bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
Authors: Jensen Paul A , Lutz Kyla A , Papin Jason A 
Published: September 2011

Abstract

Background
Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR) relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model.

Results
We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae.

Conclusion
The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.
Alu pair exclusions in the human genome
Authors: Cook George W , Konkel Miriam K , Major James D , Walker Jerilyn A , Han Kyudong , Batzer Mark A 
Published: September 2011

Abstract

Background
The human genome contains approximately one million Alu elements which comprise more than 10% of human DNA by mass. Alu elements possess direction, and are distributed almost equally in positive and negative strand orientations throughout the genome. Previously, it has been shown that closely spaced Alu pairs in opposing orientation (inverted pairs) are found less frequently than Alu pairs having the same orientation (direct pairs). However, this imbalance has only been investigated for Alu pairs separated by 650 or fewer base pairs (bp) in a study conducted prior to the completion of the draft human genome sequence.

Results
We performed a comprehensive analysis of all (> 800,000) full-length Alu elements in the human genome. This large sample size permits detection of small differences in the ratio between inverted and direct Alu pairs (I:D). We have discovered a significant depression in the full-length Alu pair I:D ratio that extends to repeat pairs separated by ≤ 350,000 bp. Within this imbalance bubble (those Alu pairs separated by ≤ 350,000 bp), direct pairs outnumber inverted pairs. Using PCR, we experimentally verified several examples of inverted Alu pair exclusions that were caused by deletions.

Conclusions
Over 50 million full-length Alu pairs reside within the I:D imbalance bubble. Their collective impact may represent one source of Alu element-related human genomic instability that has not been previously characterized.
Variation in phlebotomy techniques in emergency medicine and the incidence of haemolysed samples
Authors: Berg J E , Ahee P , Berg J D 
Published: September 2011

Background Phlebotomy is a potential cause of preanalytical errors. We have observed phlebotomy in routine practice in a busy Emergency Department, to see how current practice compares with optimal blood sampling. Methods Phlebotomy episodes were audited and compared with standard procedures. A computer-based search of the number of haemolysed samples from Emergency Medicine and hospital inpatients was reviewed. Results Four different ways of taking blood were observed: cannulation and a syringe (38%), cannula with evacuated tube and adaptor (42%), syringe and needle into vein (14%) and evacuated tube system used conventionally (6%). Where a syringe was used, two methods of transfer into the sample tube were observed; needle kept on with cap piercing (77%) and needle and evacuated cap both removed (23%). On 20 out of 50 phlebotomy episodes (40%), the potassium-EDTA tube was filled prior to the biochemistry serum gel tube. A search of the laboratory computer records for ward-based phlebotomy found 30 of 1034 samples were haemolysed (2.9%). In the 50 phlebotomy episodes in the Majors area of the Emergency Department, 24% produced a haemolysed sample ( P < 0.0001). For samples taken from all areas of Emergency Medicine over a seven-day period, 52 of 485 were haemolysed (10.7%; P < 0.0001). Conclusions This study has shown that phlebotomy techniques in the Emergency Department deviate from standard practice significantly. This may well be a reason for the much higher frequency of haemolysed samples and with the wrong order of collection the possibility of potassium-EDTA-contaminated samples.
Role of physical activity in new onset fractures after percutaneous vertebroplasty
Authors: Rad Arash Ehteshami , Gray Leigh A , Sinaki Mehrsheed , Kallmes David F 
Published: September 2011

