bluuebunny/crossref_metadata_2025 huggingface dataset:
Current Developments in the Validation of Numerical Methods for Predicting the Responses of an Ocean Thermal Energy Conversion (OTEC) System Cold Water Pipe
Authors: Halkyard John , Sheikh Rizwan , Marinho Thiago , Shi Shan , Ascari Matthew
Published: September 2014

Ocean Thermal Energy Conversion (OTEC) was a subject of intense research in the late 1970s and early 1980s in response to a historical jump in oil prices from the 1973 oil embargo. The principal author for this paper first met Prof. Paulling as a participant in a National Research Council (NRC) Panel to review OTEC Technology around 1982. Prof. Pauling had authored a frequency domain program to analyze the coupled response of a platform and OTEC pipe. The author was involved in model tests to validate the program. The United States (U.S.) Department of Energy (DoE) and National Oceanic and Atmospheric Administration (NOAA) had sponsored this work, along with the development of other numerical methods. Shortly after the NRC completed its review, oil prices fell and interest in renewable energy, including OTEC, evaporated. Fast forward to the 2000s, the price of oil skyrocketed again, and OTEC research saw a rebirth. Lockheed Martin and others have been working on new OTEC designs over the course of the last several years. As was the case thirty-five years ago, the cold water pipe remains a key technical challenge.

A commercial scale OTEC plant requires a pipe diameter of about 10-meter (m) and a length of 1,000m to pump about half the average discharge of the Colorado River from the deep ocean to the surface and through heat exchangers. Because of the large effective mass of the CWP and entrained water, the dynamic response of the OTEC CWP and the platform can only be considered as a coupled system. This conclusion is not new, but is worth repeating and doubly important to consider when the supporting platform is a semi-submersible as opposed to a large water plane ship shaped vessel.

A new generation of software is available to analyze the cold water pipe-platform responses, including the important effect of the fluid flow inside the pipe and the local effects at the connection of the pipe to the platform. The DoE and Lockheed Martin recently sponsored a 1:50 scale wave basin model test of a commercial OTEC platform with an elastically scaled model of a 10m pipe. The purpose of the test was to validate the use of current software for the large CWP diameters in the designs of a pilot or commercial systems in the near future. This paper will briefly review past work on the OTEC cold-water pipe and present the current state of the art in numerical modeling and the results of the model tests recently completed. It will include recommendations for further experimental and numerical work to be prepared for the future design of OTEC systems.
South Stream Deepwater Pipeline System: A Case for Waiving the Hydrotest
Authors: Timmermans Jeroen , Meijer Arjen , Ethembabaoglu Sakir
Published: September 2014

The traditional scope of pre-commissioning for a pipeline system includes filling the pipeline with liquid (typically water) and pressure testing to confirm the integrity and leak-tightness of the system. This methodology is described in almost all design codes, and typically represents an important criterion for the acceptance of the completed system by the owner / operator.

As the industry takes on offshore pipeline systems in deeper and deeper water, the relevance of this traditional approach has come into question. Specifically, it is not clear that the benefit of hydrotesting a deepwater pipeline system outweighs the costs, risks and potential environmental impact. For this reason DNV introduced the possibility of ‘waiving’ (= omitting) the hydrotest in OS-F101, its offshore standard for submarine pipeline design. In order to waive the system hydrotest, OS-F101 demands that specific, additional conditions be satisfied to ensure that the overall level of safety is maintained.

To date, only two smaller pipeline projects have received such a hydrotest waiver. The South Stream Offshore Pipeline project, which is presently approaching its implementation phase, will be the third. South Stream comprises four 32-inch diameter pipelines each with a length of approximately 930 km and traversing water depths up to 2,200m. The South Stream project is re-defining the state-of-the-art in offshore pipelines. Due to the extreme water depth, harsh seabed and large internal volume of the South Stream lines, traditional hydrostatic testing would not be the most environmentally friendly and risk averse solution to ensure pipeline integrity and safety.

This paper will present the main requirements and associated solutions for the South Stream pipelines in order to obtain a DNV OS-F101 hydrotest waiver, including:

• Review of the benefits and challenges for deepwater pipeline hydrotest

• Discussion of the DNV OS-F101 waiver requirements

• Implementation of the waiver requirements on South Stream
Investigation of Back Pressure Effects on Transient Gas Flow Through Porous Media via Laboratory Experiments and Numerical Simulation
Authors: Liu Xiaolei , Limpasurat Akkharachai , Falcone Gioia , Teodoriu Catalin
Published: September 2014

When developing a transient numerical reservoir simulator, it is important to consider the back pressure effects that waves propagating from one end of the porous medium will have on the temporal distribution of pore fluid pressure within the medium itself. Such waves can be triggered by changing boundary conditions at the interface between reservoir and wellbore. An example is given by the transient reservoir response following pressure fluctuations at the wellbore boundary for gas wells suffering from liquid loading.

Laboratory experiments were performed using a modified Hassler cell to mimic the effect of varying downhole pressure on gas flow in the near-wellbore region of a reservoir. Gauges were attached along a sandstone core to monitor the pressure profile. The results of the experiments are shown in this paper.

