bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data mining of enzymes using specific peptides
Authors: Weingart Uri , Lavi Yair , Horn David 
Published: December 2009

Abstract

Background
Predicting the function of a protein from its sequence is a long-standing challenge of bioinformatic research, typically addressed using either sequence-similarity or sequence-motifs. We employ the novel motif method that consists of Specific Peptides (SPs) that are unique to specific branches of the Enzyme Commission (EC) functional classification. We devise the Data Mining of Enzymes (DME) methodology that allows for searching SPs on arbitrary proteins, determining from its sequence whether a protein is an enzyme and what the enzyme's EC classification is.

Results
We extract novel SP sets from Swiss-Prot enzyme data. Using a training set of July 2006, and test sets of July 2008, we find that the predictive power of SPs, both for true-positives (enzymes) and true-negatives (non-enzymes), depends on the coverage length of all SP matches (the number of amino-acids matched on the protein sequence). DME is quite different from BLAST. Comparing the two on an enzyme test set of July 2008, we find that DME has lower recall. On the other hand, DME can provide predictions for proteins regarded by BLAST as having low homologies with known enzymes, thus supplying complementary information. We test our method on a set of proteins belonging to 10 bacteria, dated July 2008, establishing the usefulness of the coverage-length cutoff to determine true-negatives. Moreover, sifting through our predictions we find that some of them have been substantiated by Swiss-Prot annotations by July 2009. Finally we extract, for production purposes, a novel SP set trained on all Swiss-Prot enzymes as of July 2009. This new set increases considerably the recall of DME. The new SP set is being applied to three metagenomes: Sargasso Sea with over 1,000,000 proteins, producing predictions of over 220,000 enzymes, and two human gut metagenomes. The outcome of these analyses can be characterized by the enzymatic profile of the metagenomes, describing the relative numbers of enzymes observed for different EC categories.

Conclusions
Employing SPs for predicting enzymatic activity of proteins works well once one utilizes coverage-length criteria. In our analysis, L ≥ 7 has led to highly accurate results.
Activation of Retinoid X Receptor increases dopamine cell survival in models for Parkinson's disease
Authors: Friling Stina , Bergsland Maria , Kjellander Susanna 
Published: December 2009

AbstractBackgroundParkinson's disease (PD) is caused by degeneration of dopamine (DA) neurons in the ventral midbrain (vMB) and results in severely disturbed regulation of movement. The disease inflicts considerable suffering for the affected and their families. Today, the opportunities for pharmacological treatment are meager and new technologies are needed. Previous studies have indicated that activation of the nuclear receptor Retinoid X Receptor (RXR) provides trophic support for DA neurons. Detailed investigations of these neurotrophic effects have been hampered by the lack of readily available DA neuronsin vitro. The aim of this study was to further describe the potential neurotrophic actions of RXR ligands and, for this and future purposes, develop a suitablein vitro-platform using mouse embryonic stem cells (mESCs).ResultsWe studied the potential neurotrophic effects of the RXR ligand LG100268 (LG268) and the RXR-Nurr1 ligand XCT0139508 (XCT) in neuronal cultures derived from rat primary vMB and mESCs. RXR ligands protect DA neurons from stress, such as that induced by the PD-modeling toxin 6-hydroxy dopamine (6-OHDA) and hypoxia, but not from stress induced by oxidative hydrogen peroxide (H2O2) or the excitotoxic agent kainic acid (KA). The neurotrophic effect is selective for DA neurons. DA neurons from rat primary vMB and mESCs behaved similarly, but the mESC-derived cultures contained a much higher fraction of DA cells and thus provided more accessible experimental conditions.ConclusionsRXR ligands rescue DA neurons from degeneration caused by the PD simulating 6-OHDA as well as hypoxia. Thus, RXR is a novel promising target for PD research. mESC-derived DA cells provide a valid and accessiblein vitro-platform for studying PD inducing toxins and potential trophic agents.
ECRG4 is a candidate tumor suppressor gene frequently hypermethylated in colorectal carcinoma and glioma
Authors: Götze Silke , Feldhaus Valeska , Traska Thilo , Wolter Marietta , Reifenberger Guido , Tannapfel Andrea , Kuhnen Cornelius , Martin Dirk , Müller Oliver , Sievers Sonja 
Published: December 2009

Abstract

Background
Cancer cells display widespread changes in DNA methylation that may lead to genetic instability by global hypomethylation and aberrant silencing of tumor suppressor genes by focal hypermethylation. In turn, altered DNA methylation patterns have been used to identify putative tumor suppressor genes.