Background Increased mobility and physical activity after successful vertebral augmentation procedure might increase the risk of new-onset fractures. Purpose To determine whether new-onset fracture following vertebroplasty is associated with specific type of physical activity. Material and Methods A total of 107 patients underwent at least two procedures of percutaneous vertebroplasty. Among them, 30 patients who sustained a post-vertebroplasty fracture(s), were stratified by fracture-causing activity and examined the incidence of the initial and post-vertebroplasty fractures, time to post-vertebroplasty fractures, duration of anti-osteoporotic therapy, T-score, and body mass index. Results The following percentages correspond to patients with fractures sustained pre- and post-vertebroplasty, respectively; spontaneous fractures in 17% and 7% ( P = 0.20), sitting in 7% and 3% ( P = 0.50), walking or standing in 7% and 20% ( P = 0.10), housework in 3% and 3% ( P > 0.99), coughing or sneezing in 0% and 20% ( P = 0.003), exercise in 7% and 17% ( P = 0.20), lifting in 10% and 17% ( P = 0.40) and falling in 50% and 13% ( P = 0.002). Different levels of activity were not significantly associated with time to incidence of post-vertebroplasty fractures. Anti-osteoporotic medications were administered to 33% of patients before vertebroplasty and 37% after the vertebroplasty ( P = 0.78); medications were administered to these groups for 16 and 25 months, respectively ( P = 0.39). Conclusion A significantly elevated risk of new onset fracture with increased physical activity was not identified. However, patients should be carefully counseled after vertebroplasty to optimize medical therapy for osteoporosis and also to use extreme care when engaging in even moderate physical activity.
DNA Microarray Analysis Identifies CKS2 and LEPR as Potential Markers of Meningioma Recurrence
Authors: Menghi Francesca , Orzan Francesca N. , Eoli Marica , Farinotti Mariangela , Maderna Emanuela , Pisati Federica , Bianchessi Donatella , Valletta Lorella , Lodrini Sandro , Galli Giuseppe , Anghileri Elena , Pellegatta Serena , Pollo Bianca , Finocchiaro Gaetano 
Published: September 2011

Abstract
Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p &lt; .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in &lt;5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted.
Quantified Prediction of Technically Recoverable Resources for Unconventional Gas in Frontier Basins
Authors: Cheng Kun , Wu Wenyan , Holditch Stephen A. , Ayers Walter B. , McVay Duane A. 
Published: September 2011

Abstract
Along with the trend that unconventional gas resources are significant in meeting the great energy demand, it is intuitively needed to know their quantified volume, especially for the frontier basins where little exploration of unconventional resources has been undertaken. Following by our work in standardized investigation and quantified evaluation of recoverable resources in 25 mature North American basins, this paper further employs two methods to evaluate TRR (Technically Recoverable Resources) for unconventional gas in frontier basins: Source Rock method (SR) and Conventional TRR Input method (CTRRI).
The source rock method derives from the fact that source rock potential is the mechanism for generating hydrocarbons. Thus, using the relationships between TRR and source rock factors, the SR can adequately capture TRR from the indirect source rock evaluation. Combined with the ratio of unconventional and conventional hydrocarbons from our prior investigations, the method can further deduce conventional resources and unconventional resource volumes. Different from SR that provides an independent measure of TRR, conventional TRR input method requires known recoverable conventional resources for frontier basin. To calculate frontier basin TRR volume, the frontier basin’s recoverable conventional volume is divided by the fraction of conventional resources in the similar reference basin from basin analog system investigation (BASIN). It is noted that all the quantifications are regulated by the unified definition from petroleum resource investigation summary and evaluation (PRISE). Although the two methods estimate TRR for frontier basins in different conditions, the initial tests on three basins show that estimates by CTRRI are in accordance with those by SR. The results validate the resource triangle concept with distributions of different resource types (i.e., conventional oil, conventional gas, coalbed methane, shale gas, and tight gas sand), and can be further evaluated by more complete estimation of North American basin resources and international unconventional gas resources.
Injection Well – Producer Well Combinations in Application of Toe-To-Heel Steam Flooding (THSF)
Authors: Fatemi S. Mobeen , Jamaloei Benyamin Yadali 
Published: September 2011

