bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomewide characterization of non-polyadenylated RNAs
Authors: Yang Li , Duff Michael O , Graveley Brenton R , Carmichael Gordon G , Chen Ling-Ling 
Published: February 2011

Abstract
Background
RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight into the nature and expression of transcripts that lack poly(A) tails.

Results
We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from HeLa cells and H9 human embryonic stem cells (hESCs). Using stringent criteria, we found that while the majority of transcripts are poly(A)+, a significant portion of transcripts are either poly(A)- or bimorphic, being found in both the poly(A)+ and poly(A)- populations. Further analyses revealed that many mRNAs may not contain classical long poly(A) tails and such messages are overrepresented in specific functional categories. In addition, we surprisingly found that a few excised introns accumulate in cells and thus constitute a new class of non-polyadenylated long non-coding RNAs. Finally, we have identified a specific subset of poly(A)- histone mRNAs, including two histone H1 variants, that are expressed in undifferentiated hESCs and are rapidly diminished upon differentiation; further, these same histone genes are induced upon reprogramming of fibroblasts to induced pluripotent stem cells.

Conclusions
We offer a rich source of data that allows a deeper exploration of the poly(A)- landscape of the eukaryotic transcriptome. The approach we present here also applies to the analysis of the poly(A)- transcriptomes of other organisms.
Up-Regulation of PPAR-γ mRNA Expression in the Liver of Obese Patients: an Additional Reinforcing Lipogenic Mechanism to SREBP-1c Induction
Authors: Pettinelli Paulina , Videla Luis A. 
Published: February 2011

Introduction:
Triglyceride accumulation in the liver is an early feature in the development of nonalcoholic fatty liver disease (NAFLD) associated with human obesity, which is a multifactorial syndrome and whose underlying mechanisms are beginning to be understood.

Objectives:
Liver peroxisome proliferator-activated receptor-γ (PPAR-γ) mRNA expression was measured as a signaling mechanism related to steatosis in obese patients with NAFLD.

Methods:
Liver PPAR-γ and sterol receptor element-binding protein 1c (SREBP-1c) mRNA (real-time RT-PCR), serum total adiponectin (RIA), and high molecular weight (HMW)-adiponectin (ELISA) levels, and insulin resistance (IR) evolution (homeostasis model assessment-IR) were determined in 22 obese NAFLD patients (16 with steatosis and six with steatohepatitis) who underwent subtotal gastrectomy with gastrojejunal anastomosis in Roux-en-Y and 16 nonobese subjects who underwent laparoscopic cholecystectomy (controls).

Results:
Liver PPAR-γ mRNA levels were 112 and 188% higher (P &lt; 0.05) than control values in obese patients with steatosis and steatohepatitis, respectively, who also exhibited 70 and 62% increases in those of SREBP-1c, concomitantly with IR and lower levels of serum total adiponectin and HMW-adiponectin (P &lt; 0.05). Liver PPAR-γ expression showed positive associations with SREBP-1c mRNA levels (r = 0.86; P &lt; 0.0001), serum insulin levels (r = 0.39; P &lt; 0.01), and homeostasis model assessment-IR (r = 0.60; P &lt; 0.0001), and negative correlations with total adiponectin (r = −0.37; P &lt; 0.01) and HMW-adiponectin (r = −0.51; P &lt; 0.001) levels in serum.

Conclusions:
PPAR-γ is up-regulated in the liver of obese patients with NAFLD, representing an additional reinforcing lipogenic mechanism to SREBP-1c induction in the development of hepatic steatosis.
Unidirectional Alignment of Carbon Nanotube Aggregates Using Friction-transferred Polymeric Films
Authors: Inagaki Ken-ichi , Sano Masahito 
Published: February 2011

