch restraining torque, and PTO control force are shown for the Berkeley Wedge example.
ISUM for Offshore Frame Structures
Authors: Amdahl J. , Holmas T.
Published: October 2016

The paper presents the background and major ideas behind the computer program USFOS. The program is today widely used by the offshore industry to assess the resistance of oil and gas installations against abnormal environmental loads and accidental actions, such as ship collisions, fires and explosions. The assessment is normally performed in the accidental limit states; i.e. substantial yielding, buckling, partial collapse may take place, but the structure should maintain overall integrity. The features and concepts and models adopted in USFOS have also proved to be very useful in the analysis of totally different edifices. A few examples of this are given in the paper.
Wave-Body Interactions Among an Array of Truncated Vertical Cylinders
Authors: Zhong Qian , Yeung Ronald W.
Published: October 2016

A semi-analytical method is developed to investigate water-wave radiation and diffraction by an array of truncated vertical cylinders as a model for a point-absorber wave farm. Each cylinder can have independent movements in six modes. The method of matched eigenfunction expansions is applied to obtain the velocity potential for the fluid. To achieve fast computation, the effects of evanescent modes of locally scattered waves from one cylinder are neglected in the near fields of the neighboring cylinders. Wave-exciting forces and moments on an individual cylinder or a group of cylinders, situated among an array, are evaluated by a new, generalized form of Haskind relation that is applicable to an array configuration. In results, hydrodynamic coefficients and wave-exciting loads are presented for arrays of different configurations. Comparisons between wave-exciting loads obtained from the generalized Haskind relation and those from direct diffraction solutions show excellent agreements.
Passing Ship Effects in Non-Uniform Water Depth
Authors: Zhou Lilan , Yang Ji , Wang Qian , Qin Jiangtao
Published: October 2016

Waves generated by passing ships have potential adverse impacts on the environment (beach erosion, ecological disturbance, structures damage) and other waterway users (navigations, moored ships) in the coastal and sheltered areas. But issues related to waves of ships were addressed rarely in China until now. Accurate prediction of wash waves is the first step to control the washes from passing ships and it’s significant to reduce the effects of washes. A coupled method is used in this paper to simulate the washes and its effects caused by the passing ship. A potential flow theory method is adopted as the stationary wave generation model; a non-hydrostatic wave flow model is used as the wave propagation model; a time domain method is chosen as the model for simulating the forces and moments of mooring ship. The waves calculated by a potential flow theory method in the near field are used as the input for the non-hydrostatic wave-flow model to obtain the far field waves. A time-domain representation of the wave-cut at the location of the passing vessel is transformed to the frequency-domain and is used as the input for the diffraction computations. Parts of the calculated results are validated experimentally, satisfactory agreement is demonstrated.
An Arrangement Design Framework for Ships and Offshore Plants Based on Expert System and Optimization Technique
Authors: Kim Ki-Su , Roh Myung-Il , Kim Sung-Kyoon
Published: October 2016

The arrangement design of ships and offshore plants is normally being made based on data of the past design and experts’ experiences. When performing the arrangement design, experts refer the past data and add additional requirements to the data for a new design based on their experiences. During this task, delay in design can occur due to the data missing or the absence of experts. In addition, most of ships and offshore plants are operated in the ocean environment so that spaces that can be filled with components for them are restricted. In this sense, there is a need to accumulate data regarding the past design, experts’ experiences, and design rules as a systematic structure. And a demand for optimization technique for the arrangement deign of ships and offshore plants are increasing. For this, an arrangement design framework for ships and offshore plants based on expert system and optimization technique is proposed in this study. And the proposed framework is applied to a problem with regard to the arrangement design of a small size submarine, and an FPSO topside. The results shows that the proposed framework can be used as a new tool for the arrangement design of ships and offshore plants.
Development and Characterization of High Strength Austenitic Stainless Steel for Down-Hole Application in Sour Environment With Superior Corrosion and Wear Resistance
Authors: Mishra Brajendra , Lee Eunkyung
Published: October 2016

