bluuebunny/crossref_metadata_2025_split huggingface dataset:
A TargetedIn VivoRNAi Screen Reveals Deubiquitinases as New Regulators of Notch Signaling
Authors: Zhang Junzheng , Liu Min , Su Ying , Du Juan , Zhu Alan Jian 
Published: December 2012

AbstractNotch signaling is highly conserved in all metazoan animals and plays critical roles in cell fate specification, cell proliferation, apoptosis, and stem cell maintenance. Although core components of the Notch signaling cascade have been identified, many gaps in the understanding of the Notch signaling pathway remain to be filled. One form of posttranslational regulation, which is controlled by the ubiquitin-proteasome system, is known to modulate Notch signaling. The ubiquitination pathway is a highly coordinated process in which the ubiquitin moiety is either conjugated to or removed from target proteins by opposing E3 ubiquitin ligases and deubiquitinases (DUBs). Several E3 ubiquitin ligases have been implicated in ubiquitin conjugation to the receptors and the ligands of the Notch signaling cascade. In contrast, little is known about a direct role of DUBs in Notch signaling in vivo. Here, we report an in vivo RNA interference screen in Drosophila melanogaster targeting all 45 DUBs that we annotated in the fly genome. We show that at least four DUBs function specifically in the formation of the fly wing margin and/or the specification of the scutellar sensory organ precursors, two processes that are strictly dependent on the balanced Notch signaling activity. Furthermore, we provide genetic evidence suggesting that these DUBs are necessary to positively modulate Notch signaling activity. Our study reveals a conserved molecular mechanism by which protein deubiquitination process contributes to the complex posttranslational regulation of Notch signaling in vivo.
Multiple Mechanisms Contribute to Lateral Transfer of an Organophosphate Degradation (opd) Island in Sphingobium fuliginis ATCC 27551
Authors: Pandeeti Emmanuel Vijay Paul , Longkumer Toshisangba , Chakka Deviprasanna , Muthyala Venkateswar Reddy , Parthasarathy Sunil , Madugundu Anil Kumar , Ghanta Sujana , Medipally Srikanth Reddy , Pantula Surat Chameli , Yekkala Harshita , Siddavattam Dayananda 
Published: December 2012

Abstract
The complete sequence of pPDL2 (37,317 bp), an indigenous plasmid of Sphingobium fuliginis ATCC 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attP, typically seen in integrative mobilizable elements (IME). In agreement with this sequence information, site-specific recombination was observed between pPDL2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attB site at the 3′ end of the seryl tRNA gene of Sphingobium japonicum. The opd gene cluster on pPDL2 was found to be part of an active catabolic transposon with mobile elements y4qE and Tn3 at its flanking ends. Besides the previously reported opd cluster, this transposon contains genes coding for protocatechuate dioxygenase and for two transport proteins from the major facilitator family that are predicted to be involved in transport and metabolism of aromatic compounds. A pPDL2 derivative, pPDL2-K, was horizontally transferred into Escherichia coli and Acinetobacter strains, suggesting that the oriT identified in pPDL2 is functional. A well-defined replicative origin (oriV), repA was identified along with a plasmid addiction module relB/relE that would support stable maintenance of pPDL2 in Sphingobium fuliginis ATCC 27551. However, if pPDL2 is laterally transferred into hosts that do not support its replication, the opd cluster appears to integrate into the host chromosome, either through transposition or through site-specific integration. The data presented in this study help to explain the existence of identical opd genes among soil bacteria.
In VivoRegulation of E2F1 by Polycomb Group Genes inDrosophila
Authors: Ji Jun-Yuan , Miles Wayne O , Korenjak Michael , Zheng Yani , Dyson Nicholas J 
Published: December 2012

AbstractThe E2F transcription factors are important regulators of the cell cycle whose function is commonly misregulated in cancer. To identify novel regulators of E2F1 activity in vivo, we used Drosophila to conduct genetic screens. For this, we generated transgenic lines that allow the tissue-specific depletion of dE2F1 by RNAi. Expression of these transgenes using Gal4 drivers in the eyes and wings generated reliable and modifiable phenotypes. We then conducted genetic screens testing the capacity of Exelixis deficiencies to modify these E2F1-RNAi phenotypes. From these screens, we identified mutant alleles of Suppressor of zeste 2 [Su(z)2] and multiple Polycomb group genes as strong suppressors of the E2F1-RNA interference phenotypes. In validation of our genetic data, we find that depleting Su(z)2 in cultured Drosophila cells restores the cell-proliferation defects caused by reduction of dE2F1 by elevating the level of dE2f1. Furthermore, analyses of methylation status of histone H3 lysine 27 (H3K27me) from the published modENCODE data sets suggest that the genomic regions harboring dE2f1 gene and certain dE2f1 target genes display H3K27me during development and in several Drosophila cell lines. These in vivo observations suggest that the Polycomb group may regulate cell proliferation by repressing the transcription of dE2f1 and certain dE2F1 target genes. This mechanism may play an important role in coordinating cellular differentiation and proliferation during Drosophila development.
Evidence for Population-Specific Positive Selection on Immune Genes ofAnopheles gambiae
Authors: Crawford Jacob E , Bischoff Emmanuel , Garnier Thierry , Gneme Awa , Eiglmeier Karin , Holm Inge , Riehle Michelle M , Guelbeogo Wamdaogo M , Sagnon N’Fale , Lazzaro Brian P , Vernick Kenneth D 
Published: December 2012