Abstract
Aggregates of single-walled carbon nanotubes (SWCNTs) were deposited unidirectionally on highly oriented PTFE film made by friction transfer. The friction-transferred PTFE film possesses many straight channels of various sizes running along the transfer direction. SWCNT aggregates were preferentially deposited parallel to the channels when SWCNTs in a form of dry powder were sprinkled, as confirmed by Raman microscopy and anisotropic electrical resistivity. Furthermore, the SWCNT film can be transferred to another substrate surface by simply stamping the SWCNT/PTFE film on it.
Ultrasound-mediated Transfection with Liposomal Bubbles Delivers Plasmid DNA Directly into Nucleus
Authors: Kawazu Takeshi , Hakamada Kazumi , Oda Yusuke , Miyake Jun , Maruyama Kazuo , Nagasaki Takeshi 
Published: February 2011

Abstract
Transfection using ultrasound exposure in the presence of nanobubbles can overcome an important barrier for nonviral gene delivery, that is entering the nucleus without cell division. The monitoring of the relationship between fluorescent protein expression and cell division reveals that ultrasound-mediated transfection with liposomal bubbles is independent on the disappearance of nuclear membrane at mitosis.
The New EU Directives Requirements and the Innovation in Pesticide Application Techniques
Authors: Balsari Paolo , Marucco Paolo 
Published: February 2011

Abstract
The first reference to crop protection equipment dates back to the second half of the 19th century. From that time until the recent years, the evolution of sprayers had two objectives: The adaptation of machines to the needs of applying the chemicals available in the market and improving their working capacity. Only since the 1980s that the safety aspects related to the operator and to the environment have been taken into account as priority aspects. This line of evolution will be enforced in the near future especially in Europe due to the European Union (EU) Directive on Sustainable Use of Pesticides (2009/128/EC) and amendment of the EU Machinery Directive (2009/127/EC). Due to the globalisation process, developing countries are now also facing the need to promote the development of plant protection machinery in order to improve the quality of spray application and to reduce the environmental risks related to PPP dispersal. In this review paper, several examples of the use of information technologies to improve the performance of sprayers are reported as solutions for reducing water contamination of PPP due to point and diffuse sources. Finally, it is estimated that potential market improvement for sprayers and components due to the enforcement of the new EU Directive could be 1.3 billion euros for the next 7 years.
Occupational Exposure of Dentists to Extremely‐low‐frequency Magnetic Field
Authors: Huang Shu‐Min , Lin Yu‐Wen , Sung Fung‐Chang , Li Chung‐Yi , Chang Ming‐Fong , Chen Pei‐Chun 
Published: February 2011

Occupational Exposure of Dentists to Extremely‐low‐frequency Magnetic Field: Shu‐Min Huang, et al. Department of Public Health, College of Medicine, Fu‐Jen Catholic University, Taiwan—ObjectiveTo compare occupational exposure to extremely‐low‐frequency magnetic field (ELF‐MF) between dentists practicing in dental clinics and those employed in hospitals.MethodsThirty‐two dentists who worked at clinics (n=15) and 33 dentists employed at hospital dental departments (n=7) voluntarily provided their informed consent to participate in this measurement study. The study dentists were requested to wear an ELF‐MF dosimeter for some 3 h at work to determine their personal exposure. Spot measurements taken at a number of locations in each dental ofice were used to indicate the work environment exposure level. Additionally, ELF‐MF emitted from common dental equipment was also measured. All measurements were performed with EMDEX Lite meters.ResultsThe average environmental exposure to ELF‐MF is higher in clinic dental ofices than in hospital dental departments (0.55 vs. 0.15 µT, p=0.008). Personal dosimetry showed that on average, clinic dentists spent 35.71 and 19.39% of their time at exposures above 0.3 and 0.4 µT at work, respectively. The corresponding igures for hospital dentists were 19.61 and 13.92%. Additionally, ELF‐MF was greater than 0.4 µT at 30 cm from all selected equipment, but the ELF‐MF generally diminished as the distance from dental equipment increased. Uultraviolet air sterilization system produced 3 times as much ELF‐MF as other dental equipment.ConclusionsThis study suggests the possibility of over‐exposure of dentists to power frequency ELF‐MF. Additionally, certain dental equipment may produce ELF‐MF levels greater than 0.4 µT in areas where dentists usually work when treating patients.
A Primer on Winter, Ice, and Fish: What Fisheries Biologists Should Know about Winter Ice Processes and Stream-Dwelling Fish
Authors: Brown Richard S , Hubert Wayne A , Daly Steven F 
Published: February 2011

