bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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.
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.
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.
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

ABSTRACT
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

ABSTRACTPenicillinase-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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.
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

Abstract
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.
Alterations of Choline Phospholipid Metabolism in Endometrial Cancer Are Caused by Choline Kinase Alpha Overexpression and a Hyperactivated Deacylation Pathway
Authors: Trousil Sebastian , Lee Patrizia , Pinato David J. , Ellis James K. , Dina Roberto , Aboagye Eric O. , Keun Hector C. , Sharma Rohini 
Published: September 2014

AbstractMetabolic rearrangements subsequent to malignant transformation are not well characterized in endometrial cancer. Identification of altered metabolites could facilitate imaging-guided diagnosis, treatment surveillance, and help to identify new therapeutic options. Here, we used high-resolution magic angle spinning magnetic resonance mass spectroscopy on endometrial cancer surgical specimens and normal endometrial tissue to investigate the key modulators that might explain metabolic changes, incorporating additional investigations using qRT-PCR, Western blotting, tissue microarrays (TMA), and uptake assays of [3H]-labeled choline. Lipid metabolism was severely dysregulated in endometrial cancer with various amino acids, inositols, nucleobases, and glutathione also altered. Among the most important lipid-related alterations were increased phosphocholine levels (increased 70% in endometrial cancer). Mechanistic investigations revealed that changes were not due to altered choline transporter expression, but rather due to increased expression of choline kinase α (CHKA) and an activated deacylation pathway, as indicated by upregulated expression of the catabolic enzymes LYPLA1, LYPLA2, and GPCPD1. We confirmed the significance of CHKA overexpression on a TMA, including a large series of endometrial hyperplasia, atypical hyperplasia, and adenocarcinoma tissues, supporting a role for CHKA in malignant transformation. Finally, we documented several-fold increases in the uptake of [3H]choline in endometrial cancer cell lines compared with normal endometrial stromal cells. Our results validate deregulated choline biochemistry as an important source of noninvasive imaging biomarkers for endometrial cancer. Cancer Res; 74(23); 6867–77. ©2014 AACR.