Abstract
Toe-to-Heel Steam Flooding (THSF) is a new, short-distance thermal EOR process that achieves high recovery by virtue of its stable front propagation and producing mobilized oil directly into an active section of the horizontal producer. However, the wells configuration design for field development purposes still requires critical attention so as to ensure less environmental effect, efficient start-up and optimal oil recovery.
We present a series of 3-D simulated experiments using our developed PVT and rock model for KEM heavy oil reservoir in Iran to study the feasibility of THSF. Model has been validated with the published experimental observations. Then, different well configurations using Vertical (V) or Horizontal (H), Injector (I) and/or Producer (P) in direct line drive (VIHP, HIHP) or staggered line drive (VI2HP, 2VIHP) have been investigated.
The results show that THSF outperforms the conventional steam-flooding (VIVP). Different wells configurations of THSF showed superior performance over CSF in low-permeability KEM reservoir. A quasi-vertical steam condensation front exists that moved along the horizontal section in a toe-to-heel manner. Contrary to CSF, there was no or negligible steam override and channeling in different THSF configurations. Also, the horizontal injector configuration (HIHP) was the most efficient configuration for achieving rapid start-up, i.e., the shortest time to achieve stable front propagation. The single vertical injector configuration (VI2HP) was initially slow to achieve stable operation, due to the development of a much smaller steam zone. As the process continued, 2VIHP provided improved vertical, areal, and volumetric sweep efficiency associated with steam condensation front, which resulted in larger steam chamber and higher ultimate oil recovery. Finally, the sensitivity of THSF performance to the length of horizontal producer and traversal distance between producers (for VI2HP) or between injectors (for 2VIHP) has been simulated. These results indicate the optimized scenarios for the field development purposes.
"Red" vs. "Green" Scale Inhibitors For Extending Squeeze Life – A Case Study From North Sea, Norwegian Sector – Part II
Authors: Jordan M. M. , Sorhaug E. , Marlow D. 
Published: September 2011

Abstract
Over the years environmental legislation has forced changes in the types of scale inhibitor molecule that can be deployed in certain regions of the world. These regulations have resulted in changes from phosphonate scale inhibitor to polymer based chemistry, particularly in the Norwegian and UK continental shelf where phosphonates have either been on the substitution list or phased out for many applications. Over the past 10 years significant improvements in inhibitor properties of the so called "green" scale inhibitors have been made. However for one particular operator the squeeze application of this "green" scale inhibitor resulted in poorer than expected treatment lifetimes and significant operating cost due to the frequency of retreatment. To overcome the increasing operating cost an evaluation was made of the current treatment chemicals vs. the older more established phosphonate scale inhibitors. The results for the laboratory evaluation suggested that the older chemistry would extend treatment life and reduce operating cost. A case was made to the legislative authority who approved the use of the phosphonate scale inhibitor and field applications started. The squeeze lifetimes for the "red" phosphonate chemistry were shown to be significantly better than the existing "yellow/green" inhibitors. During the following months other scale inhibitors with improved environmental characteristics were developed and evaluated. One such molecule was shown to have similar coreflood retention than the applied "red" phosphonate and presented no formation damage. This paper presents the laboratory evaluation of the new scale inhibitor, illustrates the improvement observed with this new inhibitor via field squeeze treatment results from a well treated with both the "red" and new "yellow" environmental profile inhibitor chemicals.
This paper outlines the challenges with environmental legislation and how it has been possible to develop technical solutions (both in terms of environmental vs. safety issues and with new inhibitor chemicals) to meet the challenges of offshore scale control.
Thermal Gas Recovery from Coal Seam Gas Reservoirs Using Underground Coal Gasification
Authors: Salmachi Alireza , Haghighi Manouchehr , Bedrikovetsky Pavel , Xu Chaoshui 
Published: September 2011

