bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIM-Finder: A new method for identifying TIM-barrel proteins
Authors: Si Jing-Na , Yan Ren-Xiang , Wang Chuan , Zhang Ziding , Su Xiao-Dong 
Published: December 2009

Abstract

Background
The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.

Results
To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.

Conclusions
TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.
Erratum to: Image guided dose escalated prostate radiotherapy: still room to improve
Authors: Martin Jarad M , Bayley Andrew , Bristow Robert , Chung Peter , Gospodarowicz Mary , Menard Cynthia , Milosevic Michael , Rosewall Tara , Warde Padraig R , Catton Charles N 
Published: December 2009

Abstract
We regret to report that a proofreading error caused an incorrect legend and description of the contents of table 6 to appear in our original publication of this work. The correct description of table 6 is: Univariate analysis of prognostic factors for 5-year nadir + 2 biochemical outcome for men presenting with intermediate risk factors.
Chloride Ion Detection by InN Gated AlGaN/GaN High Electron Mobility Transistors
Authors: Chu Byung Hwan , Lin Hon-way , Gwo Shangjr , Wang Yu-Lin , Pearton S. J. , Johnson J. W. , Rajagopal P , Roberts J. C. , Piner E. L. , Linthicum K. J. , Ren Fan 
Published: December 2009

AbstractChloride ion concentration can be used as a biomarker for the level of pollen exposure in allergic asthma, chronic cough and airway acidification related to respiratory disease. AlGaN/GaN high electron mobility transistor (HEMT) with an InN thin film in the gate region was used for real time detection of chloride ion detection. The InN thin film provided surface sites for reversible anion coordination. The sensor exhibited significant changes in channel conductance upon exposure to various concentrations of NaCl solutions. The sensor was tested over the range of 100 nM to 100 μM NaCl solutions. The effect of cations on the chloride ion detection was also studied.
Detection of DNA Hybridization using Functionalized InN ISFETs
Authors: Lin Cheng-Yi , Lu Yen-Sheng , Peng Shih-Kang , Gwo Shangjr , Yeh J. 
Published: December 2009

AbstractUltrathin (∼10 nm) InN ion sensitive field effect transistors (ISFETs) are functionalized by immobilized label-free oligonucleotide probes with 3-mercaptopropyltrimethoxysilane (MPTMS) through molecular vapor deposition (MVD) technique. This layer on the InN surface serves the function of selectively detecting the hybridization of complementary deoxyribonucleic acid (DNA). Using MVD technique to perform the gas-phase silanization of MPTMS provided a time-saving and simple method to reach 68° water contact angle after 1.5 h treatment. High resolution X-ray photoelectron spectroscopy (HRXPS) was employed to analyze the surface characteristics after functionalization. Modified probes DNA were covalently bonded to MPTMS-covered gate surface of InN ISFETs. And further hybridized with complementary DNA For a 12-mer oligonucleotide probe, a significant drain-source current decrease (∼ 6 μA) was observed for the hybridization with complementary DNA solution of 100 nM. In contrast, the noncomplementary DNA with single-base mismatch did not show obvious current changes. Functionalized ultrathin InN ISFETs for DNA sequence detection demonstrate the promise of biological sensing and genetic diagnosis applications.
Fast Detection of Perkinsus Marinus, a Prevalent Pathogen of Oysters and Clams from Sea Waters
Authors: Wang Yu-Lin , Chu B.H. , Chen K.H. , Chang Chih-Yang , Lele Tanmay P. , Papadi George , Coleman James K. , Sheppard Barbara J. , Dungan Chris F. , Pearton S. J. , Johnson J.W. , Ren F. 
Published: December 2009

AbstractAntibody-functionalized, Au-gated AlGaN/GaN high electron mobility transistors (HEMTs) were used to detect Perkinsus marinus. The antibody was anchored to the gate area through immobilized thioglycolic acid. The AlGaN/GaN HEMT were grown by a molecular beam epitaxy system (MBE) on sapphire substrates. Infected sea waters were taken from the tanks in which Tridacna crocea infected with P. marinus were living and dead. The AlGaN/GaN HEMT showed a rapid response of drain-source current in less than 5 seconds when the infected sea waters were added to the antibody-immobilized surface. The recyclability of the sensors with wash buffers between measurements was also explored. These results clearly demonstrate the promise of field-deployable electronic biological sensors based on AlGaN/GaN HEMTs for Perkinsus marinus detection.
Experimental Observation of Sequential Tunneling Transport in GaN/AlGaN Coupled Quantum Wells Grown on a Free-Standing GaN Substrate
Authors: Sudradjat Faisal , Driscoll Kristina , Liao Yitao , Bhattacharyya Anirban , Thomidis Christos , Zhou Lin , Smith David J. , Moustakas Theodore D. , Paiella Roberto 
Published: December 2009