Stainless steel alloys were made in the present study for application in Qatar gas wells which contain significant amounts of sour acid gas, a very corrosive environment. The alloys made in the present project contain very small amounts of nickel compared to the commercial available high-nickel alloys. In the present work, nickel is replaced with the elements nitrogen and carbon which are very abundant and are inexpensive. Because of the low nickel content of the alloys from the present study, the alloys should be economical to produce. The study showed that the new alloys resist attack by sour acid gas very effectively. Specifically, the alloys exhibit equal or better resistance to attack than commercially available high-nickel alloys made for application in sour gas environments.
Mechanics Modeling and Inverse Analyses of Pulse Wave System From the View-Point of Traditional Chinese Medicine
Authors: Wang Lili , Wang Hui
Published: October 2016

Follow the holism concept of traditional Chinese medicine (TCM), the pulse wave system is considered as an entire system of life energy propagating within the blood in the form of wave. A corresponding mechanics model is established, showing that a pulse phenomenon includes both the blood flow and the energy wave propagating within the blood. The former is a visible matter-flow with lower velocity, while the latter is an invisible energy-flow with much higher velocity, corresponding respectively to the “blood” and the “Qi” in TCM. Moreover the method of inverse analysis in the wave propagation theory is generalized to deal with the pulse wave signals. Once anyone form of pulse wave, e.g. the pressure wave, is measured, the other forms of pulse wave such as the particle velocity wave, the specific volume wave and the internal energy wave can all be deduced, and finally the constitutive equation of the system can be determined. The propagating characters of pulse wave are mainly determined by the constitutive equation of the system, which may correspond to the “body constitution” in TCM. Some intrinsic relationship may exist between them and should be further investigated.
Numerical Study of Flow Around a Smooth Circular Cylinder at Reynold Number=3900 With Large Eddy Simulation Using CFD Code
Authors: Khan Niaz B. , Jameel Mohammed , Mohamad Badry Ahmad Badarudin Bin , Ibrahim Zainah B.
Published: October 2016

The study of flow around circular cylinders is one of the challenges in marine hydrodynamics. Many offshore structures are of cylindrical shape such as spar hull, risers and pipelines. Furthermore, the flow around cylinder open the path for studying more complex shape structures like ellipses, flat plat and other complex geometries. The aim of the study is to understand the flow field around these structures and calculation of forces acting on them. In current study, flow over a circular cylinder is investigated numerically using the turbulent model Large Eddy simulation (LES) and SIMPLE pressure-velocity coupling. In LES option, Smagorinksy-lilly subgrid scale model with dynamic stress is used. Mesh is generated using ICEM CFD tool and analysis is performed using ANSYS fluent. Velocity profiles are investigated in the cylinder wake up to ten diameters and compared with the experimental results. Hydrodynamic values and pressure distribution on the cylinder wall are also analyzed.

The numerical results extracted from the simulation agreed well with the experimental results available in the literature. Furthermore, the spanwise mesh resolution study shows that flow around cylinder at Reynold number Re = 3900 is highly 3dimensional study and 2D study or coarse mesh in spanwise direction will deteriorate the results.
Dynamic Response of Sandwich Panels With Functionally Graded Aluminum Foam Cores Subjected to Underwater Explosion
Authors: Zhang Changzai , Zhang Pan , Liu Jun , Pan Jianqiang , Zhao Yanjie , Cheng Yuansheng
Published: October 2016

Numerical investigations were conducted using the MSC.Dytran software on the dynamic response of functionally graded sandwich panels when subjected to underwater explosion. The effects of the number of layers and density distribution of graded cores on the blast performance were analyzed in several aspects under the constraint of equivalent mass. The simulation results have demonstrated that sandwich panels experience both bending and large plastic stretching deformation. Compared to single layered sandwich panel, those panels with graded cores overall possess smaller central permanent displacement and better energy absorption capability. Central deflection of bottom face sheet decreases as the density of cores descends from top to bottom face. A large proportion of the energy dissipates in the plastic deformation of top face sheet by the end of response, followed by the bottom face sheet, and core compression absorbers the minimum. Utilizing the high efficiency of energy absorption by adjusting those cores with greater density near to the top face sheet can further mitigate the damage from explosion.
Idealized Methods for Nonlinear Welding Mechanics
Authors: Murakawa Hidekazu
Published: October 2016