A numerical code for modelling transient flow in the near-wellbore region was run to mimic the experiments. The comparisons of simulations and laboratory test results are presented here, for the initial and final steady-state flowing conditions, and where the inlet pressure was maintained constant while initiating a transient pressure build up at the core outlet.

The concept of the U-shaped pressure profile along the near-wellbore region of a reservoir under transient flow conditions, originally proposed by Zhang et al. [1], was experimentally and numerically reproduced for single-phase gas flow. This is due to a combination of inertia and compressibility effects, leading to the reservoir response not being instantaneous. The results suggest that, in two phase gas-liquid conditions, liquid re-injection could occur during liquid loading in gas wells. From the experimental results, the U-shaped curves were more obvious and of longer duration in the case of greater outlet pressure. The transition from the initial to the final steady state condition occurred rapidly in all the cases shown here, with the U-shaped pressure profile appearing only over a relatively short time (at the small scale and low pressures tested in this study).
Diffraction Corrections for Platform Wave Measurements
Authors: Forristall George Z. , Aubault Alexia
Published: September 2014

Many measurements of hurricane waves have been made from deep water production facilities in the Gulf of Mexico. Measurements made on different sides of the platforms differ from one another and the incident wave field because the platforms diffract and radiate waves. For many purposes, we would like to know the incident wave field. Forristall and Aubault (OMAE2013-10860) used WAMIT diffraction calculations to successfully invert wave spectra measured under a TLP model in the Marin offshore basin. We have now used similar techniques to invert spectra measured at offshore platforms during Hurricanes Gustav and Ike. We do not have any measurements of the undisturbed wave spectra for testing the results. The tests were made by checking whether inverse calculations on all the gauges deployed at different locations on the platforms could produce the same undisturbed wave field.

Wave directions are needed for the diffraction calculations. Information from the wave gauges can be used to find the directions by optimizing the agreement among the inverted power spectra. To perform the optimization, we varied both the mean direction and spreading at each spectral frequency. The rms difference between the inverted probe spectral densities was minimized at each spectral frequency.

When spectra from four gauges on a platform are inverted, they agree reasonably well with each other. The average of the inverted significant wave heights is slightly lower than the average of the measured significant wave heights. But when spectra from pairs of the four probes are inverted, the results differ depending on which pair is used. This result implies that our inversion method cannot be used on data from platforms with two probes, and casts doubt on the accuracy of four probe inversions.
Assess the Seismic Wave Influence on Buried Pipelines With ASCE Soil-Spring Model
Authors: Zhang Fan , Wang Yong-Yi
Published: September 2014

The propagation of seismic waves introduces strains in buried pipelines. Considerable amount of work was performed in 1970’s and early 1980’s in this subject area. A good representative of such work is the model developed by Shinozuka and Koike in 1979. The analytical models developed during this period are still the major tools in assessing the influence of seismic waves on buried pipelines. The foundations of these models are the assumptions and some simplified soil and pipe interaction models available at the time. In 1984 a spring model representing the interaction between soil and buried pipes was introduced by American Society of Civil Engineers (ASCE) in Guidelines for the Seismic Design of Oil and Gas Pipeline Systems. An improved version of the ASCE model was later published in Guidelines for the Design of Buried Steel Pipe by American Lifelines Alliance in 2001. Since then, the spring model has become one of the most widely used models by various industries and has been incorporated into commercial software, such as AutoPIPE®. Most of the soil properties in fields are represented by the parameters of the ASCE soil-spring model. However, it is inconvenient to assess the influence of seismic waves on pipelines with soil properties described by parameters of the ASCE model. There are differences between the ASCE soil-spring model and the soil-pipe interactions in the seismic wave analysis model. In this paper the foundation of Shinozuka and Koike model is first reviewed. The model is then revised to accommodate the ASCE soil-spring model. Some unnecessary assumptions in the Shinozuka and Koike model are removed to make the model more generally applicable to various field conditions. Finally, the revised model is verified by finite element analysis under several typical pipeline field conditions, including straight segments and segments with bends and tees.
Experimental Investigation of Reservoir Stress Path Hysteresis During Production-Injection Periods
Authors: Shahri Mojtaba P. , Miska Stefan Z.
Published: September 2014

There has been an increasing consciousness regarding stress changes associated with reservoir depletion as the industry moves towards more challenging jobs in deep-water or depleted reservoirs. These stress changes play a significant role in the design of wells in this condition. Therefore, accurate prediction of reservoir stress path, i.e., change in horizontal stresses with pore pressure, is of vital importance.