Abstract
Stream-dwelling fish face highly-variable environmental conditions from fall to winter due to fluctuations in water temperatures, discharge, and ice conditions. We provide an in-depth description of the interactions between these complex environmental conditions and behaviors of stream-dwelling salmonids during winter. Fisheries managers should be aware of the conditions that fish confront during winter in order to make appropriate management decisions. Diverse habitats, including deep pools with low water velocities, coarse rock substrate, and abundant cover, as well as side channels and backwaters, aid in the survival of overwintering fish. The inflow of relatively warm groundwater into the water column can be an important factor affecting winter habitat. Considering the length of winter and the vulnerability of fish during winter, a broad understanding of winter ice process and their effects on stream dwelling fish can aid in the preservation and improvement of winter habitats.
Human Population Increase, Economic Growth, and Fish Conservation: Collision Course or Savvy Stewardship?
Authors: Limburg Karin E , Hughes Robert M , Jackson Donald C , Czech Brian 
Published: February 2011

Abstract
Globally, fishes and fisheries are in severe decline, driven in large part by economic and human population growth. Despite progress in environmental philosophies, legislation, and protection, conflicts between economic/human population growth and fish conservation remain and are intensifying at continental and global scales. The growth of the human enterprise ad infinitum is impossible because of dependence on finite resources; hence policies should leave a margin of error when dealing with the biophysical environment. We suggest a re-definition of Earth stewardship to serve as a conceptual bridge between ecology and economics, recognizing the hubris behind most economic models, which assume that the biosphere is a subset of the economy or else an externality, when in fact Homo sapiens is a species operating within the biosphere. Additional indicators that focus on a different suite of values (e.g., social justice, corporate responsibility, and ethics) would underscore the complexity of economic and human population growth effects on societies and ecosystems, and could help guide us away from unsustainable actions toward those that are “savvier” in terms of co-existence with the resources upon which we depend.
An Expert System Approach to Real-Time Diagnosis of Drill Bit Condition and Preventing its Damage
Authors: Salakhov Tagir R. , Yamaliev Vil U. , Dubinsky Vladimir 
Published: February 2011

Abstract
Introduction of modern computer technologies to drilling control systems opened new opportunities for real-time diagnosis of the drill bit conditions and preventing any further damage. While usage of MWD systems equipped with corresponding downhole sensors significantly increases the efficiency and accuracy of downhole drilling monitoring and diagnosis, there remains a niche in the market for much less expensive drilling monitoring systems based mainly on the surface measurements. These measurements usually include such parameters as static and dynamic hook load, stand pipe pressure measurements, surface torque, differential mud flow rate, and possibly some surface vibration data.
The expert system approach suggested in this paper offers an efficient way of combining some basic measurements provided by the surface sensors for early diagnosis and prevention of possible damage of the downhole drilling equipment, primarily the drill bit itself. This paper addresses both aspects of the proposed methodology – the system configuration and some details of the data analysis algorithms. The fundamental theory behind the proposed approach is based on certain elements of fractal analysis as well as artificial neural networks. A huge amount of data needs to be collected and organized in a database to cover different operational and varying drill bit conditions.
The data analysis is performed for multiple time frames in order to identify both a big picture and more specific details. Application of the fractal performances allows obtaining important practical information during standard field operations, without conducting a special controlled field experiment.
We present some real field data examples used for training our model and assessing the current drill bit conditions by using the proposed methodology. We believe that this methodology opens new opportunities for real-time drilling optimization that can be efficiently implemented within the scope of the existing drilling practice.
Classification of Oil and Gas Reservoirs Based on Recovery Factor: A Data-Mining Approach
Authors: Sharma A. , Srinivasan S. , Lake L. W. 
Published: February 2011