Computational Welding Mechanics is established by Prof. Yukio Ueda and it has become an indispensable and powerful method for understanding complex mechanical phenomena in welding. To tackle practical engineering problem, large scale transient nonlinear problem must be solved. For this, various “Idealized Methods” for welding mechanics were proposed. Among them, Iterative Substructure Method for transient nonlinear welding problem and Inherent Deformation Method for prediction of welding distortion of large structures are presented together with their application to practical problems.
Multiphase Transient Slugging Flow in Subsea Oil and Gas Production
Authors: Zhang Zhenhua , Tao Longbin
Published: October 2016

Slug flow in horizontal pipelines and riser systems in deep sea has been proved as one of the challenging flow assurance issues. Large and fluctuating gas/liquid rates can severely reduce production and, in the worst case, shut down, depressurization or damage topside equipment, such as separator, vessels and compressors.

Previous studies are primarily based on experimental investigations of fluid properties with air/water as working media in considerably scaled down model pipes, and the results cannot be simply extrapolated to full scale due to the significant difference in Reynolds number and other fluid conditions. In this paper, the focus is on utilizing practical shape of pipe, working conditions and fluid data for simulation and data analysis. The study aims to investigate the transient multiphase slug flow in subsea oil and gas production based on the field data, using numerical model developed by simulator OLGA and data analysis.

As the first step, cases with field data have been modelled using OLGA and validated by comparing with the results obtained using PIPESYS in steady state analysis. Then, a numerical model to predict slugging flow characteristics under transient state in pipeline and riser system was set up using multiphase flow simulator OLGA. One of the highlights of the present study is the new transient model developed by OLGA with an added capacity of newly developed thermal model programmed with MATLAB in order to represent the large variable temperature distribution of the riser in deep water condition. The slug characteristics in pipelines and temperature distribution of riser are analyzed under the different temperature gradients along the water depth. Finally, the depressurization during a shut-down and then restart procedure considering hydrate formation checking is simulated. Furthermore, slug length, pressure drop and liquid hold up in the riser are predicted under the realistic field development scenarios.
An Innovative FPSO Design Hosting SCRs in the North Sea Harsh Environment
Authors: Mansour Alaa M. , Zuccolo Ricardo , Peng Cheng , Wu Chunfa , Greiner Bill , Kumar Dhiraj , Azevedo Jefferson
Published: October 2016

Floating Production Storage and Offloading (FPSO) floaters have the advantages of providing the required storage in the hull and direct offloading to tankers of opportunity in deep and ultra-deep water in areas lacking infra-structure.

Steel Catenary Risers (SCRs) are the preferred solution in wet-tree applications due to their simplicity, robustness and low Capital costs (CAPEX) and Operational costs (OPEX) compared to other riser options. However, due to its relatively high dynamic motions, FPSO is not a feasible host for SCRs in most environments and especially so in the North Sea very harsh environment. Also, for efficient production from rich reservoirs, large diameter and number of risers are typically required. This makes it more challenging to find a robust and commercially attractive riser solution.

In this paper a novel design for an FPSO with the ability to host SCRs in the North Sea very harsh environment is presented and evaluated. The novel design, namely, Low Motion FPSO (LM-FPSO), has a hull form with a generally rectangular cross-section. The platform is moored in-place using a conventional mooring system. The LM-FPSO performance is enhanced with the robust low-tech feature, namely, free-hanging solid ballast tank (SBT). The SBT is located certain distance below hull keel and connected to the hull through four groups of short tendons. All tendon components are the same as those used in conventional TLPs. Through the mass and added mass of the SBT, the LM-FPSO provides significantly improved heave, roll and pitch responses.

The paper presents detailed description of the novel North Sea LM-FPSO design and its in-service performance. The SCR’s feasibility is discussed. The identified risks and associated mitigations for the new design compared to the conventional FPSO are investigated and reported. The paper concludes with discussions on the project execution plan and cost benefit when developing fields using this novel design.
A Study on Small Scale Associated Gas FLNG Utilizing Small Scale LNG Carriers to Near-By Onshore LNG Plant
Authors: Nguyen X. C. , Miheaye Komla , Kim Mun-gyu , Newman Howard , Yoo Dong-hoon , Cho Ho-young , de Regt Cees , Kim Jin-ki , Lee Wang-keun
Published: October 2016

This study describes a FLNG specifically designed to monetize Associated Gas (AG) of producing oil fields located within convenient distance of an existing LNG Plant or Port with LNG storage facility.