In this study, the current stress path formulation is investigated using a Tri-axial Rock Mechanics Testing Facility. The reservoir depletion scenario is simulated through experiments and provides a better perspective on the currently used formulation and how it’s applicable during production and injection periods. The effect of fluid re-injection into reservoirs on the horizontal stress is also analyzed using core samples. According to the results, formation fracture pressure would not be equal to its initial value if pressure builds up using re-injection. The irrecoverable formation fracture pressure has a power law relation with pore pressure drawdown range. In order to avoid higher permanent fracture pressure reduction, it’s recommended to start the injection process as soon as possible during the production life of reservoirs. According to the experimental results, rocks behave differently during production and injection periods. Poisson’s ratio is greater during pressure build-up as compared to the depletion period. According to the current industry standards, Poisson’s ratio is usually obtained using fracturing data; i.e., leak-off test or mini-fracture test, or well logging methods. However, we are not able to use the same Poisson’s ratio for both pressure drawdown and build-up scenarios according to the experimental data. Corresponding to Poisson’s ratio values, the change in horizontal stress with pore pressure during drawdown (production) is higher than during build-up (injection) period. The outcomes of this study can significantly contribute to well planning and design of challenging wells over the life of reservoirs.
Pozzolanic Reactions in Cementitious Materials for Subsurface Applications
Authors: Ukrainczyk Neven , Zlopaša Jure , Koenders Eduardus , Rocha Camila Aparecida Abelha , Toledo Filho Romildo Dias
Published: September 2014

Silica fume (SF) is used as a constituent to formulate cementitious materials for subsurface (oil-well) applications, e.g. by the offshore industry. Using green supplementary pozzolanic materials like silica fume could both improve the material’s performance and the footprint of the sustainable solution. X-ray diffraction and isothermal calorimetry were employed to investigate the evolution of cement paste hydration (water to binder ratio 0.44) after 14 h, 3, 7, and 28 days of curing. Experimental results are presented for both cement pastes made of Class G Portland cement and for a blended paste system where 8% of the Class G cement has been replaced by silica fume. The results indicate beneficial effects of SF on the microstructural development of the slurry.
Application of 2D Finite Element Analysis on Subsea Pipe-Soil Interaction Assessment
Authors: Thomaz Tianna , Carneiro Daniel , Ellwanger Gilberto , Nascimento Leonardo , Pereira Sergio
Published: September 2014

The behavior of a subsea pipeline when submitted to external loads is governed by the well predictable physical properties of the pipe and the not-so-well predictable pipe-soil interaction behavior. Understanding of the pipe-soil interaction behavior has advanced over the last years, however, the level of uncertainty in the available models is still high.

This paper presents a series of detailed two-dimensional nonlinear finite element analyses investigating the soil resistance to pipeline lateral displacement. Parametric analyses were used to compare the influence of some important parameters such as the maximum (breakout) resistance, initial stiffness and mobilization displacements for example. Results are compared to the analytical models proposed by Verley, Lund and Bruton [1,2].

The results revealed some aspects not foreseen by the analytical models: The displacement under which the maximum lateral load is mobilized is not straightforwardly linked to the pipeline diameter, as some authors would say; the embedment seems to play a much more important role than the diameter itself in the maximum force derivation. Some other results are discussed through the paper and the main findings are listed in the conclusions.
The Experiences From the First Rounds of Offshore Wind Farm Installation in the German EEZ (Both Baltic and North Sea) and Lessons Learnt to Achieve Serial Production Status: A Consultant’s Perspective
Authors: Stade Ekkehard
Published: September 2014

Offshore wind farms present a lesser safety risk to operators and contractors than traditional oil and gas installations. In the post Macondo world this does not come as a surprise since the risks involved in construction, operation and maintenance of an offshore wind farm are by far lower.

Even with higher probability of incidents and near misses (due to serial construction) the severity/ impact of those is considerably lower.

On the other hand projects are complex, profit margins are what they are called: marginal. Hence there is no room for errors, perhaps in form of delays. If, for example, the installation completion of the turbines and the inner array cabling/ export cables are not perfectly in tune, the little commercial success that can be achieved is rapidly diminishing by costly compensation activities.

The paper will try to present solutions to the most pressing challenges and elaborate on the effect those would have had, had they been implemented at the beginning of the projects.

How can a sustainable new industry evolve by learning from established industries? Presently, there is a view that offshore wind is a short-lived business. Particularly representatives of the oil and gas industry raise such concern. Apart from the obvious bias of those voices, this controversy is also caused by the fact that offshore wind seems to have a tendency to try and re-invent the wheel rather than using established procedures. Even with a relatively stable commitment to the offshore wind development regardless of the respective government focus within European coastal states the industry suffers from financing issues, subsidies, over-regulation due to lack of expertise within authorities and other challenges. The avoidance of those is key to a successful development for this industry in other areas of the planet. In conjunction with a stable commitment this is essential in order to attract the long lead-time projects and to establish the complex supply chains to achieve above goals. The paper will look at the short but intensive history of the industry and establish mitigation to some of the involved risks of offshore wind farm EPCI.
The Effect of Constant and Variable Eccentricity on the Spacer Performance During Primary Well Cementing
Authors: Zulqarnain Muhammad , Tyagi Mayank
Published: September 2014

Spacers are the intermediate fluids in the primary cementing process, preceded by the mud and followed by the cement. They help in mud removal, keep mud and cement separated and prepare the annulus walls for a good cement bond. The focus of this study is to analyze the spacer performance in keeping mud and cement separated in the vertical and horizontal well sections with eccentricity. Several combinations of eccentricity variation and displacement rates are simulated using Computational Fluid Dynamics (CFD) tool to analyze the temporal and spatial fluid volume fraction distributions in the annulus and validated against multi-fluid displacement experiments. A 50 ft vertical section with annular gap of 1.5″ and casing standoff from 5% to 100% and a horizontal section with variable eccentricity are studied. For initial conditions the annulus is modeled as filled with mud and subsequently swept by one annular volume of spacer and cement each respectively. Mud and cement are treated as Herschel Bulkley fluids and spacer as a Newtonian fluid.