AbstractA GaN/AlGaN multiple-quantum-well structure based on an asymmetric triple-quantum-well repeat unit was grown by molecular beam epitaxy, and its vertical electrical transport characteristics were investigated as a function of temperature. To minimize the density of dislocations and other structural defects providing leakage current paths, homoepitaxial growth on a free-standing GaN substrate was employed. The measured vertical-transport current-voltage characteristics were found to be highly nonlinear, especially at low temperatures, consistent with sequential tunneling through the ground-state subbands of weakly coupled adjacent quantum wells. Furthermore, different turn-on voltages were measured depending on the polarity of the applied bias, in accordance with the asymmetric subband structure of the sample repeat units.
Does a Diflufenzopyr Plus Dicamba Premix Synergize Russian Knapweed (Acroptilon repens) Control with Auxinic Herbicides?
Authors: Enloe Stephen F. , Kniss Andrew R. 
Published: December 2009

AbstractDiflufenzopyr is a synergist that improves broadleaf weed control when mixed with certain auxinic herbicides. In nonagricultural settings, it is only available in a premix with dicamba, which is labeled for noncrop sites, pasture, hay, and rangeland. Our objectives were to determine the influence of diflufenzopyr + dicamba when applied with auxinic herbicides for Russian knapweed control. Studies were conducted near Ethete, WY, from 2005 to 2008 in a pasture heavily infested with Russian knapweed. Treatments were applied in the fall (September) and included aminopyralid, clopyralid, clopyralid + 2,4-D, clopyralid + triclopyr, and picloram at standard and reduced rates, with and without diflufenzopyr + dicamba. At 12 and at 24 mo after treatment (MAT), diflufenzopyr + dicamba did not influence Russian knapweed control when applied with standard rates of aminopyralid, clopyralid, clopyralid + 2,4-D, clopyralid + triclopyr, or picloram. All of these treatments except clopyralid + 2,4-D consistently provided ≥ 80% control 24 MAT. Reduced-rate herbicide interactions with diflufenzopyr + dicamba were also not significant at 12 MAT. However, at 24 MAT, aminopyralid applied with diflufenzopyr + dicamba controlled Russian knapweed 83% compared with 59% when aminopyralid was applied alone. Russian knapweed control with all other reduced-rate treatments, except picloram, fell below 80%. These results indicate that diflufenzopyr + dicamba does not generally improve Russian knapweed control at 12 or 24 MAT with either standard or reduced rates of typical fall, auxinic herbicide treatments.
Selective Water Shutoff in Gas Well Turns a Liability into an Asset: A Successful Case History from East Kalimantan, Indonesia
Authors: Junesompitsiri Chat , Berel Antoine , Curtice Richard , Riyanto Latief , Thouvenin Etienne , Cheneviere Pascal 
Published: December 2009

Abstract
This case history describes a procedure in which a polymer sealant and a bridge plug were used to shut off water production from upper zones to enable gas production from productive lower zones. Offshore gas fields operated in East Kalimantan were producing gas and water. When water production increased, gas production was greatly reduced. This paper presents a case history of water-shutoff work performed in the Peciko field, offshore East Kalimantan, Indonesia.
Typically, the production of these wells is commingled with multiple perforations inside the production casing and the water breakthrough could happen at any layer; therefore, a selective shutoff is required. A production-logging tool (PLT) was run to identify the source of the water influx, and the uppermost set of perforations was identified to be the main contributor to the water production.
The objective was to completely shut off the uppermost zones with sealant, without a cement tail-in. The chosen sealant was an organically crosslinked polymer system and tail-in with a particle-gel system (PGS) to increase near-wellbore shutoff integrity. Because the target shutoff zone was the uppermost set of perforations, a retrievable bridge plug was used to provide isolation from all the lower zones while pumping the sealant.
The operation sequence consists of (1) setting the retrievable bridge plug, (2) performing an injectivity test, (3) pumping the sealants, (4) shutting-in to allow the polymer to develop strength, (5) cleaning out excess particle gel inside the wellbore (without milling), (6) retrieving the bridge plug in an underbalanced condition, and then (7) flowing the well.
The job was initially evaluated by flowing the well and observing the well performance. Later, a PLT was run to confirm the amount of influx from the shutoff zone. Results from both were very satisfactory, as is detailed in the paper.
Investigation on Crude Oil Migration in Surface and Subsurface Environment: Impact and Solution
Authors: Amro Mohammed M. , Benzagouta Mohammed S. , Karnanda Wimpy 
Published: December 2009

