bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of matrix metalloproteinase-2 (mmp-2) transcriptional repression by progesterone in jar choriocarcinoma cells
Authors: Goldman Shlomit , Lovett David H , Shalev Eliezer 
Published: May 2009

Abstract

Background
Although the MMP-2 promoter lacks a canonical progesterone response element (PRE), the hormone inhibits MMP-2 expression and is part of treatment protocols in gynecological invasive pathologies, including endometriosis and endometrial hyperplasia. This study aimed to explore the mechanism by which progesterone inhibits MMP-2 expression.

Methods
The effect of progesterone on MMP-2 expression in the JAR human choriocarcinoma cell line was analyzed by gelatin zymography. MMP-2 transcript expression was studied using Northern blot and semi-quantitative RT-PCR. Rat promoter deletion analysis, electrophoretic mobility shift and chromatin immuno-precipitation assays were performed in order to locate the DNA binding site and the transcription factors involved in MMP-2 regulation.

Results
Progesterone significantly decreased secretion of pro-MMP-2 and MMP-2 transcript expression level in a dose-dependent manner. Progesterone (1 microM) significantly decreased both human and rat MMP-2 promoter activity (80.1% +/- 0.3 and 81.3% +/- 0.23, respectively). Progesterone acts through the SP1 family transcription factors-binding site, located between -1433 and -1342 bp region from the transcriptional start site of the rat MMP-2 promoter, which are present in the orthologous human MMP-2 promoter. Progesterone receptor (PR), SP2, SP3 and SP4 proteins are constitutively bound to this consensus sequence.

Conclusion
Progesterone reducesPR and SP4 binding to the MMP-2 promoter, thereby suppressing transcription. Progesterone also promotes SP4 degradation. These novel mechanisms of MMP-2 regulation by progesterone provide the biological rationale for the use of progesterone in clinical settings associated with increased MMP-2 expression.
Network analysis of human glaucomatous optic nerve head astrocytes
Authors: Nikolskaya Tatiana , Nikolsky Yuri , Serebryiskaya Tatiana , Zvereva Svetlana , Sviridov Eugene , Dezso Zoltan , Rahkmatulin Eugene , Brennan Richard J , Yankovsky Nick , Bhattacharya Sanjoy K , Agapova Olga , Hernandez M Rosario , Shestopalov Valery I 
Published: May 2009

AbstractBackgroundAstrocyte activation is a characteristic response to injury in the central nervous system, and can be either neurotoxic or neuroprotective, while the regulation of both roles remains elusive.MethodsTo decipher the regulatory elements controlling astrocyte-mediated neurotoxicity in glaucoma, we conducted a systems-level functional analysis of gene expression, proteomic and genetic data associated with reactive optic nerve head astrocytes (ONHAs).ResultsOur reconstruction of the molecular interactions affected by glaucoma revealed multi-domain biological networks controlling activation of ONHAs at the level of intercellular stimuli, intracellular signaling and core effectors. The analysis revealed that synergistic action of the transcription factors AP-1, vitamin D receptor and Nuclear Factor-kappaB in cross-activation of multiple pathways, including inflammatory cytokines, complement, clusterin, ephrins, and multiple metabolic pathways. We found that the products of over two thirds of genes linked to glaucoma by genetic analysis can be functionally interconnected into one epistatic network via experimentally-validated interactions. Finally, we built and analyzed an integrative disease pathology network from a combined set of genes revealed in genetic studies, genes differentially expressed in glaucoma and closely connected genes/proteins in the interactome.ConclusionOur results suggest several key biological network modules that are involved in regulating neurotoxicity of reactive astrocytes in glaucoma, and comprise potential targets for cell-based therapy.
On Evaluating Information Revelation Policies in Procurement Auctions: A Markov Decision Process Approach
Authors: Greenwald Amy , Kannan Karthik , Krishnan Ramayya 
Published: May 2009