Qualitative results from simulations are shown in the form of volume fraction contour plots at different sections of the annulus and quantitative results in the form of temporal and spatial volume fraction of each fluid at specific planes in the entire annulus. For a vertical annular section with constant eccentricity, some unswept mud is observed on the narrow side and eventually becomes trapped after the eccentricity is increased above a threshold value. It is also observed that increasing displacement rate helps in displacing some of this trapped mud. After a threshold eccentricity value, the trapped mud cannot be displaced and the spacer and cement follow the path of least resistance and flow occurs mainly on the wider side of the annulus. For a horizontal section with variable eccentricity (maximum at the mid distance between centralizers), the flow is observed to move towards wider side around the center and then returning to the other side (narrow part) after passing through middle section. Some trapped mud is also observed in the vicinity of the middle section due to local maximum eccentricity.
Dynamic Response of a Spar-Type Floating Wind Turbine at Power Generation
Authors: Utsunomiya Tomoaki , Yoshida Shigeo , Kiyoki Soichiro , Sato Iku , Ishida Shigesuke
Published: September 2014

In this paper, dynamic response of a Floating Offshore Wind Turbine (FOWT) with spar-type floating foundation at power generation is presented. The FOWT mounts a 100kW wind turbine of down-wind type, with the rotor’s diameter of 22m and a hub-height of 23.3m. The floating foundation consists of PC-steel hybrid spar. The upper part is made of steel whereas the lower part made of prestressed concrete segments. The FOWT was installed at the site about 1km offshore from Kabashima Island, Goto city, Nagasaki prefecture on June 11th, 2012. Since then, the field measurement had been made until its removal in June 2013. In this paper, the dynamic behavior during the power generation is presented, where the comparison with the numerical simulation by aero-hydro-servo-mooring dynamics coupled program is made.
Effect of Ship Forward Speed on Ship Response Statistics in Extreme Seas
Authors: Guo Bingjie , Bitner-Gregersen Elzbieta M.
Published: September 2014

Earlier investigations have indicated that proper prediction of nonlinear responses due to nonlinear waves is important for ship safety in extreme seas. Nonlinearities may increase significantly ship responses in steep sea-states, particularly when rogue waves are present. So far most of the model tests in rogue waves have been performed without ship forward speed. Therefore the effect of forward speed on ship responses is still not sufficiently investigated. The present study is addressing this topic by taking an LNG tanker as an example. Ship responses of the LNG tanker with/without forward speed are studied with both model test and numerical simulations. The model test is carried out in the sea-keeping tank of the Technical University of Berlin (TUB), and numerical simulations are performed using the 3D Panel code. The statistical uncertainty of the ship responses due to different time spans is investigated also. The study shows that ship forward speed increases the ship motions and hogging moment. The change of sagging moment due to the forward speed is very small at slow speed. After the ship forward speed is increased to a certain value, the sagging moment increases significantly with ship speed.
Theoretical Study on Hydroelastic Responses of Very Large Floating Structures Near Islands and Reefs
Authors: Tian Chao , Ni Xinyun , Ding Jun , Yang Peng , Wu Yousheng
Published: September 2014

In order to explore the fishery, oil and gas, and tourism resources in the ocean, Very Large Floating Structures (VLFS) can be deployed near islands and reefs as a logistic base with various functions such as a floating harbor, accommodation, fishery processing, oil and gas exploration, environment surveillance, airplane landing and taking off, etc. However, in addition to the complicated hydroelastic coupling effects between the hydrodynamic loads and structural dynamic responses, when tackling the hydroelastic problems of floating structures deployed near islands and reefs, several other environmental effects and numerical techniques should be taken into account: 1) The influences of the non-uniform incident waves (multi-directions, different wave frequencies); 2) Complex seabed profile and its impact on the incident waves; 3) Nonlinear second order wave exciting forces in the complex mooring system, shallow water and coral reef geological conditions; 4) Parallel computing technology and fast solving methods for the large scale linear equations, accounting for the influence of dramatic increase of number of meshes to the computation efforts and efficiency. In the present paper the theoretical investigation on the hydroelastic responses of VLFS deployed near islands and reefs has been presented. In addition, based on the pulsating source Green function, the high performance parallel fast computing techniques and other numerical methods, in solving large scale linear equations, have been introduced in the three-dimensional hydroelastic analysis package THAFTS. The motions, wave loads, distortions and stresses can be calculated using the present theoretical model and the results can be used in the design and safety assessment of VLFS.
State-of-the-Art Techniques for Seismic Soil-Structure Interaction Analysis of Steel Gravity Structures
Authors: Tajirian Frederick , Tabatabaie Mansour , Sumodobila Basilio , Paulson Stephen , Davies Bill
Published: September 2014

The design of steel jacket fixed offshore structures in zones of moderate seismicity is typically governed by Metocean loads. In contrast the steel gravity structure (SGS) presented in this paper, is a heavy and stiff structure. The large mass results in foundation forces from seismic events that may exceed those created by extreme cyclonic storm events. When computing the earthquake response of such structures it is essential to account for soil-structure interaction (SSI) effects.