Abstract
Natural degradation of crude oil is very slow and might take several years to be degraded. However, its impact on the environment will last as long as neither treatment nor solutions are undertaken. When further migration of crude oil is occurring, it will harm the soil and might contact the subsurface water or groundwater. The most relevant in that respect would be the type of fluids (Contaminants), mode of fluid transport, type of soil, environmental importance of the concerned sites, and weathering effect. Therefore, the main objectives of this study are investigation and observation of crude oil migration as toxic fluid, its penetration, and weathering effect.
Achievement of the abovementioned objectives necessitates the design of an experimental model. This model consists of two separated columns, which were filled with soil and other types of rocks. One setup column contains soil in dry condition (dry system); while the other was filled with soil material in wet conditions (wet system).
During its progress, crude oil penetration was recorded versus time by taking soil samples, whereas water samples were collected from the wet system. This was aimed to report a possible migration of hydrocarbons dissolved in water.
Results show that the penetration depth was more performed in wet system during early stages rather than in dry system. However, with time this progress becomes more developed in both systems. Based on observation, it is important to notify that the duration of this progress will last for long time in dry system. However, the overall penetration at final stage has been found significantly higher in the dry system. In addition, it was observed that during crude oil migration in dry system, chromatographic separation of crude oil components has occurred obviously.
The obtained results reveal that immediate treatment action has to be performed in both systems with particular attention to the wet system, owing to its high initial penetration rate.
Net Pay: What is it? What does it do? How do we quantify it? How do we use it?
Authors: Worthington Paul F. 
Published: December 2009

Abstract
A knowledge of Net Pay is important in the volumetric estimation of hydrocarbon Resources, a practice that underpins the value of the petroleum industry. Yet, there is no universal definition of Net Pay, there is no general acceptance of its role in integrated reservoir studies, there is no recognized method for evaluating it, and there are disparate views on how to make use of it. Partly for these reasons, Net-to-Gross Pay constitutes a major source of uncertainty in volumetric Resources estimates, second only to gross rock volume. With the aim of improving this unsatisfactory state of affairs, this presentation charts a critical path of Net-Pay understanding and application by exploding some of the unhelpful myths that abound within the industry and replacing them with a defensible rationale to guide the quantification of Net Pay (thickness). Central to this process is the identification of Net-Pay cut-offs, themselves the subject of much controversy over the years. The approach is data-driven, in that it uses what we know, and also fit-for-purpose, in that it takes account of reservoir conditions. The outcome is a sounder basis for incorporating Net Pay into volumetric estimates of ultimate recovery and thence petroleum Resources.
Pazflor, A World Technology First in Deep Offshore Development
Authors: Bon Louis 
Published: December 2009

Abstract
PAZFLOR is TOTAL's ongoing largest oil development, and was launched in December 2007. After the success of Girassol, Dalia and Rosa, PAZFLOR represents a major new step in the development of Block 17, offshore Angola as it will raise the installed production capacity of the Block to over 700,000 barrels per day.
PAZFLOR main technical challenge consists in producing two very different types of oils from four reservoirs, on a single FPSO. The heavy and viscous oil from the three Miocene reservoirs with low energy potential will be produced using the innovative technology of gas/liquid subsea separation.
The three subsea gas/liquid separation and pumping units on the sea bed will constitute a World Technology First for a development of this scale. After separation, the liquids will be pumped to the surface using hybrid pumps, specially designed and qualified for PAZFLOR. Such development scheme also allows a different strategy with respect to hydrates preservation based on depressurisation rather than live oil replacement.
The selection of a subsea gas/liquid separation concept raised new challenges, due to the relatively poor quality of the oil: a) the efficiency of the gas/liquid separation with viscous fluids, and b) the design of the subsea pumps which must be gas tolerant. Dedicated test programs were conducted in cooperation with oil industry partners and concluded in the qualification of a full scale hybrid pump as well as on separator internals.
Successful Second Stage Cementation of a Multilateral Junction, After Floating in the Casing
Authors: McWilliam Ian , Tandy Polly , McCaffrey Martin , Brooks Robert T. 
Published: December 2009

Abstract
This paper presents a practical solution for successfully floating in the casing and performing second stage cementing of a multilateral junction. The drilling and completion objectives required a successful cement job on the 9-5/8"x 10-3/4" casing that would: Isolate the reservoir at the 9-5/8" shoe.Isolate both production legs and provide a secondary barrier against future potential B annulus communication.Provide support for the 9-5/8" casing during exit window milling operations.
Due to the distance between the 9-5/8" shoe and the multilateral junction point it was identified early in the planning stages that the chances of success for a good single stage cement job over the whole interval, whilst maintaining ECDs below formation fracture gradient, was minimal.
With this in mind it was decided to perform the 9-5/8" cementing in 2 stages. The first stage was a conventional cement job with a total column length of 1500 ft. The next stage was conducted through a locking Port Collar with metal to metal (MTM) seals, situated at 4442ft MD. A successful cement job was achieved with a cement column of 1342ft, which was above the depth required to meet all of the objectives.
After displacement of the cement the operating tool was picked up to close and lock the Port Collar. A successful casing pressure test confirmed the Port Collar was closed. All objectives were met; a world first was achieved for this combined operation.
Is the Focus too Low on Issues That Have a Potential to Lead to a Major Incident?
Authors: Leistad Gunnar H. , Bradley Adam R. 
Published: December 2009