Each market session in a reverse electronic marketplace features a procurer and many suppliers. An important attribute of a market session chosen by the procurer is its information revelation policy. The revelation policy determines the information (such as the number of competitors, the winning bids, etc.) that will be revealed to participating suppliers at the conclusion of each market session. Suppliers participating in multiple market sessions use strategic bidding and fake their own cost structure to obtain information revealed at the end of each market session. The information helps to reduce two types of uncertainties encountered in future market sessions, namely, their opponents' cost structure and an estimate of the number of their competitors. Whereas the first type of uncertainty is present in physical and e-marketplaces, the second type of uncertainty naturally arises in IT-enabled marketplaces. Through their effect on the uncertainty faced by suppliers, information revelation policies influence the bidding behavior of suppliers which, in turn, determines the expected price paid by the procurer. Therefore, the choice of information revelation policy has important consequences for the procurer. This paper develops a partially observable Markov decision process model of supplier bidding behavior and uses a multiagent e-marketplace simulation to analyze the effect that two commonly used information revelation policies—complete information policy and incomplete information policy—have on the expected price paid by the procurer. We find that the expected price under the complete information policy is lower than that under the incomplete information policy. The integration of ideas from the multiagents literature, the machine-learning literature, and the economics literature to develop a method to evaluate information revelation policies in e-marketplaces is a novel feature of this paper.
Glycosylation- and phosphorylation-dependent intracellular transport of lysosomal hydrolases
Authors: Pohl Sandra , Marschner Katrin , Storch Stephan , Braulke Thomas 
Published: May 2009

Abstract
Lysosomes contain more than 50 soluble hydrolases that are targeted to lysosomes in a mannose 6-phosphate (Man6P)-dependent manner. The phosphorylation of man- nose residues on high mannose-type oligosaccharides of newly synthesized lysosomal enzymes is catalyzed by two multimeric enzymes, GlcNAc-1-phosphotransferase and GlcNAc-1-phosphodiester-α-N-acetylglucosaminidase, allowing the binding to two distinct Man6P receptors in the Golgi apparatus. Inherited defects in the GlcNAc-1-phosphotransferase complex result in missorting and cellular loss of lysosomal enzymes, and the subsequent lysosomal dysfunction causes the lysosomal storage disorders mucolipidosis types II and III. Biosynthetic studies and the availability of Man6P receptor-deficient mouse models have provided new insights into the structural requirements for preferential binding of subsets of lysosomal enzymes to Man6P receptors as well as the identification of alternative targeting pathways.
Brain development needs sugar: the role of polysialic acid in controlling NCAM functions
Authors: Mühlenhoff Martina , Oltmann-Norden Imke , Weinhold Birgit , Hildebrandt Herbert , Gerardy-Schahn Rita 
Published: May 2009

Abstract
Polysialic acid (polySia) is a major regulator of cell-cell interactions in the developing nervous system and a key factor in maintaining neural plasticity. As a polyanionic molecule with high water binding capacity, polySia increases the intercellular space and creates conditions that are permissive for cellular plasticity. While the prevailing model highlights polySia as a non-specific regulator of cell-cell contacts, this review concentrates on recent studies in knockout mice indicating that a crucial function of polySia resides in controlling interactions mediated by its predominant protein carrier, the neural cell adhesion molecule NCAM.
Pore Network Modeling of Saudi Aramco Rocks: A Comparative Study
Authors: Suicmez Sander , Funk James , Cinar Yildiray , Knackstedt Mark 
Published: May 2009