Limited production capacity combined with short range small capacity shuttles and limited LNG storage capacity, provide a cost effective means for LNG production.

This FLNG is designed to service an existing industry and does not require development of stranded gas discoveries.
Middle-ear function in the chinchilla: Circuit models and comparison with other mammalian species
Authors: Lemons Charlsie , Meaud Julien
Published: October 2016

The middle ear efficiently transmits sound from the ear canal into the inner ear through a broad range of frequencies. Thus, understanding middle-ear transmission characteristics is essential in the study of hearing mechanics. Two models of the chinchilla middle ear are presented. In the first model, the middle ear is modeled as a lumped parameter system with elements that represent the ossicular chain and the middle-ear cavity. Parameters of this model are fit using available experimental data of two-port transmission matrix parameters. In an effort to improve agreement between model simulations and the phase of published experimental measurements for the forward pressure transfer function at high frequencies, a second model in which a lossless transmission line model of the tympanic membrane is appended to the original model is proposed. Two-port transmission matrix parameter results from this second model were compared with results from previously developed models of the guinea pig, cat, and human middle ears. Model results and published experimental data for the two-port transmission matrix parameters are found to be qualitatively similar between species. Quantitative differences in the two-port transmission matrix parameters suggest that the ossicular chains of chinchillas, cats, and guinea pigs are less flexible than in humans.
No change in the acoustic reflex threshold and auditory brainstem response following short-term acoustic stimulation in normal hearing adults
Authors: Brotherton Hannah , Plack Christopher J. , Schaette Roland , Munro Kevin J.
Published: October 2016

Unilateral auditory deprivation or stimulation can induce changes in loudness and modify the sound level required to elicit the acoustic reflex. This has been explained in terms of a change in neural response, or gain, for a given sound level. However, it is unclear if these changes are driven by the asymmetry in auditory input or if they will also occur following bilateral changes in auditory input. The present study used a cross-over trial of unilateral and bilateral amplification to investigate changes in the acoustic reflex thresholds (ARTs) and the auditory brainstem response (ABR) in normal hearing listeners. Each treatment lasted 7 days and there was a 7-day washout period between the treatments. There was no significant change in the ART or ABR with either treatment. This null finding may have occurred because the amplification was insufficient to induce experience-related changes to the ABR and ART. Based on the null findings from the present study, and evidence of a change in ART in previous unilateral hearing aid use in normal hearing listeners, the threshold to trigger adaptive changes appears to be around 5 days of amplification with real ear insertion gain greater than 13–17 dB.
Relative contribution of envelope and fine structure to the subcortical encoding of noise-degraded speech
Authors: Bidelman Gavin M.
Published: October 2016

Brainstem frequency-following responses (FFR) were elicited to the speech token /ama/ in noise containing only envelope (ENV) or fine structure (TFS) cues to assess the relative contribution of these temporal features to the neural encoding of degraded speech. Successive cue removal weakened FFRs with noise having the most deleterious effect on TFS coding. Neuro-acoustic and response-to-response correlations revealed speech-FFRs are dominated by stimulus ENV for clean speech, with TFS making a stronger contribution in moderate noise levels. Results suggest that the relative weighting of temporal ENV and TFS cues to the neural transcription of speech depends critically on the degree of noise in the soundscape.
A PilZ domain protein for chemotaxis adds another layer to c-di-GMP–mediated regulation of flagellar motility
Authors: Orr Mona W. , Lee Vincent T.
Published: October 2016

Chemotaxis of an opportunistic pathogen is regulated by a c-di-GMP receptor (Xu
et al
., in 18 October 2016 issue).
Science Signaling
Podcast for 18 October 2016: ALK combination therapies for lung cancer
Authors: Haura Eric B. , VanHook Annalisa M.
Published: October 2016

Network analysis reveals potential targets for treating lung cancers driven by ALK fusion proteins (Zhang
et al
., in 18 October 2016 issue).
Vitamin D–mediated cancer therapy needs p62
Authors: Ferrarelli Leslie K.
Published: October 2016