Abstract
Rigorous flow simulations to obtain estimates for recovery are infeasible given many combinations of reservoir and development scenarios. This motivates an alternative approach to calibrate likelihood of recovery using reservoir datasets. A proxy model relating reservoir, well, and operational factors to the ultimate recovery factor could guide subsequent field-scale flow simulations. There are two reservoir datasets that we have used for the classification and estimation of ultimate recovery: the Tertiary Oil Recovery Information System (TORIS) database for oil reservoirs and the Gas Information System (GASIS) database for gas reservoirs.
For oil reservoirs, 19 predictor variables were used to estimate the ultimate recovery factor. Cluster analysis was followed by linear regression analysis within the identified clusters that provided a reliable deterministic model for predicting the recovery factor. The linear regression model was compared with the empirical correlations given by Arps et al. (1967) and Guthrie et al. (1995). Analysis showed that geological and engineering parameters are correlated and both are important to the prediction of recovery factor. Later, we used a naive Bayesian approach on principal scores of the predictors for the calibration of recovery factor likelihood. The likelihood function of the recovery factor for oil reservoirs provided the uncertainty in recovery. It was computed to be multimodal and non-Gaussian.
In case of the gas reservoirs, good deterministic estimation was achieved by introducing cluster analysis to the data. The robustness of the linear regression model was tested on tight gas reservoirs. The likelihood of recovery factor was multimodal and non-Gaussian. It also indicates that gas reservoirs are less complex.
Vital Role of Nanopolymers in Drilling and Stimulations Fluid Applications
Authors: Singh Subodh , Ahmed Ramadan 
Published: February 2011

Abstract
Production of hydrocarbons from conventional, as well as unconventional resources, is becoming increasingly more difficult and expensive. Drilling fluid stability and performance in deeper, high-temperature high-pressure (HTHP) formations are still problematic, even for environmentally safer synthetic fluids.
Recent research has demonstrated that nano fluids have attractive properties for applications where heat transfer, drag reduction, formation consolidation, gel formation, wettability alteration, and corrosive control are of interest.
Nano fluids can be designed by adding nano-sized particles in low volumetric fractions to a fluid. The nano particles modify the fluid properties, and suspensions of nano-sized particles can provide numerous advantages. Nano-sized particles can impart sedimentary, thermal, optical, mechanical, electrical, rheological, and/or magnetic properties to a base material that can enhance its performance.
This paper presents an extensive literature review to assess the application of nanotechnology in drilling and completion applications and evaluates the potential technical and economic benefits that this technology might provide to the industry.
Improving Efficiency of Coiled Tubing Operations on Vankor Field
Authors: Sitdikov Suleyman , Von Hertzberg Bert , Zagranichniy Stanislav 
Published: February 2011

Abstract
Coiled tubing is commonly used as an intervention tool for treatment delivery in long horizontal wells. As with any intervention tool, however, coiled tubing has operational limitations. Depending on the diameter of the horizontal sections and the well trajectory, accessing laterals greater than 1,000 m is often problematic or not possible due to helical friction lock-up. The well profiles in Vankor, a new frontier oil and gas field in East Siberia, are designed with a reverse bend in it allowing the horizontal section of more than 1,000 m the wellbore to be directly beneath the wellhead. There is an 800 m thick layer of perma-frost which is coupled with extremely low reservoir temperatures that complicates the intervention causing the wax precipitation in tubing.
Conventionally, it is possible to change the geometry of the intervention (CT OD), optimize the string design, utilize lubricants (metal to metal friction reducers), straighten the coiled tubing string, use downhole tractors and vibration tools. The use of different methods yields incremental reach of 5 – 20% in some cases. This paper highlights an approach that has been implemented in Vankor field to enable the coiled tubing intervention to access the horizontal lateral with the methods of string design optimization and utilization of downhole BHA vibration.
The coiled tubing string design requires the special attention for successful intervention in horizontal and extended reach wells. The optimized tapered string allows increasing the advance of coiled tubing to 5-15% compared to traditional design.
The vibrator tool can effectively increase CT access to the extended reach hole by reducing the implied friction coefficient of the wellbore up to additional 10 %. The tool is actually delaying the helical shape and reducing the number of coiled tubing contact points dragging on the well bore.
This paper reviews the engineering and operational challenges related to utilizing coiled tubing in Vankor field and the solutions required to overcome these issues.
Investigation of Oil-Trapping Mechanisms in Deepwater Gulf of Mexico
Authors: Li Xin , Lach Joseph , McMillen Kenneth 
Published: February 2011