Seismic SSI analysis of the SGS platform was performed using state-of-the-art SSI software, which analyzed a detailed three-dimensional model of the SGS supported on layered soil system. The results of this analysis were then compared with those using industry standard impedance methods whereby the layered soil is replaced by equivalent foundation springs (K) and damping (C). Differences in calculated results resulting from the different ways by which K and C are implemented in different software are presented.

The base shear, overturning moment, critical member forces and maximum accelerations were compared for each of the analysis methods. SSI resulted in significant reduction in seismic demands. While it was possible to get reasonable alignment using the different standard industry analysis methods, this was only possible after calibrating the KC foundation model with software that rigorously implements SSI effects. Lessons learned and recommendations for the various methods of analysis are summarized in the paper.
The Reliability of an Instrumented Start Block Analysis System
Authors: Tor Elaine , Pease David L. , Ball Kevin A.
Published: September 2014

The swimming start is highly influential to overall competition performance. Therefore, it is paramount to develop reliable methods to perform accurate biomechanical analysis of start performance for training and research. The Wetplate Analysis System is a custom-made force plate system developed by the Australian Institute of Sport—Aquatic Testing, Training and Research Unit (AIS ATTRU). This sophisticated system combines both force data and 2D digitization to measure a number of kinetic and kinematic parameter values in an attempt to evaluate start performance. Fourteen elite swimmers performed two maximal effort dives (performance was defined as time from start signal to 15 m) over two separate testing sessions. Intraclass correlation coefficients (ICC) were used to determine each parameter’s reliability. The kinetic parameters all had ICC greater than 0.9 except the time of peak vertical force (0.742). This may have been due to variations in movement initiation after the starting signal between trials. The kinematic and time parameters also had ICC greater than 0.9 apart from for the time of maximum depth (0.719). This parameter was lower due to the swimmers varying their depth between trials. Based on the high ICC scores for all parameters, the Wetplate Analysis System is suitable for biomechanical analysis of swimming starts.
Emerging from the shade of p53 mutants: N-terminally truncated variants of the p53 family in EMT signaling and cancer progression
Authors: Engelmann David , Pützer Brigitte M.
Published: September 2014

Truncated variants of the p53 family alter the tumor microenvironment to promote tumor vascularization, growth, and metastasis.
Inhibitors of Nucleotidyltransferase Superfamily Enzymes Suppress Herpes Simplex Virus Replication
Authors: Tavis John E. , Wang Hong , Tollefson Ann E. , Ying Baoling , Korom Maria , Cheng Xiaohong , Cao Feng , Davis Katie L. , Wold William S. M. , Morrison Lynda A.
Published: September 2014

Herpesviruses are large double-stranded DNA viruses that cause serious human diseases. Herpesvirus DNA replication depends on multiple processes typically catalyzed by nucleotidyltransferase superfamily (NTS) enzymes. Therefore, we investigated whether inhibitors of NTS enzymes would suppress replication of herpes simplex virus 1 (HSV-1) and HSV-2. Eight of 42 NTS inhibitors suppressed HSV-1 and/or HSV-2 replication by >10-fold at 5 μM, with suppression at 50 μM reaching ∼1 million-fold. Five compounds in two chemical families inhibited HSV replication in Vero and human foreskin fibroblast cells as well as the approved drug acyclovir did. The compounds had 50% effective concentration values as low as 0.22 μM with negligible cytotoxicity in the assays employed. The inhibitors suppressed accumulation of viral genomes and infectious particles and blocked events in the viral replication cycle before and during viral DNA replication. Acyclovir-resistant mutants of HSV-1 and HSV-2 remained highly sensitive to the NTS inhibitors. Five of six NTS inhibitors of the HSVs also blocked replication of another herpesvirus pathogen, human cytomegalovirus. Therefore, NTS enzyme inhibitors are promising candidates for new herpesvirus treatments that may have broad efficacy against members of the herpesvirus family.
Penicillinase-Producing Plasmid Types in Neisseria gonorrhoeae Clinical Isolates from Australia
Authors: Whiley David , Trembizki Ella , Buckley Cameron , Freeman Kevin , Lawrence Andrew , Limnios Athena , Pearson Julie , Smith Helen , Stevens Kerrie , Lahra Monica M.
Published: September 2014

Penicillinase-producingNeisseria gonorrhoeae(PPNG) carrying theblaTEM-135gene is of particular concern, as it is considered a stepping stone toward resistance to extended-spectrum cephalosporins. Here, we sought to characterize plasmid types and the occurrence of theblaTEM-135gene forN. gonorrhoeaeclinical isolates from Australia. We found thatblaTEM-135was prevalent in Australian PPNG and was detected on all three major plasmid types.
Enterococcus faecalis Infection Activates Phosphatidylinositol 3-Kinase Signaling To Block Apoptotic Cell Death in Macrophages
Authors: Zou Jun , Shankar Nathan
Published: September 2014