Abstract
3D imaging and pore network modeling is a potential breakthrough reservoir engineering tool that allows the prediction of petrophysical properties of a reservoir from small sample sizes not suited for laboratory testing (e.g, drill cuttings, sidewall core or damaged core). If a reasonable sample size (5mm-1cm) can be obtained, micro-CT scanning can be undertaken at resolutions of 2-4 microns. Using advanced image analysis techniques the pore structure and an equivalent pore network model of the rock can be extracted. This model retains key properties of the pore space of the rock sample in 3D. We then conduct flow simulations to predict key petrophysical properties such as porosity, permeability, formation factor, capillary pressure and resistivity.
In this work, a number of Saudi Aramco core plugs were chosen. A series of experimental measurements were also undertaken on the plugs. Smaller pieces of rocks (8mm diameter) were cut from the plugs and CT scanned at 4 microns resolution. Corresponding topologically equivalent networks were then constructed. Petrophysical properties were analyzed directly on the images and the pore network models.
The numerical results are compared with experimental counterparts. While porosity and resistivity data is in agreement, the predictions of capillary pressure and permeability can be significantly different. Reasons for the differences are explored. A key observation is that the modeling and experimental data may not match when comparing measurements at varying length scales — core scale heterogeneity should be accounted for. The need for incorporation of spatial information at varying length scales is discussed. An example of data integration on multiple scales is given. Necessary improvements to pore scale modeling techniques are discussed to address improved reliability in carbonate samples.
Innovative Progressive Cavity Pump Design for Brown Fields in South of Oman
Authors: Al Shukri Mahmoud Said , Abou-ElKhair Abdel-Monaim 
Published: May 2009

Abstract
Most of the fields located in south of Oman are mature, sub-hydrostatic, producing viscous, and sandy oil. This has raised the need to deploy different artificial lifting mechanisms. Progressive Cavity Pump (PCP) is one of the lifting methods in use and unlike other lifting methods it has proved its capability to produce viscous oil and tolerates more with sand production. Besides, PCPs can be run deeper in deviated wells for better drawdown. Currently in South of Oman we have more than 400 PCP wells and by the end of 2013 the PCP population is expected to reach 1000 units.
South of Oman fields are characterised by being geologically complex and extremely heterogeneous due to existence of faults and fractures. Water flooding project was started to enhance oil recovery in those fields. To evaluate the success of water flood performance the wells require well intervention work such as coil tubing and wireline for well bore cleaning, well logging, selective water shut-off, re-perforation, and well stimulation. As completions needed to be removed, therefore in the past work could never be performed concurrently with production. The inability to evaluate water flood performance caused remedial work to become ineffective. The need for surveillance and an intervention string for the PCP drive completions were identified.
This paper presents the ideas developed to make concurrent production and well-intervention work with PCP completions is possible without interrupting production, including well kill. In this process, we looked at all aspects of PCP completions (Surface/ Subsurface) from running the completion to its maintenance. The design needed to overcome serious engineering challenges such as extremely tight surface tolerances with restricted geometries. The new design consists of an eccentric PCP drive head at surface, a downhole dual receptacle style torque anchor and housing for two parallel tubing strings. The innovative design was done locally by a multi-disciplinary team of PDO and local service companies. There was no appropriate solution available in the international market. The technology has been proven reliable on 10 wells and is now an integral part of a standard well design with 58 wells in planning as part of the Program Build for the year 2009.
Open Hole Sidetrack: A Transformation in Drilling Dual Lateral Khuff Reservoir Gas Wells in the Kingdom of Saudi Arabia
Authors: Nawaz Khalid , Al-Faraj Omar A. , Ajmi Naser A. , Awan A. H. , Verma Jaywant , Ganda Sukesh 
Published: May 2009