The autophagy-associated adaptor protein p62 is involved in vitamin D–mediated regulation of gene expression.
Paper of note in
Science Translational Medicine
Authors: Ferrarelli Leslie K.
Published: October 2016

This week’s article describes a mechanism to overcome resistance to VEGF-targeted therapy in patients with metastatic colorectal cancer.
Papers of note in
Science
Authors: VanHook Annalisa M.
Published: October 2016

This week’s articles feature new insights into phosphorylation and the evolution of this posttranslational modification.
Preventing white fat from wasting away
Authors: Wong Wei
Published: October 2016

Cachexia-inducing tumors trigger white adipose tissue wasting by decreasing the abundance of AMPK.
Safety, Tolerability, and Pharmacokinetics of MEDI4893, an Investigational, Extended-Half-Life, Anti-Staphylococcus aureus Alpha-Toxin Human Monoclonal Antibody, in Healthy Adults
Authors: Yu Xiang-Qing , Robbie Gabriel J. , Wu Yuling , Esser Mark T. , Jensen Kathryn , Schwartz Howard I. , Bellamy Terramika , Hernandez-Illas Martha , Jafri Hasan S.
Published: October 2016

MEDI4893 is an investigational immunoglobulin G1(κ) monoclonal antibody that specifically binds to and neutralizes alpha-toxin, a key
Staphylococcus aureus
virulence factor. A triple-amino-acid substitution, M252Y/S254T/T256E, was engineered into the MEDI4893 Fc region to extend its serum half-life. A phase 1, double-blind, dose escalation study was designed to evaluate the safety, tolerability, pharmacokinetics, anti-alpha-toxin-neutralizing activity, and antidrug antibody (ADA) response of MEDI4893 following a single intravenous infusion in healthy adults 18 to 65 years of age. Thirty-three subjects were randomly assigned to receive MEDI4893 at 225 mg (
n
= 3), 750 mg (
n
= 3), 2,250 mg (
n
= 8), or 5,000 mg (
n
= 12) or placebo (
n
= 7) and were followed for 360 days. Adverse events were mild or moderate in severity; none were serious. The MEDI4893 peak serum concentration increased dose proportionally from 77.2 μg/ml (225-mg dose) to 1,784 μg/ml (5,000-mg dose). The area under the concentration-time curve from 0 to 360 days also increased dose proportionally, from 4,840 μg · day/ml (225-mg dose) to 91,493 μg · day/ml (5,000-mg dose), indicating linear pharmacokinetics. MEDI4893's terminal half-life was estimated to be 80 to 112 days, which is approximately 4-fold longer than the half-lives of other human immunoglobulin G antibodies. The alpha-toxin-neutralizing activity in serum correlated highly with the MEDI4893 concentrations in serum. Three adults transiently tested positive for ADA on day 151, but this did not have an impact on MEDI4893 serum concentrations or the MEDI4893 safety profile; no subjects exhibited serum ADA at the study end. These data support the continued development of MEDI4893 for the prevention of
S. aureus
-mediated pneumonia. (This study has been registered at ClinicalTrials.gov under identifier NCT02296320.)
Preclinical Characterization and Human Microdose Pharmacokinetics of ITMN-8187, a Nonmacrocyclic Inhibitor of the Hepatitis C Virus NS3 Protease
Authors: Rajagopalan Ravi , Pan Lin , Schaefer Caralee , Nicholas John , Lim Sharlene , Misialek Shawn , Stevens Sarah , Hooi Lisa , Aleskovski Natalia , Ruhrmund Donald , Kossen Karl , Huang Lea , Yap Sophia , Beigelman Leonid , Serebryany Vladimir , Liu Jyanwei , Sastry Srikonda , Seiwert Scott , Buckman Brad
Published: October 2016