Methods
In a methylation screening approach, we identified ECRG4 as a differentially methylated gene. We analyzed different cancer cells for ECRG4 promoter methylation by COBRA and bisulfite sequencing. Gene expression analysis was carried out by semi-quantitative RT-PCR. The ECRG4 coding region was cloned and transfected into colorectal carcinoma cells. Cell growth was assessed by MTT and BrdU assays. ECRG4 localization was analyzed by fluorescence microscopy and Western blotting after transfection of an ECRG4-eGFP fusion gene.

Results
We found a high frequency of ECRG4 promoter methylation in various cancer cell lines. Remarkably, aberrant methylation of ECRG4 was also found in primary human tumor tissues, including samples from colorectal carcinoma and from malignant gliomas. ECRG4 hypermethylation associated strongly with transcriptional silencing and its expression could be re-activated in vitro by demethylating treatment with 5-aza-2'-deoxycytidine. Overexpression of ECRG4 in colorectal carcinoma cells led to a significant decrease in cell growth. In transfected cells, ECRG4 protein was detectable within the Golgi secretion machinery as well as in the culture medium.

Conclusions

ECRG4 is silenced via promoter hypermethylation in different types of human cancer cells. Its gene product may act as inhibitor of cell proliferation in colorectal carcinoma cells and may play a role as extracellular signaling molecule.
Phytalgic®, a food supplement, vs placebo in patients with osteoarthritis of the knee or hip: a randomised double-blind placebo-controlled clinical trial
Authors: Jacquet Alain , Girodet Pierre-Olivier , Pariente Antoine , Forest Karelle , Mallet Laurent , Moore Nicholas 
Published: December 2009

Abstract
Introduction
The medicinal treatment of osteoarthritis (OA) is mostly symptomatic to relieve pain and incapacity with analgesics and non-steroidal anti-inflammatory drugs (NSAIDs), drugs with well-known risks. Complementary medicines might reduce the symptoms of OA and decrease the need for NSAIDs. This study tested the effects of a food supplement, Phytalgic®, on pain and function in patients with osteoarthritis and their use of analgesic and NSAIDs.

Methods
A randomized double-blind parallel-groups clinical trial compared Phytalgic® (fish-oil, vitamin E, Urtica dioica) to a placebo for three months, in 81 patients with OA of the knee or hip using NSAIDs and/or analgesics regularly. The main outcome measures were use of NSAIDs (in Defined Daily Doses per day - DDD/day) or analgesics (in 500 mg paracetamol-equivalent tablets per week (PET/week) measured each month, and Western Ontario-McMaster University Osteo-Arthritis Index (WOMAC) function scales.

Results
After three months of treatment, the mean use of analgesics in the active arm (6.5 PET/week) vs. the placebo arm (16.5) was significantly different (P < 0.001) with a group mean difference of -10.0 (95% CI: -4.9 to -15.1). That of NSAIDs in the active arm (0.4 DDD/day) vs the placebo arm (1.0 DDD/day) was significantly different (P = 0.02) with a group mean difference of - 0.7 DDD/day (95% CI: -0.2 to -1.2). Mean WOMAC scores for pain, stiffness and function in the active arm (respectively 86.5, 41.4 and 301.6) vs the placebo arm (resp. 235.3, 96.3 and 746.5) were significantly different (P < 0.001) with group mean differences respectively of -148.8 (95% CI: -97.7 to -199.9), -54.9 (95% CI: -27.9 to -81.9) and -444.8 (95% CI: -269.1 to -620.4).

Conclusions
The food supplement tested appeared to decrease the need for analgesics and NSAIDs and improve the symptoms of osteoarthritis.