Apoptosis is an intrinsic immune defense mechanism in the host response to microbial infection. Not surprisingly, many pathogens have evolved various strategies to manipulate this important pathway to benefit their own survival and dissemination in the host during infection. To our knowledge, no attempts have been made to explore the host cell survival signals modulated by the bacterium
Enterococcus faecalis
. Here, we show for the first time that during early stages of infection, internalized enterococci can prevent host cell (RAW264.7 cells, primary macrophages, and mouse embryonic fibroblasts [MEFs]) apoptosis induced by a wide spectrum of proapoptotic stimuli. Activation of caspase 3 and cleavage of the caspase 3 substrate poly(ADP-ribose) polymerase were inhibited in
E. faecalis
-infected cells, indicating that
E. faecalis
protects macrophages from apoptosis by inhibiting caspase 3 activation. This antiapoptotic activity in
E. faecalis
-infected cells was dependent on the activation of the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway, which resulted in the increased expression of the antiapoptotic factor Bcl-2 and decreased expression of the proapoptotic factor Bax. Further analysis revealed that active
E. faecalis
physiology was important for inhibition of host cell apoptosis, and this feature seemed to be a strain-independent trait among
E. faecalis
isolates. Employing a mouse peritonitis model, we also determined that cells collected from the peritoneal lavage fluid of
E. faecalis
-infected mice showed reduced levels of apoptosis compared to cells from uninfected mice. These results show early modulation of apoptosis during infection and have important implications for enterococcal pathogenesis.
Coordinate Regulation of the Suf and Isc Fe-S Cluster Biogenesis Pathways by IscR Is Essential for Viability of Escherichia coli
Authors: Mettert Erin L. , Kiley Patricia J.
Published: September 2014

Fe-S cluster biogenesis is essential for the viability of most organisms. In
Escherichia coli
, this process requires either the housekeeping Isc or the stress-induced Suf pathway. The global regulator IscR coordinates cluster synthesis by repressing transcription of the
isc
operon by [2Fe-2S]-IscR and activating expression of the
suf
operon. We show that either [2Fe-2S]-IscR or apo-IscR can activate
suf
, making expression sensitive to mainly IscR levels and not the cluster state, unlike
isc
expression. We also demonstrate that in the absence of
isc
, IscR-dependent
suf
activation is essential since strains lacking both the Isc pathway and IscR were not viable unless Suf was expressed ectopically. Similarly, removal of the IscR binding site in the
sufA
promoter also led to a requirement for
isc
. Furthermore,
suf
expression was increased in a Δ
isc
mutant, presumably due to increased IscR levels in this mutant. This was surprising because the iron-dependent repressor Fur, whose higher-affinity binding at the
sufA
promoter should occlude IscR binding, showed only partial repression. In addition, Fur derepression was not sufficient for viability in the absence of IscR and the Isc pathway, highlighting the importance of direct IscR activation. Finally, a mutant lacking Fur and the Isc pathway increased
suf
expression to the highest observed levels and nearly restored [2Fe-2S]-IscR activity, providing a mechanism for regulating IscR activity under stress conditions. Together, these findings have enhanced our understanding of the homeostatic mechanism by which cells use one regulator, IscR, to differentially control Fe-S cluster biogenesis pathways to ensure viability.
Structures of Bacterial Polynucleotide Kinase in a Michaelis Complex with Nucleoside Triphosphate (NTP)-Mg
2+
and 5′-OH RNA and a Mixed Substrate-Product Complex with NTP-Mg
2+
and a 5′-Phosphorylated Oligonucleotide
Authors: Das Ushati , Wang Li Kai , Smith Paul , Munir Annum , Shuman Stewart
Published: September 2014

Clostridium thermocellum
polynucleotide kinase (
Cth
Pnk), the 5′-end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from a nucleoside triphosphate (NTP) donor to a 5′-OH polynucleotide acceptor, either DNA or RNA. Here we report the 1.5-Å crystal structure of
Cth
Pnk-D38N in a Michaelis complex with GTP-Mg
2+
and a 5′-OH RNA oligonucleotide. The RNA-binding mode of
Cth
Pnk is different from that of the metazoan RNA kinase Clp1.
Cth
Pnk makes hydrogen bonds to the ribose 2′-hydroxyls of the 5′ terminal nucleoside, via Gln51, and the penultimate nucleoside, via Gln83. The 5′-terminal nucleobase is sandwiched by Gln51 and Val129. Mutating Gln51 or Val129 to alanine reduced kinase specific activity 3-fold. Ser37 and Thr80 donate functionally redundant hydrogen bonds to the terminal phosphodiester; a S37A-T80A double mutation reduced kinase activity 50-fold. Crystallization of catalytically active
Cth
Pnk with GTP-Mg
2+
and a 5′-OH DNA yielded a mixed substrate-product complex with GTP-Mg
2+
and 5′-PO
4
DNA, wherein the product 5′ phosphate group is displaced by the NTP γ phosphate and the local architecture of the acceptor site is perturbed.
Rare case of severe cholangiopathy following critical illness
Authors: Patel Kamal Vijaykant , Zaman Sameer , Chang Fuju , Wilkinson Mark
Published: September 2014