The current paradigm for the treatment of chronic hepatitis C virus (HCV) infection involves combinations of agents that act directly on steps of the HCV life cycle. Here we report the preclinical characteristics of ITMN-8187, a nonmacrocyclic inhibitor of the NS3/4A HCV protease. X-ray crystallographic studies of ITMN-8187 and simeprevir binding to NS3/4A protease demonstrated good agreement between structures. Low nanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 1, 2b, 4, 5, and 6. In cell-based potency assays, half-maximal reduction of genotype 1a and 1b HCV replicon RNA was afforded by 11 and 4 nM doses of ITMN-8187, respectively. Combinations of ITMN-8187 with other directly acting antiviral agents
in vitro
displayed additive antiviral efficacy. A 30-mg/kg of body weight dose of ITMN-8187 administered for 4 days yielded significant viral load reductions through day 5 in a chimeric mouse model of HCV. A 3-mg/kg oral dose administered to rats, dogs, or monkeys yielded concentrations in plasma 16 h after dosing that exceeded the half-maximal effective concentration of ITMN-8187. Human microdose pharmacokinetics showed low intersubject variability and prolonged oral absorption with first-order elimination kinetics compatible with once-daily dosing. These preclinical characteristics compare favorably with those of other NS3/4A inhibitors approved for the treatment of chronic HCV infection.
The Helicobacter pylori Autotransporter ImaA Tempers the Bacterium's Interaction with α
5
β
1
Integrin
Authors: Sause William E. , Keilberg Daniela , Aboulhouda Soufiane , Ottemann Karen M.
Published: October 2016

The human pathogen
Helicobacter pylori
uses the host receptor α
5
β
1
integrin to trigger inflammation in host cells via its
cag
pathogenicity island (
cag
PAI) type IV secretion system (T4SS). Here, we report that the
H. pylori
ImaA protein (HP0289) decreases the action of the
cag
PAI T4SS via tempering the bacterium's interaction with α
5
β
1
integrin. Previously,
imaA
-null mutants were found to induce an elevated inflammatory response that was dependent on the
cag
PAI T4SS; here we extend those findings to show that the elevated response is independent of the CagA effector protein. To understand how ImaA could be affecting
cag
PAI T4SS activity at the host cell interface, we utilized the Phyre structural threading program and found that ImaA has a region with remote homology to bacterial integrin-binding proteins. This region was required for ImaA function. Unexpectedly, we observed that
imaA
mutants bound higher levels of α
5
β
1
integrin than wild-type
H. pylori
, an outcome that required the predicted integrin-binding homology region of ImaA. Lastly, we report that ImaA directly affected the amount of host cell β1 integrin but not other cellular integrins. Our results thus suggest a model in which
H. pylori
employs ImaA to regulate interactions between integrin and the T4SS and thus alter the host inflammatory strength.
Purine Biosynthesis Metabolically Constrains Intracellular Survival of Uropathogenic Escherichia coli
Authors: Shaffer Carrie L. , Zhang Ellisa W. , Dudley Anne G. , Dixon Beverly R. E. A. , Guckes Kirsten R. , Breland Erin J. , Floyd Kyle A. , Casella Daniel P. , Algood Holly M. Scott , Clayton Douglass B. , Hadjifrangiskou Maria
Published: October 2016

The ability tode novosynthesize purines has been associated with the intracellular survival of multiple bacterial pathogens. UropathogenicEscherichia coli(UPEC), the predominant cause of urinary tract infections, undergoes a transient intracellular lifestyle during which bacteria clonally expand into multicellular bacterial communities within the cytoplasm of bladder epithelial cells. Here, we characterized the contribution of the conservedde novopurine biosynthesis-associated locuscvpA-purFto UPEC pathogenesis. Deletion ofcvpA-purF, or ofpurFalone, abolishedde novopurine biosynthesis but did not impact bacterial adherence propertiesin vitroor in the bladder lumen. However, upon internalization by bladder epithelial cells, UPEC deficient inde novopurine biosynthesis was unable to expand into intracytoplasmic bacterial communities over time, unless it was extrachromosomally complemented. These findings indicate that UPEC is deprived of purine nucleotides within the intracellular niche and relies onde novopurine synthesis to meet this metabolic requirement.
Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene
Authors: Yu Qinli , Cai Hanlin , Zhang Yanfeng , He Yongzhi , Chen Lincai , Merritt Justin , Zhang Shan , Dong Zhiyang
Published: October 2016