AbstractHost-pathogen interactions can be powerful drivers of adaptive evolution, shaping the patterns of molecular variation at the genes involved. In this study, we sequenced alleles from 28 immune-related loci in wild samples of multiple genetic subpopulations of the African malaria mosquito Anopheles gambiae, obtaining unprecedented sample sizes and providing the first opportunity to contrast patterns of molecular evolution at immune-related loci in the recently discovered GOUNDRY population to those of the indoor-resting M and S molecular forms. In contrast to previous studies that focused on immune genes identified in laboratory studies, we centered our analysis on genes that fall within a quantitative trait locus associated with resistance to Plasmodium falciparum in natural populations of A. gambiae. Analyses of haplotypic and genetic diversity at these 28 loci revealed striking differences among populations in levels of genetic diversity and allele frequencies in coding sequence. Putative signals of positive selection were identified at 11 loci, but only one was shared by two subgroups of A. gambiae. Striking patterns of linkage disequilibrium were observed at several loci. We discuss these results with respect to ecological differences among these strata as well as potential implications for disease transmission.
A Pilot Study of the Impact of Housing First–Supported Housing for Intensive Users of Medical Hospitalization and Sobering Services
Authors: Srebnik Debra , Connor Tara , Sylla Laurie 
Published: December 2012

Objectives. We examined changes in service use in a Housing First (HF) pilot program for adults who were homeless with medical illnesses and high prior acute-care use relative to a similar comparison group. Methods. We used a 1-year pre–post comparison group design. The 29 participants and 31 comparison group members were adults who were homeless with inpatient claims of at least $10 000 or at least 60 sobering “sleep off” center contacts in the prior year. Results. Participants showed a significantly greater reduction in emergency department and sobering center use relative to the comparison group. At a trend level, participants had greater reductions in hospital admissions and jail bookings. Reductions in estimated costs for participants and comparison group members were $62 504 and $25 925 per person per year—a difference of $36 579, far outweighing program costs of $18 600 per person per year. Conclusions. HF participants showed striking reductions in acute-care use relative to the comparison group, demonstrating that HF can be a successful model for people with complex medical conditions and high prior acute-care use. Despite notable methodological limitations, these findings could be used to inform a larger multisite study that would establish greater generalizability.
Laboratory Investigation of Dynamic Growth of Asphaltene Deposition and Formation Damage on Sandstone Cores
Authors: Ali Mohammad A. , Kholosy S. M. , Al-Haddad A. A 
Published: December 2012

Abstract
A live oil sample was subjected to a solid detection system (SDS) to measure asphaltene onset point (AOP) at 3850 psi, and asphaltene content of 1.3%. A high-resolution digital camera was used to measure asphaltene particle size distribution. The result showed that asphaltene particles were not uniform in size, but has a normal distribution of 100–120 μm. Asphaltene reversibility to dissolved back into the oil with increasing pressure was only 35% of the original deposition. Two core samples were examined for formation damage due to asphaltene deposition. A Low permeability core showed significant permeability reduction exceeding 50% of its baseline permeability, and the higher permeability core showed less permeability decline, even with the same asphaltene precipitation.
Laboratory Challenges of Sand Production in Unconsolidated Cores
Authors: Ali Mohammad A. , Al-Hamad K.. , Al-Haddad A.. , AlKholosy S.. , Sennah H. Abu , Sanyal T.. , Aniel J.. 
Published: December 2012