Trial registration
Clinicaltrials.gov NCT00666523.
Changes in Care and Support Needs Following Community-Based Intervention for Individuals With Acquired Brain Injury
Authors: Sloan Sue , Callaway Libby , Winkler Dianne , McKinley Kirsten , Ziino Carlo , Anson Katie 
Published: December 2009

AbstractObjective:To examine the care and support and participation outcomes for individuals with severe Acquired Brain Injury (ABI) provided with three consecutive years of Community Approach to Participation (CAP) intervention.Method:A case series study design was undertaken with a total of 43 participants from two private occupational therapy practices specialising in community-based, CAP rehabilitation for people with severe ABI. Data were collected at four time points: January 2004 (Baseline), January 2005 (T1), January 2006 (T2), and January 2007 (T3) and included rating on the Care and Needs Scale (CANS); number of hours of paid and gratuitous weekly support; FIM™ and Community Integration Questionnaire scores; and number of current life roles (as recorded on Part 1 of the Role Checklist). Participants were an average of 6.73 years post injury and were living in a range of community environments and residential facilities.Results:There was considerable change in participants' CANS rating across the intervention period, with statistically significant decreases occurring from Baseline to T1 and T1 to T2. Ninety-five per cent of participants received some level of weekly paid support throughout the intervention period, with the amount varying considerably. Paid care decreased by an average of 10.78 hours per week from 85.85 hours per week at Baseline to 75.06 at T3. Although not statistically significant, this equated to an average cost saving of AU$324.84 per participant per week by the end of CAP intervention. There was an overall mean reduction of 4.96 hours of gratuitous care per week per participant over the intervention period, which was statistically significant. Increases in functional independence, community integration, and role participation were also found. On the FIM™, statistically significant improvement occurred between Baseline and T1 and on the CIQ between Baseline and T1 and T1 and T2. Significant increase on the Role Checklist occurred between Baseline and T1 and between T2 and T3. The number of life roles in which participants engaged increased by an average of 1.65 roles by the end of the intervention period. A reduction in care and support needs (measured by the CANS) was significantly associated with: (1) a reduction in total care hours, (2) and an increase in functional independence on the FIM™, and (3) an increase in community integration on the CIQ.Conclusion:With a long term approach and contextualised intervention targeted at skill development in the areas that underpin personally valued participation, increased role performance and community integration can be achieved by people with severe ABI, even many years post injury. This increased capacity has been found to be associated with a reduction in care and support needs, including paid and gratuitous care hours, over time.
The Development of Novel Down-Hole Intervention Tools, a Change in Well Technology
Authors: Heijnen W. H. P. M. 
Published: December 2009

Abstract
Well Technology is traditionally dealing with drilling and completion as well as with well intervention and well integrity during the well life. The drilling and production engineers are the main players in this arena covering the full life cycle from design to abandonment of the well. The high-level governing factors in well design and well lifetime are the production forecast together with the PVT data and the geology based well trajectory. These three major data sets combined with historical drilling and production data is the basis for well design and its associated technology. The latter methodology was applied at oil prices, starting at 2 USD, mid of the last century to the 2008 price of 140 USD plus per barrel of oil.
The paradigm shift in well technology is driven by the disappearing vision that the hydrocarbon resources are unlimited. Well Technology is now not a function of executing a field development plan but becomes a tool to tap into older fields which were closed in or even abandoned at an oil price around 20 USD per barrel. This paper will demonstrate how Maersk Oil's Well Technology shifts the paradigm, that decline cannot be reversed in an offshore environment, where well intervention and well design became so expensive that, even at elevated oil prices, the wells became economically unattractive.
This paper will in detail describe a tool box, developed by Maersk Oil engineers. The tool box varies from shutting off water, which is conveyed by fractures between injectors and producers, seal off (stuck open) sliding side doors, overcome lubricator height limitations, to how to abandon the long horizontal section of a well which acts as a water highway resulting in an increasing water cut in several sound producers, leaving pockets of oil behind.
The goal of this effort by Maersk Oil is to increase the ultimate recovery and thereby increase the amount of hydrocarbons produced.
Analysis of Inflow Control Devices
Authors: Aadnoy Bernt S. , Hareland Geir 
Published: December 2009