Abstract
This paper describes application of openhole sidetrack (OHSDTR) technique to drill deep gas multilateral horizontal wells in Saudi Arabia. The drawbacks of earlier whipstock exits were studied and an alternate technique was proposed and implemented.
The typical approach to drilling Khuff dual laterals was to drill the lower lateral and then set whipstock, and cut a window in the base Khuff-B and drill the upper lateral. Various problems observed using this technique were: Problem setting whipstock.Premature setting while running in holeProblem cutting the window. Mill twist offs leading to a long fishing operation; in some cases setting another whipstock and cutting another window.Milling the top of the whipstock while cutting the window leading to a severe problem in retrieving the whipstock.
Whipstock from different companies were tried, however, we could not get rid of multiple failures while milling and retrieving the whipstock. Even with modifications, a new whipstock system was tried in which milling was done in two parts; a first run with the milling machine to mill only the casing, and a second run with different mills to cut the window through to formation, but problems continued. Saudi Aramco and Schlumberger D&M came up with the idea of drilling dual laterals using an OHSDTR technique to avoid complication due to whipstock failure. Well HRDH-XYZ was the first successful dual lateral horizontal Khuff-C gas producer drilled with the open hole sidetrack technique, in a record time of 98.8 days against the 165 days planned, the technique saved $975,000 and two weeks of rig time.
This was a step change in drilling practice, to drill dual laterals saving considerable rig days to Saudi Aramco, and removing the time consuming whipstock operation to the extent of losing the well, due to unsuccessful whipstock retrieval. This technique brought a transformation in the way dual lateral wells were drilled in deep gas drilling in Saudi Arabia, later on similar technique was applied in drilling dual laterals in Khuff-B reservoir as well. Since the introduction of this technique on well HRDH-XYZ, 50 wells have been drilled successfully saving (approximately) 735 days to Saudi Aramco. This paper further details challenges; lesson learnt and success story about introduction of Open Hole Sidetrack in deep Gas drilling.
Evolution of Roller Cone Bit Design to Improve Performance in Carbonates
Authors: Senger Jim , AlRamahi Basil , Taha Islam Ahmed , Waheed Tamer 
Published: May 2009

Abstract
In the long tophole section of vertical wells in Abu Dhabi, formation challenges historically have caused roller cone bits to suffer impact and fatigue damage to the gage and cutting structure. As a result, at least two bits have been required to drill the 4000-foot section, which is composed mainly of carbonates with a thick anhydrite section.
In addition to high impact damage, the carbonates also generate high friction on bits that exacerbates thermal degradation to the cutting materials, launching a series of consequences that inevitably result in premature bit failure.
In addition, lost circulation is very common in this application, so determining optimum operating parameters is more challenging.
Given these conditions, the operator's stated objective was to drill the 17-1/2-in. interval "shoe-to-shoe" in a single bit run, optimizing penetration rate without compromising hole quality or cleaning efficiency.
Revitalization of Old Asset Oil Fields into I-Fields
Authors: Al-Khamis Mohammed N. , Zorbalas Konstantin I. , Al-Matouq Hassan M. , Almahamed Saleh M. 
Published: May 2009

AbstractRecent evolution in oil field technologies has made a great revolution in the oil and gas industry all over the world leading to the emerging development of intelligent fields (I-Fields)1,2,3,4. The integration of I-Field technologies whether downhole or at surface, coupled with communication networks along with sophisticated simulation and monitoring applications has lead to significant advancements not only in monitoring and control capabilities, but rather also in decision making processes5. Therefore, the overall system upgrade has resulted in an enhancement of the field surveillance, which will lead to higher levels of oil production in these assets as a consequence of Saudi Aramco's development strategy for these fields.A comprehensive redevelopment and I-Field transformation of three elderly remote onshore oil fields in Saudi Arabia has taken place where extensive drilling and workover programs have been reinitiated to complete both oil production and peripheral water injection wells, and equip them with the latest downhole production technologies. The project has also involved construction of new oil and gas processing and water injection facilities, which are being linked with the wells via a state of the art fiber optic communication network for controlling both subsurface and surface parameters and data surveillance in real-time. Further integration of I-Field components, such as Permanent Downhole Monitoring Systems (PDHMS), Smart Well Systems, Multiphase Flow Meters (MPFM), Single Phase Flow Meters, pressure and temperature sensors with specially tailored monitoring, and simulation software has facilitated the development and implementation of optimized production and injection strategies.This paper will discuss the development strategy of the three fields sharing the lessons learned from this project. Moreover, examples, such as well performance monitoring and validation, crude blend assessment and assurance and reservoir pressure mapping, which are all being performed in real-time will be presented. In addition, this paper will also illustrate how the integration of I-Field components has effectively helped in optimizing the production from a portfolio of developed reservoirs.
Seismic Inversion Workflow for Sand Stringers Characterization in Offshore Saudi Arabia
Authors: Tonellot Thierry , Burnstad Roy , Fitzmaurice John 
Published: May 2009