Abstract
Oil recovery depends on geologic complexity – structure, stratigaphy and deposition – and rock and fluid properties. The work reported here illustrates the oil trapping mechanisms for 450 reservoirs in 83 mature deepwater fields in the Gulf of Mexico (DW GoM). The evaluation of trapped or forecast remaining was a precursor to determining improved oil recovery concepts as part of a project for the group RPSEA (Research Partnership to Secure Energy for America).
Neogene age reservoirs in the DW GoM are characterized as over-pressured with generally good rock and fluid properties. Drive energy is typically from a combination of rock compaction with some assistance from aquifer influx. Only a few engineered water injection projects have been implemented and no gas injection has been used to add drive energy. Oil recovery is reasonable with an average of 32% of original oil in-place (OOIP) with a 95% confidence and range between 21% and 42% of OOIP.
Several field examples of estimated trapped oil mechanisms are used to illustrate typical reservoir performance and the calculation methodology. Trapped oil is determined for the categories of capillary bound, non-connected to wells, high abandonment pressure or low abandonment water cut, limited drive energy, and poor sweep. The results indicate the improved recovery initiatives should focus on aqueous phase injection, pumping and artificial lift technology, and well and intervention technology.
Human Decision-Making in the Oil and Gas Industry
Authors: Mackie S. I. , Begg S. H. , Smith C. , Welsh M. B. 
Published: February 2011

Abstract
Business under-performance in the upstream oil and gas industry, and the failure of many decisions to return expected results, has led to a growing interest over the past few years in understanding the impacts of current decision-making tools and processes and their relationship with decision outcomes. A primary observation is that different decision types require different decision-making approaches to achieve optimal outcomes.
Optimal decision-making relies on understanding the types of decisions being made and matching the type of decision with the appropriate tools and processes. Yet the industry lacks both a definition of decision types and any guidelines as to what tools and processes should be used for what decisions types. It is argued that maximizing the chances of a good outcome in real world decisions requires the implementation of such matching. Comparing a "real world" decision-making model used by the upstream oil and gas industry with a theoretical model yields various prescriptions for optimal decision-making.
Further implications are examined in relation to a variety of oil and gas decisions by documenting both a definition of decision types as well as guidelines to what decision-making processes should be used with what decision types. The paper looks at a comparison between what tools and processes companies are now using for some of the decision types and compare these with what they should be using in order to lead to optimal decision-making.
Acid-resistant Foamer Used to Control Gas Breakthrough for CO2 Drive Reservoir
Authors: Liu XiangBin , Wang FengShan , Zhang ZongYu , Xin Wang , Zhou WanFu , ZhongLian Han , HaiJing Wang , DeFu Zou , Guo Li , HaiRong Fu 
Published: February 2011

Abstract
Due to the prone gas breakthrough in CO2 immiscible flooding, the development effect was poor. In order to block off gas breakthrough channels, improve gas injection/production profile, and increase sweep volume & efficiency, two different acid-resistant and oil-resistant foam systems were developed according to reservoir characteristics and fluid features in Daqing peripheral oilfield. The foam system swelled 4times, the half-life was 83h, and core resistance coefficient was 120 under the condition of PH=3 and 60% oil saturation. Filed test results showed that the systems can effectively block off gas channels, decrease inefficient circulation, increase CO2 sweep volume & efficiency as well as displacement efficiency. The tested well gas injection pressure rose by 3.5MPa after resuming injection. Dominant injection direction changed obviously and gas sweep area increased enormously. Connected wells’ gas oil ratio decreased with an average valid period of 11 months and cumulative oil increment of 467t. This gas breakthrough blocking off technology is suitable for gas flooding development of Daqing peripheral oilfields which have ultra-low permeability, and has the advantages of high efficiency and low costs. It provides a sound technique support for gas flooding development.