Ectoine has osmoprotective effects on
Sinorhizobium meliloti
that differ from its effects in other bacteria. Ectoine does not accumulate in
S. meliloti
cells; instead, it is degraded. The products of the
ehuABCD-eutABCDE
operon were previously discovered to be responsible for the uptake and catabolism of ectoine in
S. meliloti
. However, the mechanism by which ectoine is involved in the regulation of the
ehuABCD-eutABCDE
operon remains unclear. The
ehuR
gene, which is upstream of and oriented in the same direction as the
ehuABCD-eutABCDE
operon, encodes a member of the MocR/GntR family of transcriptional regulators. Quantitative reverse transcription-PCR and promoter-
lacZ
reporter fusion experiments revealed that EhuR represses transcription of the
ehuABCD-eutABCDE
operon, but this repression is inhibited in the presence of ectoine. Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions overlapping the −35 region of the
ehuA
promoter and the +1 region of the
ehuR
promoter. Surface plasmon resonance assays further demonstrated direct interactions between EhuR and the two promoters, although EhuR was found to have higher affinity for the
ehuA
promoter than for the
ehuR
promoter.
In vitro
, DNA binding by EhuR could be directly inhibited by a degradation product of ectoine. Our work demonstrates that EhuR is an important negative transcriptional regulator involved in the regulation of ectoine uptake and catabolism and is likely regulated by one or more end products of ectoine catabolism.

IMPORTANCE
Sinorhizobium meliloti
is an important soil bacterium that displays symbiotic interactions with legume hosts. Ectoine serves as a key osmoprotectant for
S. meliloti
. However, ectoine does not accumulate in the cells; rather, it is degraded. In this study, we characterized the transcriptional regulation of the operon responsible for ectoine uptake and catabolism in
S. meliloti
. We identified and characterized the transcription repressor EhuR, which is the first MocR/GntR family member found to be involved in the regulation of compatible solute uptake and catabolism. More importantly, we demonstrated for the first time that an ectoine catabolic end product could modulate EhuR DNA-binding activity. Therefore, this work provides new insights into the unique mechanism of ectoine-induced osmoprotection in
S. meliloti
.
Cell-Biological Studies of Osmotic Shock Response in Streptomyces spp
Authors: Fuchino Katsuya , Flärdh Klas , Dyson Paul , Ausmees Nora
Published: October 2016

Most bacteria are likely to face osmotic challenges, but there is yet much to learn about how such environmental changes affect the architecture of bacterial cells. Here, we report a cell-biological study in model organisms of the genusStreptomyces, which are actinobacteria that grow in a highly polarized fashion to form branching hyphae. The characteristic apical growth ofStreptomyceshyphae is orchestrated by protein assemblies, called polarisomes, which contain coiled-coil proteins DivIVA and Scy, and recruit cell wall synthesis complexes and the stress-bearing cytoskeleton of FilP to the tip regions of the hyphae. We monitored cell growth and cell-architectural changes by time-lapse microscopy in osmotic upshift experiments. Hyperosmotic shock caused arrest of growth, loss of turgor, and hypercondensation of chromosomes. The recovery period was protracted, presumably due to the dehydrated state of the cytoplasm, before hyphae could restore their turgor and start to grow again. In most hyphae, this regrowth did not take place at the original hyphal tips. Instead, cell polarity was reprogrammed, and polarisomes were redistributed to new sites, leading to the emergence of multiple lateral branches from which growth occurred. Factors known to regulate the branching pattern ofStreptomyceshyphae, such as the serine/threonine kinase AfsK and Scy, were not involved in reprogramming of cell polarity, indicating that different mechanisms may act under different environmental conditions to control hyphal branching. Our observations of hyphal morphology during the stress response indicate that turgor and sufficient hydration of cytoplasm are required forStreptomycestip growth.