Abstract
Improved oil recovery for heavy oil reservoirs is becoming a new research study for Kuwaiti reservoirs. There are two mechanisms for improved oil recovery by thermal methods. The first method is to heat the oil to higher temperatures, and thereby, decrease its viscosity for improved mobility. The second mechanism is similar to water flooding, in which oil is displaced to the production wells. While more steam is needed for this method than for the cyclic method, it is typically more effective at recovering a larger portion of the oil.
Steam injection heats up the oil and reduce its viscosity for better mobility and higher sweep efficiency. During this process, the velocity of the moving oil increases with lower viscosity oil; and thus, the heated zone around the injection well will have high velocity. The increase of velocity in an unconsolidated formation is usually accompanied with sand movement in the reservoir creating a potential problem.
The objective of this study was to understand the effect of flowrate and viscosity on sand production in heavy oil reservoir that is subjected for thermal recovery process. The results would be useful for designing completion under steam injection where the viscosity of the oil is expected to change due to thermal operations.
A total of 21 representative core samples were selected from different wells in Kuwait. A reservoir condition core flooding system was used to flow oil into the core plugs and to examine sand production. Initially, the baseline liquid permeability was measured with low viscosity oil and low flowrate. Then, the flowrate was increased gradually and monitored to establish the value for sand movement for each plug sample. At the end of the test, the produced oil containing sand was filtered for sand content.
The result showed that sand production increased with higher viscosity oil and high flowrate. However, sand compaction at the injection face of the cores was more significant than sand production. In addition, high confining pressure contributes to additional sand production. The average critical velocity was estimated ranged from 18 to 257 ft/day for the 0.74 cp oil, 2 to 121 ft/day for the 16 cp oil, and 1 to 26 ft/day for the 684 cp oil.
Laboratory Evaluation of Organically Crosslinked Polymer for Water Shutoff in High-Temperature Well Applications
Authors: Salgaonkar Lalit , Das Prasanta 
Published: December 2012

Abstract
Excessive water production from unwanted zones in oil producing wells is one of the major challenges faced by the oil industry. The applicability of organically crosslinked polymer (OCP) systems as sealants for water shutoff treatments in temperatures up to 350°F is well documented. However, their effectiveness at temperatures above 350°F has not been evaluated. This paper presents experimental data from using an OCP system for water shutoff treatments at 400°F.
At temperatures around 400°F, crosslinking is expected to happen faster and can lead to premature gelation of the recipe before the entire treatment is in place. Thus, controlling the gelation time at such temperatures is extremely crucial. Optimizing the amount of retarder is essential to provide adequate time for placement of the treatment fluid. This paper provides gelation time data at temperatures between 350 and 400°F with different amounts of retarder. With an optimum amount of retarder, the OCP showed a gelation time of 1 hr 20 min.
This paper also describes the experimental setup used to study and determine the long-term stability of the OCP system at 400°F. Sand packs measuring 1-ft long were used for the test to simulate formation conditions. Once the optimized OCP recipe was gelled inside the sand pack, measurements were taken by gradually applying incremental differential pressure (ΔP) to evaluate the sealant at temperature, as well as the threshold ΔP the system could withstand. Even after one month at 400°F, the OCP recipe was able to sustain a AP of 950 psi over the sand pack.
The data indicates the applicability of this system as an effective conformance product to shut off water-producing zones over an extended period of time at 400°F.
Optimization of Polymer Flood Performance by Preflush Injection - Numerical Investigation
Authors: Abedi M.. , Algharaib M.. 
Published: December 2012

Abstract
Currently, many reservoirs in the region approach the end of primary recovery phase where new techniques are needed to enhance recovery. Therefore, the need to optimize oil recovery from the current resources is very well understood by regional oil companies. To enhance oil recovery from current oil resources, field operators need to overcome the forces responsible for oil entrapment. Enhanced Oil Recovery techniques (EOR) introduce new energy into oil reservoirs to reduce the influence of these forces. Most of these resources contain light oil and are considered suitable candidates for either miscible or chemical EOR techniques. The first technique is challenged by the availability of suitable miscible gas. While, chemical EOR techniques are challenges by the high salt concentrations in the maturing oil reservoirs. The high salinity conditions encourage deficiencies in the performance of chemical EOR processes. Therefore, minimizing the effect of in situ salt on the injected chemical would impose tremendous improvement that leads to higher oil recovery. One way to diminish salt effect is to condition the oil reservoirs by injecting a slug of preflush water prior to chemical injection.
In this paper, the performance of polymer flooding, after preflush slug, in high salinity reservoir is investigated by numerical simulation means. The injected slugs, both preflush and polymer, are driven by water. The objective is to identify the relationship between preflush, polymer, and drive water characteristics and oil recovery. Seven parameters were considered: preflush slug size, preflush salinity, polymer slug size, polymer concentration, polymer slug salinity, and drive water salinity. The results show that these parameters have various degree of influence on oil recovery. For example, increasing the preflush slug size would results in more oil recovery especially during the early time. Detailed findings will be presented in the paper.
Efficient Polynomial Chaos Proxy-based History Matching and Uncertainty Quantification for Complex Geological Structures
Authors: Bazargan Hamid , Christie Mike 
Published: December 2012