Abstract
Inflow Control Devices (IDCs) were initially developed to avoid water coning problems in long horizontal wells. They have been used with success the past 15 years. There are, however, issues that needs to be resolved.
A pressure drop model of the ICD is presented herein. The physical model of the ICD consists of pressure drop equations from the reservoir, through the screen, through the flow conduit, through the ICD nozzle and into the production tubing, and, pressure drop through the lower completion system. Evaluation of the model shows that for current commercial tools, turbulent flow through the ICD dominates the pressure drop, leading to a density controlled flow. This is fortunate as density varies much less than viscosity over the production life of a field.
Due to the inherent non-linear nature of a production system, the pressure drop versus flow rate will vary with degree of depletion. An ICD may be optimal initially, but not when the reservoir pressure is depleted. This paper also presents a new designer IDC concept which maintains constant flow regardless of the degree of field depletion. It is based on a hydraulic feedback principle, and ensures controlled flow throughout the life of the oil field.
A Novel Diverting Acid Stimulation Treatment Technique for Carbonate Reservoirs in China
Authors: Zhou Fujian , Liu Yuzhang , Zhang Shaoli , Li Xiangdong , Xiong Chunming , Yang Xianyou , Liu Xiongfei , Shi Yang , Li Xiuhui , Zhang Fuxiang , Shi Hongxiang , Shen Jianxin , Yuan Xuefang 
Published: December 2009

Abstract
Carbonate reservoirs are wildly distributed in China, and the reserve is very large. Bulk of big and middle oil fields were discovered in Sichuan Basin, BoHai Gulf Basin, Ordos Basin, Tarim Basin and so on. The cumulative demonstrated geological oil reserve reaches 1.62 billion ton, and the gas reserve is 1.42 trillion.
Formations of the newly discovered carbonate oil/gas fields have the following features: deep buried (&gt;5000m); serious heterogeneity; full of pores, caves and cracks; long well section. So, it's difficult for acid stimulation treatment. And the treatment effect using traditional polymer-based acid fluid system is not very good.
Based on surfactant, this paper develops a novel diverting acid stimulation treatment for carbonate formation. This kind of self-diverting acid system contains a special visco-elastic surfactant. The viscosity of fresh acid is very low. However, when it enters into the pores or cracks of carbonate formation and reacts with rocks, the viscosity will increase rapidly as the concentration of acid decreases, because the surfactant molecules will aggregate to baculate micelle along with the consuming of acid. The structure will increase the viscosity of system, and prevent the fluid from leaking off into wormholes and cracks which have been etched. The micelle structure of surfactant can be used as a diverting agent in the process of acid treatment, and can also be used to control the fluid leaking off in acid fracturing stimulation. This technique has been used in 5 carbonate oil fields on land in China. 38 wells were acid fractured and 25 wells were treated. The effect is very well.
Research on the Application of Environment Acceptable Modified Natural Macromolecule Based Drilling Fluid
Authors: He Xiaoqing , Zheng Lihui 
Published: December 2009

Abstract
Environment acceptable modified natural macromolecule based drilling fluid is mainly composed of shale inhibitor agent IND30, fluid loss control agent NAT20, bloomless white asphalt NFA-25 and dry powder of polyalcohols PGCS-1, which are biodegradable and environment acceptable. Results of rheological property tests of based mud, IND30 mud, NAT20 mud, NFA-25 mud and environment acceptable modified natural macromolecule based drilling fluid provide us with the best of dosage of each component and confirm that the drilling fluid system meets requirements of petroleum drilling. Other experiments indicate that environment acceptable modified natural macromolecule based drilling fluid has five merits. Firstly, it can bear a high temperature of 140□. Secondly, it has very good anti-contamination ability. Thirdly, inhibit ability of the system is very strong. Fourthly, it can control formation damage. Last but not least, both of the drilling fluid and the basic components are environment acceptable. Field applications of environment acceptable modified natural macromolecule based drilling fluid indicate that not only did the drilling fluid solve a series of complex problems it did not disturb other works such as well logging, casing and production. What's more, it is a kind of environment acceptable drilling fluid that can be used both on dryland operation and in marine drilling for different well types.
Geomechanical Modeling Integrating Subseismic Faults
Authors: Fouladvand Arash , Baroni Axelle , Cangémi Laurent , Deflandre Jean-Pierre , Bernard Pascal 
Published: December 2009