IMPORTANCEPolar growth is an intricate manner of growth for accomplishing a complicated morphology, employed by a wide range of organisms across the kingdoms of life. The tip extension ofStreptomyceshyphae is one of the most pronounced examples of polar growth among bacteria. The expansion of the cell wall by tip extension is thought to be facilitated by the turgor pressure, but it was unknown how external osmotic change influencesStreptomycestip growth. We report here that severe hyperosmotic stress causes cessation of growth, followed by reprogramming of cell polarity and rearrangement of growth zones to promote lateral hyphal branching. This phenomenon may represent a strategy of hyphal organisms to avoid osmotic stress encountered by the growing hyphal tip.
Characterization of a Novel Iron Acquisition Activity That Coordinates the Iron Response with Population Density under Iron-Replete Conditions in Bacillus subtilis
Authors: Roy Emily M. , Griffith Kevin L.
Published: October 2016

Iron is an essential micronutrient required for the viability of many organisms. Under oxidizing conditions, ferric iron is highly insoluble (∼10
−9
to 10
−18
M), yet bacteria typically require ∼10
−6
M for survival. To overcome this disparity, many bacteria have adopted the use of extracellular iron-chelating siderophores coupled with specific iron-siderophore uptake systems. In the case of
Bacillus subtilis
, undomesticated strains produce the siderophore bacillibactin. However, many laboratory strains, e.g., JH642, have lost the ability to produce bacillibactin during the process of domestication. In this work, we identified a novel iron acquisition activity from strain JH642 that accumulates in the growth medium and coordinates the iron response with population density. The molecule(s) responsible for this activity was named
e
lemental
Fe
(II/III) (Efe) acquisition factor because
efeUOB
(
ywbLMN
) is required for its activity. Unlike most iron uptake molecules, including siderophores and iron reductases, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur repressor. Restoring bacillibactin production in strain JH642 inhibits the activity of Efe acquisition factor, presumably by sequestering available iron. A similar iron acquisition activity is produced from a mutant of
Escherichia coli
unable to synthesize the siderophore enterobactin. Given the conservation of
efeUOB
and its regulation by catecholic siderophores in
B. subtilis
and
E. coli
, we speculate that Efe acquisition factor is utilized by many bacteria, serves as an alternative to Fur-mediated iron acquisition systems, and provides cells with biologically available iron that would normally be inaccessible during aerobic growth under iron-replete conditions.

IMPORTANCE
Iron is an essential micronutrient required for a variety of biological processes, yet ferric iron is highly insoluble during aerobic growth. In this work, we identified a novel iron acquisition activity that coordinates the iron response with population density in laboratory strains of
Bacillus subtilis
. We named the molecule(s) responsible for this activity elemental Fe(II/III) (Efe) acquisition factor after the
efeUOB
(
ywbLMN
) operon required for its uptake into cells. Unlike most iron uptake systems, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur, the master regulator of the iron response. We speculate that Efe acquisition factor is highly conserved among bacteria and serves as a backup to Fur-mediated iron acquisition systems.
EssD, a Nuclease Effector of the Staphylococcus aureus ESS Pathway
Authors: Ohr Ryan Jay , Anderson Mark , Shi Miaomiao , Schneewind Olaf , Missiakas Dominique
Published: October 2016

Specialized secretion systems of bacteria evolved for selective advantage, either killing microbial competitors or implementing effector functions during parasitism. Earlier work characterized the
E
SAT-6
s
ecretion
s
ystem (ESS) of
Staphylococcus aureus
and demonstrated its contribution to persistent staphylococcal infection of vertebrate hosts. Here, we identify a novel secreted effector of the ESS pathway, EssD, that functions as a nuclease and cleaves DNA but not RNA. EssI, a protein of the DUF600 family, binds EssD to block its nuclease activity in the staphylococcal cytoplasm. An
essD
knockout mutant or a variant lacking nuclease activity,
essD
L546P
, elicited a diminished interleukin-12 (IL-12) cytokine response following bloodstream infection of mice, suggesting that the effector function of EssD stimulates immune signaling to support the pathogenesis of
S. aureus
infections.

IMPORTANCE
Bacterial type VII or ESAT-6-like secretion systems (ESS) may have evolved to modulate host immune responses during infection, thereby contributing to the pathogenesis of important diseases such as tuberculosis and methicillin-resistant
S. aureus
(MRSA) infection. The molecular mechanisms whereby type VII secretion systems achieve their goals are not fully elucidated as secreted effectors with biochemical functions have heretofore not been identified. We show here that MRSA infection relies on the secretion of a nuclease effector that cleaves DNA and contributes to the stimulation of IL-12 signaling during infection. These results identify a biological mechanism for the contribution of the ESS pathway toward the establishment of MRSA disease.