Secondary sclerosing cholangitis is a rare condition caused by disorders directly damaging the biliary tree. We present a case of a 34-year-old man with no pre-existing hepatobiliary disease who developed significant cholestasis and subsequent cholangitis while in the intensive care unit for multiorgan failure secondary to H1N1 influenza A (swine flu). After discharge from the intensive care unit, jaundice, fevers, abdominal pain, pruritus and ongoing cholestasis persisted, consistent with recurrent cholangitis. Secondary sclerosing cholangitis was confirmed by liver biopsy and endoscopic retrograde cholangiopancreatography. This is a case of the recently described syndrome of secondary sclerosing cholangitis following critical illness, with associated severe hypoxic and ischaemic injury. He subsequently developed recognised complications of sclerosing cholangitis, including fat-soluble vitamin deficiencies, recurrent cholangitis and liver fibrosis. To the best of our knowledge, this is the first reported case of secondary sclerosing cholangitis following critical illness in the UK.
Hepatocellular carcinoma in a patient with chronic lymphocytic leukaemia involving the liver
Authors: Ezigbo Chika , Sy Alexander M , Popescu-Martinez Andrea , Boma Noella , Bergasa Nora V
Published: September 2014

A relationship between hepatocellular carcinoma and chronic lymphocytic leukaemia has been reported. This is a case of a 75-year-old woman with stable chronic lymphocytic leukaemia, not on treatment with an increased activity of serum alkaline phosphatase and negative liver disease work up. A liver biopsy revealed leukaemic infiltration without evidence of cirrhosis or fatty liver. Four years later, she presented with a rapidly progressive liver mass which was diagnosed as hepatocellular carcinoma histologically.
Ocular toxoplasmosis: a very rare presentation in an immunocompetent patient
Authors: Matias Margarida , Gomes Antonia , Marques Tiago , Fonseca Ana Claudia
Published: September 2014

A 28-year-old man presented with a 2-week history of red eye, photophobia, pain and decreased visual acuity of the right eye. The ophthalmological examination revealed hypertensive non-granulomatous panuveitis, retinal vasculitis with focus of retinochoroiditis with pigmented central area suggestive of ocular toxoplasmosis in the active phase. He started treatment with azithromycin, pyrimethamine, topical steroids and measures for control of intraocular pressure. Serology forToxoplasma gondiiwas positive and for HIV, negative. For headache and vomiting, he was hospitalised in order to exclude cerebral toxoplasma. The cerebral CT scan, MRI and lumbar puncture were negative and treatment was changed to pyrimethamine, sulfadiazine and prednisolone. For persistence of vomiting he started clindamycin with clinical and ophthalmological improvement. The patient is currently under prophylaxis with co-trimoxazol for 1 year, and maintains clinical improvement. This case illustrates the rarity of presentation of ocular toxoplasmosis, without cerebral in an immunocompetent patient.
Instantons and vortices on noncommutative toric varieties
Authors: Cirio Lucio S. , Landi Giovanni , Szabo Richard J.
Published: September 2014

We elaborate on the quantization of toric varieties by combining techniques from toric geometry, isospectral deformations and noncommutative geometry in braided monoidal categories, and the construction of instantons thereon by combining methods from noncommutative algebraic geometry and a quantized twistor theory. We classify the real structures on a toric noncommutative deformation of the Klein quadric and use this to derive a new noncommutative four-sphere which is the unique deformation compatible with the noncommutative twistor correspondence. We extend the computation of equivariant instanton partition functions to noncommutative gauge theories with both adjoint and fundamental matter fields, finding agreement with the classical results in all instances. We construct moduli spaces of noncommutative vortices from the moduli of invariant instantons, and derive corresponding equivariant partition functions which also agree with those of the classical limit.
Development of the coastal systems of the easternmost Gulf of Finland, and their links with Neolithic–Bronze and Iron Age settlements
Authors: Ryabchuk D. , Zhamoida V. , Amantov A. , Sergeev A. , Gusentsova T. , Sorokin P. , Kulkova M. , Gerasimov D.
Published: September 2014

We examine three questions concerning the post-glacial geological history of the eastern Gulf of Finland: (1) the amplitude of the Holocene sea-level regressions; (2) the time and mechanism of the development of large sand accretion forms (bars and spits), including dunes; and (3) the sea-level changes and coastal development over the last 4 kyr. Recent on-land geoarchaeological studies, as well as detailed marine geological research of the Gulf of Finland nearshore bottom, have provided new data for developing a hypothesis about the palaeogeographical development of the area. Geoarchaeological studies carried out around Sestroretsky Artificial Lake and within Okhta Cape, as well as analyses of previous studies of the Neolithic–Early Metal settlements, have shed new light on some aspects of coastal system development. Geographical information system (GIS)-based modelling of Holocene shorelines for the different time periods can be useful for future archaeological research. A series of submarine terraces was found at the bottom of the Gulf (sea depths from 10 to 2 m). The analysis of marine geological data (submarine terraces) and distribution of archaeological sites can be explained by a possible rise in relative sea level in the Gulf of Finland at 5 ka BP and a regression around 3 ka BP.
Numerical Characterization of the Performance of Fluid Pumps Based on a Wankel Geometry
Authors: Wan Stephen , Leong Jason , Ba Te , Lim Arthur , Kang Chang Wei
Published: September 2014