Abstract
Injection of gas in a saline aquifer reservoir modifies fluid saturation and pore pressure, and consequently changes effective stresses into but also around the reservoir: the mechanical equilibrium of the geological structure is affected. Stress variations depend on site characteristics: rock properties, fracturing, existing faults, fracture networks, …, and on the exploitation activity: injected volumes, exploitation rates, reservoir pressure…. The effective stress modifications on natural fractures and faults, can be monitored by measure of surface displacement, measure of pressure changes in overburden, and record of induced seismic activity…
The goal of our work is to develop techniques to exploit such information to calibrate and constrain coupled hydro-mechanical modeling. The mechanical phenomena have to be precisely identified, quantified and eventually associated with specific major discontinuities like faults. The way, investigated in this paper, is to validate and constrain geomechanical modeling, by exploiting interpreted results from passive seismic data. The scope of the paper is to present our approach and to discuss preliminary results. In this first step of the methodology, we focus on the integration of a subseismic fault in a 3D earth model, assuming simple mechanical law and no geochemical phenomena. Coupled hydro-mechanical modeling is achieved using a commercial software.
Deepwater Development Production and Export Options
Authors: Hartell W. D. , Greenwald J. R. 
Published: December 2009

Abstract
Deepwater discovery development activities can be located in remote locations far from existing infrastructure like other facilities and pipelines. Major deepwater developments typically consist of subsea wells tied back to floating surface production facilities such as semisubmersibles, SPARs, TLPs, or FPSOs. The choice of production and export options for liquid hydrocarbons and gas is important and is affected by the distance to other infrastructure, the waterdepths involved, geohazards, reservoir fluid characteristics, production rates, and reserves. Another important factor is whether adjacent undeveloped discoveries exist to potentially share facilities and export options. Conventional production and export options involve oil and gas production facilities and pipelines with shipping pumps or compression as required to reach the closest transmission pipelines or onshore markets. In SE Asia, deepwater developments are often located in remote locations hundreds of kilometers from markets onshore, so the development production and export options must be wider in order to obtain economic and timely choices. In addition to pipeline options, liquid hydrocarbons can be stored offshore in the floating production facility or in an adjacent FSO, then offloaded and shuttled to markets by tankers. Gas production and export options can include long distance gas pipelines, Compressed Natural Gas (CNG) vessels, purity product (butane and propane) liquefied petroleum gas (LPG) FPSOs, methanol/DME FPSOs, and floating LNG FPSOs. This paper will show some of the technical concepts, risks, costs, and economics involved in making these choices.
Wellbore Stability Study: Lessons and Learnings From a Tectonically Active Field
Authors: Han Gang , Henson Jo , Timms Andrew , Aziz Ilyah Abdul 
Published: December 2009

Abstract
Shales account for 75% of the formations drilled worldwide, while drilling troubles associated with shale represents 90% of wellbore stability problems reported. In this paper, a traditional wellbore stability study has been implemented at an onshore gas field in a tectonically active region. Despite following the program however, the drilling experienced significant challenges, particularly in the shales where the sonic logs have shown high velocity and therefore high rock strength.
To investigate the root cause, several mechanisms for the wellbore instabilities have been investigated, such as overpressure, weak bedding plane, chemical activity, insufficient mud weight, and fractured shales. The cavings collected and preserved from the wells, as big as several inches in size, have undergone XRD, SEM, thin-section, and strength tests. While most mechanisms have been ruled out, focus has turned to the fractured shales. With the evidence from the lab and collaborated with drilling experience in the field, it has found the troublesome shale formation has been extensively fractured during past and present tectonic movements. The presence of the fissure network becomes so significant that it dominates rock mechanical behavior and wellbore stability. More interestingly, it seems the sonic logs have overlooked the existence of fissures and still shown the response from a typical strong rock. Based on those findings, modified drilling strategies have been suggested and implemented in the region.
The field case presents a new challenge to the log-based wellbore stability interpretation routinely implemented in current drilling society. Being open-minded, closely monitoring and testing cavings, and updating the model with drilling experience may be as important as the model development itself.