Abstract
The paper is based on the proposition that offshore workers are not sufficiently focused on issues that have the potential to lead to a major incident. On the contrary, for many years offshore workers have been motivated to focus on issues that could lead to personal injuries and lost time incidents. The most severe consequence of these personal injuries would be one fatality, as compared with the tens or hundreds of potential fatalities potentially associated with a major incident.
Significant manpower has been used both on and offshore to train personnel to protect themselves and others to avoid personal injuries. This often involves simple actions, that are easy to understand and with little cost to the company. By contrast, the resources used on prediction and avoidance of issues that could lead to major accidents are not sufficient at many levels in offshore organisations.
In order to reduce the risk of major accidents the required actions are often complex, sometimes expensive, and not easy for everybody to understand. The risk of major failure is limited, but the consequences are large if a failure should occur. As an example of this principle, records show that since 1967 fatalities due to major accidents have been 53% of the total number of fatalities on the Norwegian continental shelf. If helicopter accidents are included the percentage is 73 %.
These issues have been illustrated by a survey of several hundred personnel on offshore facilities. The results from the survey are clear and show that there is a need for change in the daily focus of the safety work on offshore installations.
Application of Reelwell Drilling Method in Offshore Drilling to Address Many Related Challenges
Authors: Rajabi M. Mir , Nergaard A. I. , Hole O. , Vestavik O. M. 
Published: December 2009

AbstractIn recent years, operators have been drilling wells in ever increasing water depths. Drilling wells in deepwaters is a daunting task due to both downhole drilling hazards and excessive floating rig packages. Traditionally, these challenging wells are drilled with a low-pressure 21" drilling riser stretching from mudline to surface. A high day-rate gigantic floating rigs with high weight, space, and tensioning requirement is essential to handle this huge and long LP marine riser in deepwaters.Today, the industry is contemplating drilling in water depths of 10,000 ft and beyond, while current equipment can hardly (or even not) take the industry into such depths without changes. The 21" marine drilling riser cannot be pushed much further by existing rigs, and even if the rig could support the riser length and weigh, the riser itself cannot withstand the stresses. Furthermore, if all of these problems are tackled, many downhole drilling challenges are yet to be answered.So, needs for change in current deepwater drilling technology seems to be necessary if the industry is to reach deep targets successfully in deepwaters. Our approach to this problem is changing drilling method; we intend to introduce a newly born drilling technology called Reelwell Drilling Method which is a riserless drilling method by nature and facilitates drilling at any water depth by smaller and less expansive floating rigs, with fewer difficulties.RDM is also promising in delivering closed circulation system which turns it into a competent tool for Managed Pressure Drilling. This feature of RDM can make a big difference in drilling operations in environments with narrow pressure margin which is the case in deepwaters, HPHT, and depleted reservoirs.
Control and Safety System (ESD, F&G and PCS) Obsolescence, a Practical Solution for System Migration Taking Account of Aging Facilities while Maintaining Safety Standards
Authors: Koh A. , Macleod A. , Gallacher M. , Lewis J. 
Published: December 2009

Abstract
This paper will describe, through an actual project experience, adopted methodology, which has been developed through close cooperation between Operator and system designer, to enable migration of obsolete Emergency Shutdown System, Fire &Gas Protection System and Process Control Systems to latest generation equipment, while avoiding production downtime, by live transfer and minimal uninterrupted production during migration process.
This type of system migration is taking place on Northern North Sea offshore facilities, and has proven to be cost effective in what normally would be an expensive transfer operation, during extended shutdown periods.
This system has been developed with the original equipment manufacturer to enable live transfers and have manageable downgraded safety during the transfer period. The benefits included no planned loss of production during the transfer of old to new systems, re-use of existing system footprints, wiring, marshalling and operating Philosophy.
System migration can be phased to suit other parallel planned works, and even re-phased if operational constraints dictate.
The paper will describe an actual live project which has utilised this technology and methodology, and has enabled the operator to manage major fabric maintenance and modifications in parallel with control system migration.
The paper will go further in describing and concluding the tangible benefits, success stories, lessons learnt, and safety records, on an actual live project.