Abstract
We describe an optimized seismic inversion workflow for an improved characterization of mid-Cretaceous sand stringers in the northern offshore area of Saudi Arabia. The first step of the workflow consists of analyzing the impact on inversion results for critical processing steps such as random and coherent noise reduction or prestack time migration. In a second step, a new "inversion friendly" processing sequence, including a patented in-house data reconstruction technique, is then defined in order to mitigate noise while preserving the recorded seismic amplitude variation with offset. The last step of the workflow consists of inverting the processed seismic dataset for Vp/Vs, and interpreting the results in terms of sand stringer probability. This workflow is illustrated on a dataset covering an area where one extended reach lateral is to be drilled.
Prediction of Sand Body Trend Based on Stratigraphic Dip Pattern from Microresistivity Images in Permian Sandstone Reservoir, Oman
Authors: Wang Da-Li , Al-Busaidi Salim , Lee Desmond N.H. 
Published: May 2009

Abstract
Stratigraphic dip patterns from high-resolution microresistivity images can indicate the paleocurrent direction of sediments transported by water and the associated depositional environment such as sand-filled stream channel and flood plain. This information was successfully used in the prediction of sand body orientation trends of an oil field in Oman. The interpretation and analysis of the stratigraphic dip patterns from the images complemented conventional seismic data and well logs in the sand body characterization. The sand body orientation trends were predicted from the oriented stratigraphic dip patterns of the sedimentary sandstone beddings observed on the images and the depositional energy analysis through the dip magnitudes of the beddings on the images, and the associated depositional environments were reconstructed using the sedimentary structures and textures on the images. The prediction and analysis of the sand body orientation trend finally provided the classification of the sand bodies that correspond to the different reservoir parameters for further field development.
The main contributor to hydrocarbon reserves and production in the field of North Oman is the sandstone reservoir of the Permian formation, which was dominantly formed in the fluvial and floodplain depositional environment. The uncertain sediment supply direction and complicated faults or sedimentologically confined compartments make reservoir characterization and modeling in the oil field very difficult, if not impossible, with only the traditional seismic data and well logs. In fact, the current field development demonstrates that in the oil field, the Permian sandstone reservoir contains structural traps and stratigraphic traps. Detailed sand body orientation trend is very important in further field development, but almost impossible using only conventional well logs and seismic data.
For the prediction of sand body trend in the case studies, firstly, the interpretation of the stratigraphic dip patterns was performed on each of the 30 wells, and secondly, the correlation of oriented sand bodies was analyzed within the multiwell scale of the field. Finally, from the multiwell correlation of oriented sand bodies, the sand body orientation trend was established. An improved understanding of sand body characterization and modeling in the field was obtained to reduce the risk of drilling unsuccessful wells.
Wettability Studies at the Pore Level of Saudi Aramco Reservoirs
Authors: Al-Shafei Mansour A. , Okasha Taha M. 
Published: May 2009

Abstract
The wettability of rocks is of critical importance in understanding reservoir dynamics. Several studies of wettability evaluation on Saudi Aramco reservoir rocks were reported, but to our knowledge, none of them have attempted to study wettability on the pore scale level. In this study wettability evaluation of carbonate rock samples of Saudi Aramco reservoirs were investigated using environmental scanning electron microscope (ESEM). The data obtained gives access to the distribution of oil and water in relation with mineral interface which can not be observed by normal techniques. It also improves the understanding of rock/fluid interaction.
In this study preserved rock samples from two distinct reservoirs (Arab-C and Shu'aiba) were used. The mineralogical analysis showed that the predominant minerals were calcite and dolomite in both samples. Determination of wettability using ESEM method is very cost effective. It is unlike other traditional methods. It doesn't use any chemical or even generate by-products; it is not time-consuming and provides better quality data at much lower cost.