The performance of fluid pumps based on Wankel-type geometry, taking the shape of a double-lobed limaçon, is characterized. To the authors’ knowledge, this is the first time such an attempt has been made. To this end, numerous simulations for three different pump sizes were carried out and the results were understood in terms of the usual scaling coefficients. The results show that such pumps operate as low efficiency (<30%) valveless positive displacements pumps, with pump flow-rate noticeably falling at the onset of internal leakage. Also, for such pumps, the mechanical efficiency varies linearly with the head coefficient, and, within the onset of internal leakage, the capacity coefficient holds steady even across pump efficiency. Simulation of the flow field reveals a structure rich in three-dimensional vortices even in the laminar regime, including Taylor-like counterrotating vortex pairs, pointing towards the utility of these pumps in microfluidic applications. Given the planar geometry of such pumps, their applications as microreactors and micromixers are recommended.
Attitude of Healthcare Professionals: A Major Limiting Factor in Organ Donation from Brain-Dead Donors
Authors: Kosieradzki Maciej , Jakubowska-Winecka Anna , Feliksiak Michal , Kawalec Ilona , Zawilinska Ewa , Danielewicz Roman , Czerwinski Jaroslaw , Malkowski Piotr , Rowiński Wojciech
Published: September 2014

Public attitude toward deceased donor organ recovery in Poland is quite positive, with only 15% opposing to donation of their own organs, yet actual donation rate is only 16/pmp. Moreover, donation rate varies greatly (from 5 to 28 pmp) in different regions of the country. To identify the barriers of organ donation, we surveyed 587 physicians involved in brain death diagnosis from regions with low (LDR) and high donation rates (HDR). Physicians from LDR were twice more reluctant to start diagnostic procedure when clinical signs of brain death were present (14% versus 5.5% physicians from HDR who would not diagnose death, resp.). Twenty-five percent of LDR physicians (as opposed to 12% of physicians from HDR) would either continue with intensive therapy or confirm brain death and limit to the so-called minimal therapy. Only 32% of LDR physicians would proceed with brain death diagnosis regardless of organ donation, compared to 67% in HDR. When donation was not an option, mechanical ventilation would be continued more often in LDR regions (43% versus 26.7%;P<0.01). In conclusion, low donation activity seems to be mostly due to medical staff attitude.
Noncontact Measurement for Radius of Curvature of Unpolished Lens
Authors: Liang Haifeng
Published: September 2014

A noncontact mathematical model to measure radius of curvature (ROC) of an unpolished spherical lens was proposed and also proved by experiments. This model gives ROC as a function of arcs radii and their separation distance, where the radii of the corresponding arcs could be acquired by taking coordinates of points on the arcs when two parallel lines of light project onto a lens surface. Our experiments demonstrated that the measured maximum relative error was 0.027% for a concave surface with a 38.19 mm ROC and 0.021% for a convex surface with a 97.75 mm ROC, which were all in agreement with those of theory prediction error. The suggested method presented a fast noncontact method for testing ROC of lens during coarse grinding and fine grinding.
Peroneal Arteriovenous Fistula and Pseudoaneurysm: An Unusual Presentation
Authors: Ching Kevin C. , McCluskey Kevin M. , Srinivasan Abhay
Published: September 2014

Peroneal artery arteriovenous fistulas and pseudoaneurysms are extremely rare with the majority of reported cases due to penetrating, orthopedic, or iatrogenic trauma. Failure to diagnose this unusual vascular pathology may lead to massive hemorrhage or limb threatening ischemia. We report an interesting case of a 14-year-old male who presented with acute musculoskeletal pain of his lower extremity. Initial radiographs were negative. Further imaging workup revealed a peroneal arteriovenous fistula with a large pseudoaneurysm. After initial endovascular intervention was unsuccessful, the vessels were surgically ligated in the operating room. Pathology revealed papillary endothelial hyperplasia consistent with an aneurysm and later genetic testing was consistent with Ehlers-Danlos syndrome Type IV. This case illustrates an unusual cause of acute atraumatic musculoskeletal pain and uncommon presentation of Ehlers-Danlos syndrome.
Strength Gains as a Result of Brief, Infrequent Resistance Exercise in Older Adults
Authors: Fisher James , Steele James , McKinnon Pat , McKinnon Stephen
Published: September 2014

Chronological aging is associated with a decrease in skeletal muscle mass and bone mineral density, an increase in fat mass, frequency of falls and fractures, and the likelihood of obesity, diabetes, and coronary heart disease. Resistance exercise has been shown to counter all of these effects of aging and, in turn, reduce the risk of all-cause mortality. However, variables such as volume and frequency have become contentious issues, with recent publications suggesting that similar physiological adaptations are possible with both high- and low-volume approaches. The aim of this research was to consider strength increases as a result of brief, infrequent resistance exercise. The present study offers data from 33 (14 male and 19 female) older adults (M=55years) who underwent brief (<15 minutes per exercise session), infrequent (2×/week), resistance exercise to a high intensity of effort (6-repetition maximum) at a controlled repetition duration (10 seconds concentric : 10 seconds eccentric) on 5 resistance machines (chest press, leg press, pull-down, seated row, and overhead press). Data is presented for training interventions of 12 weeks (male) and 19 weeks (female). Significant strength increases were identified for all exercises. With the detailed health benefits obtainable, the present study suggests that resistance exercise can be efficacious in much smaller volumes than previously considered.