Abstract
Gas production from coal seam gas reservoirs initiates by dewatering operation. Reservoir pressure reduction activates gas desorption and gas diffuses from micropores to macropores and consequently coal cleats. Dewatering operation provides the required driving force for the gas to desorb. In this research, in situ coal combustion is introduced as an enhanced gas recovery method.
Methane desorption from coal matrix is an endothermic process. Heating disturbs thermal equilibrium of the coal and more gas is released at higher temperature. A numerical transport model is applied to investigate thermal effect on gas desorption and diffusion in coal. Desorption-diffusion properties of the coal are modeled at non isothermal condition. Due to extremely low thermal conductivity of coal, convection is the dominant mechanism responsible for heat transfer in coal seam. Physical properties of the coal, Langmuir pressure and volume, porosity, density and initial diffusivity control methane mobility in thermal treatment.
Underground coal gasification which is a known technology in coal mining is proposed to be used as the source of heat. Controlled air injection into different wells in a coal seam reservoir can generate some hot spots in the reservoir. Heat flux generated from underground coal gasification sites has the potential to be transferred within the reservoir and locally increases reservoir temperature.
It is shown that the combination of underground coal gasification and coal seam gas production has the potential to develop a new technology that not only reduces the dewatering operation but also enhances gas recovery. Results show that thermal recovery can significantly increase gas desorption and diffusion in coal seam gas reservoirs. Thermal treatment causes higher desorption rate and ultimate recovery factor, lower water production and higher wellhead pressure.
Injectivity of Hydrophobically Modified Water Soluble Polymers for IOR: Controlled Resistance Factors vs. Flow-Induced Gelation
Authors: Dupuis Guillaume , Rousseau David , Tabary René , Grassl Bruno 
Published: September 2011

Abstract
The associative properties of Hydrophobically Modified Water Soluble Polymers (HMWSP) are known to be attractive for IOR, both because of their enhanced thickening capability as compared to classical water soluble polymers (for mobility control) and of their marked adsorptions on surfaces (for well treatments). In previous works, we have studied HMWSP injectivity in the dilute regime and shown, in particular, that adsorption played a major role in controlling injectivity. In this paper, we report new experimental data on the injectivity of HMWSP solutions in the semi-dilute regime.
From membrane filtration tests at imposed flow rate, we have firstly observed the formation of a filter-cake made of HMWSP physical gel, which remained largely permeable to polymers. This "gel-filtration" entailed modifications of the solution's viscosimetric properties, which can be explained by a rearrangement of the intra- and inter-chain hydrophobic bonds in the solution. The second part of our work consisted in injectivity tests in model granular packs. We have performed comparative experiments in porous media with variable permeabilities but at the same shear rate in the pore throats. Results show that, above a critical pore throat radius, rpC, HMWSP injection lead to stable resistance factors, with values close to the solution's viscosity, and that, below rpC, gelation occurs during injection. Furthermore, resistance factors measured on the cores internal sections evidence for in-depth gel formation. These insights could represent a new step towards the tuning of HMWSP injection conditions to the application targeted: mobility control or profile/conformance control.
High-Efficiency Boron Crosslinkers for Low-Polymer Fracturing Fluids
Authors: Sun Hong , Qu Qi 
Published: September 2011

Abstract
Guar-based fracturing fluids are the most commonly used fluids in reservoir stimulation. To provide high viscosity, boron crosslinked gels are preferred for their ability to heal after mechanical shearing and their favorable environmental properties. However, polymer loading determines amount of polymer residue, which can damage the formation and proppant pack. New, efficient boron crosslinking chemistry promises to reduce polymer loading in fracturing fluids and therefore minimize polymer residue and damage.
As a first step toward improving crosslinking efficiency, several diboronic acids were tested as model compounds in a series of guar solutions against boric acid. The results demonstrated that such chemistry could effectively reduce C* (critical overlap concentration for polymer chains), C** (critical entangle concentration for polymer chains) and Ccc (critical crosslinking concentration) of guar solutions. Further observations show crosslinking efficiency is a function of the crosslinking sites and chemical structures of the crosslinkers.
A new chemistry was developed to produce crosslinkers more cost-effective than the model compounds, whereby boron was incorporated via reactions between organometallic intermediates and boron reagents. Amines and polyimines were used as the base scaffolds and derivatized under mild conditions. The resulting compounds contain more crosslinking sites than the existing chemistry and can connect multiple guar chains to form a much more complex network for more efficient proppant transport.
A series of crosslinkers based on the new amine derivatization were synthesized and evaluated. This paper will show the lab test results of model compounds and new crosslinkers versus the conventional boric acid crosslinker. Analysis and discussion of the chemistry, crosslinking performance and economics will be presented.