Abstract
The purpose of history matching is to achieve geological realizations calibrated to the historical performance of the reservoir. For complex geological structures it is usually intractable to run tens of thousands of full reservoir simulation to trace the most probable geological model. Hence the inadequacy of the history-matching results frequently leads to poor estimation of the true model and high uncertainty in production forecasting. Reduced-order modeling procedures, which have been applied in many application areas including reservoir simulation, represent a promising means for constructing efficient surrogate models. Nonlinear dimensionality reduction techniques allow for encapsulating the high-resolution complex geological description of reservoir into a low-dimensional subspace, which significantly reduces number of unknowns and provides an efficient way to construct a proxy model based on the the reduced-dimension parameters.
Polynomial Chaos Expansions (PCE) is a powerful tool to quantify uncertainty in dynamical system when there is probabilistic uncertainty in the system parameters. In reservoir simulation it has been shown to be more accurate and efficient compared to traditional experimental design (ED). PCEs have a significant advantage over other response surfaces as the convergence to the true probability distribution is proved when the order of the PCE is increased. Accordingly PCE proxy can be used as the pseudo-simulator to represent the surface responses of the uncertain variables. When the objective and constraints of a reservoir model is described by multivariate polynomial functions, there are very efficient algorithms to compute the global solutions. We have developed a workflow at which incorporates PCE to find the global minimum of the misfit surface and assess the uncertainty associated with. The accuracy of the PCE proxy increases with the additional trial runs of the reservoir simulator.
We conduct a two dimensional synthetic case study of a fluvial channel as well as a real field example to demonstrate the effectiveness of this approach. Kernel Principal Component Analysis (KPCA) is used to parameterize the complex geological structure. The study has revealed useful reservoir information and delivered more reliable production forecasts. PCE-based history match enhances the quality and efficiency of the estimation of the most probable geological model and improve the confidence interval of production forecasts.
Utilising Process Safety Management to Reduce Risks in E&P Operations - Long Term Commitment Required.
Authors: Gopaul G. A. , Al-Kandari H.. , Al Qallaf H.. 
Published: December 2012

Abstract
In April 2010 we were reminded that Drilling operations are amongst the most hazardous in the world, having the potential for Major Incidents, with the Deepwater Horizon rig fire and explosion. This incident resulted in 11 lives being lost, almost 5,000,000 million barrels of oil being spilt into the Gulf of Mexico over an 87 day period and significant financial loss for bp. This Major Incident also served to remind us that while traditional "Personal Safety" programs are important to achieve safe drilling operations, these alone cannot effectively manage Major Incident Hazards. E&P Operations can learn valuable lessons from the Process Industry in this regard.
This paper looks at how "Process Safety Management" implementation, aimed at reducing the potential for Major Incidents, has commenced at an onshore E&P operation. It also discusses the challenges of integrating the culture of Process Safety into existing company culture for operations involving over 60 land rigs comprising both local and international Drilling Contractors and Service Companies.
Process Safety Management system is used to describe those parts of an organisation’s management system intended to prevent major incidents arising out of the production, storage and handling of dangerous substances (UK HSE, 2012). It addresses the potential release of these substances caused by: Mechanical FailuresProcess UpsetsProcedures/Human Error.
Third Generation Glass Barrier Technology: Improving Well Completion Integrity and Reliability
Authors: Gimre Rune , Maitre Shawn Le 
Published: December 2012

Abstract
In recent times the topic of well barrier integrity has become increasingly salient. Within the well completion arena, there have traditionally been two main alternatives for barrier plugs used for packer setting or temporary well abandonment; these are the metallic flapper or ball type isolation plugs. This paper describes the evolution of an innovative glass type barrier plug from its first appearance in the oilfield in 2004, to the deployment of third generation prototype systems into wells in the North Sea today.
Traditional ball or flapper type plug systems need to operate in two states: open and closed. This functionality typically necessitates the use of dynamic seals, which also have to compensate for the pressure differential applied across the plug. Plugs built in this manner can be prone to malfunctions in the dynamic seals and have limitations as to the pressure differentials that can be applied to them when opening. Additionally as the balls or flappers themselves are traditionally manufactured using metallic alloys, in the event that a plug fails to open the only alternative is milling, which if successful, will still leave a restriction in the well limiting options for future well interventions.
Glass barrier plugs have to operate in two slightly different states, solid or shattered. When the plug is run in hole the glass is in a solid state with pressure integrity maintained using static elastomeric seals. Once well operations have progressed to the stage when the plug needs to be opened, a preinstalled trip saver can be activated which would shatter the glass and open well communication. Operating in this manner avoids the use of dynamic seals thereby increasing plug reliability. Other major advantages are that the differential pressure applied across the plug when opening has no effect on the plugs functionality and since the plug is made out of glass, in the event of a trip saver malfunction the plug can be opened using a shoot down tool, a spear, or milled within approximately 10 minutes using a wireline tractor (Welltec, 2011) leaving a full bore ID for future well interventions.
This paper describes how BP Norway and TCO used the lessons learned from two generations of Glass Barrier Plugs (GBPs) to develop a system with increased debris tolerance, improved redundancy and a larger inner diameter.