bluuebunny/crossref_metadata_2025_split huggingface dataset:
The `dnet’ approach promotes emerging research on cancer patient survival
Authors: Fang Hai , Gough Julian 
Published: August 2014

AbstractWe present the `dnet’ package and apply it to the `TCGA’ mutation and clinical data of >3,000 patients. We uncover the existence of an underlying gene network that at least partially controls cancer `survivalness’, with mutations that are significantly correlated with patient survival, yet independent of tumour origin and type. The survivalness network has natural community structure corresponding to tumour hallmarks, and contains genes that are potentially druggable in the clinic. This network has evolutionary roots in Deuterostomia identifying PTK2 and VAV1 as under-valued relative to more studied genes from that era. The `dnet’ R package is available at http://cran.r-project.org/package=dnet.
Massive Gravity
Authors: de Rham Claudia 
Published: August 2014

AbstractWe review recent progress in massive gravity. We start by showing how different theories of massive gravity emerge from a higher-dimensional theory of general relativity, leading to the Dvali-Gabadadze-Porrati model (DGP), cascading gravity, and ghost-free massive gravity. We then explore their theoretical and phenomenological consistency, proving the absence of Boulware-Deser ghosts and reviewing the Vainshtein mechanism and the cosmological solutions in these models. Finally, we present alternative and related models of massive gravity such as new massive gravity, Lorentz-violating massive gravity and non-local massive gravity.
Perception, Non-Propositional Content and the Justification of Perceptual Judgments
Authors: Almäng Jan 
Published: August 2014

AbstractIt is often argued that for a perceptual experience to be able to justify perceptual judgments, the perceptual experience must have a propositional content. For, it is claimed, only propositions can bear logical relations such as implication to each other. In this paper, this claim is challenged. It is argued that whereas perceptions and judgments both have intentional content, their contents have different structures. Perceptual content does not have a propositional structure. Perceptions and judgments can nevertheless have the same cognitive significance. So the veridicality of a certain perceptual experience, can imply the truth of certain propositions. Consequently, perceptions can have non-propositional content, but even so justify perceptual judgments which have a propositional structure.
About Aboutness
Authors: Rasmussen Joshua 
Published: August 2014

Abstract
I develop a new theory of the nature of aboutness. I begin by presenting an “aboutness” puzzle that exposes a problem for many theories of aboutness. I then develop the components for a theory of aboutness that can help us solve the puzzle. The theory of aboutness I offer depends upon a theory of propositions as ordered complexes of properties. I develop this theory of propositions and show how it relates to, or builds upon, some of the most recent theories of propositions in the literature. My end goal is to deepen our understanding of how the things we say and think relate to the things we say and think about.
Modal Realism, Counterpart Theory, and Unactualized Possibilities
Authors: Baltimore Joseph A. 
Published: August 2014

Abstract
It is a commonsense thesis that unactualized possibilities are not parts of actuality. To keep his modal realism in line with this thesis, David Lewis employed his indexical account of the term “actual.” I argue that the addition of counterpart theory to Lewis’s modal realism undermines his strategy for respecting the commonsense thesis. The case made here also reveals a problem for Lewis’s attempt to avoid haecceitism.
The Natures of Types and Tokens: On the Metaphysical Commitments of Non-Reductive Physicalism
Authors: van Riel Raphael 
Published: August 2014

Abstract
Non-reductive physicalism has become the dominant view in the philosophy of mind. Some of its metaphysical underpinnings, however, have not been studied in detail yet. The present paper suggests that non-reductive physicalism is committed to a particular view on the connection between the natures of types and the natures of their tokens – thereby defending non-reductive physicalism against an argument recently put forward by Susan Schneider.
Correlating optical coherence tomography images with dose distribution in late oral radiation toxicity patients
Authors: Davoudi Bahar , Bizheva Kostadinka , Wong Alexander , Dinniwell Robert , Levin Wilfred , Vitkin Alex 
Published: August 2014

AbstractBackground and objective:Late oral radiation toxicity occurs in about half of the patients who undergo head-and-neck radiotherapy, reducing the quality of life drastically. The total delivered radiation dose has been shown to be one of the predictors of these late complications. To demonstrate this, the studies carried out so far have used either visual observation together with symptom-based scoring systems or histology to evaluate the tissue response. However, the former lacks imaging information on tissue subsurface and the latter is invasive and exposes the patients to additional risks. Therefore, there is a need for a non-hazardous, non-invasive subsurface monitoring tool that can provide more objective information on dose-dependent response of normal oral tissue to radiation.Materials and methods:To address this unmet clinical need, optical coherence tomography (OCT) was used. A clinical study was conducted on 14 late oral radiation toxicity patients and 5 age-matched healthy volunteers. OCT structural images were acquired from different oral regions in both cohorts and were then de-speckled in order to provide a better visualization of the subsurface layers and features. The alterations in patients’ de-speckled OCT images compared to the healthy cohort are reviewed, and potential correlations between the total dose to specific regions and the abnormal features observed in the OCT images of the same sites are discussed.Results:OCT images were acquired from 32 sites in 14 patients, 15 of these sites belonged to the regions which received >50 Gy radiation dose and the rest to the region which was irradiated to <50 Gy. The de-speckled OCT images from the former group showed major differences, such as total layer disruption, compared to the images of healthy oral tissue. The de-speckled OCT images from all but one of the regions which received <50 Gy showed normal features and layer definition compared to healthy oral OCT images. Same results were observed in an intra-patient comparison of the ipsilateral (dose >70 Gy) and contralateral (dose <25 Gy) soft palate of one of the patients, suggesting the results are independent of anatomical differences between individuals.Conclusion:This preliminary clinical study showed the ability of OCT to differentiate subsurface features in the oral regions that received high radiation dose (>50 Gy) compared to healthy oral tissue. These results can be used to design a prospective study to monitor oral subsurface changes periodically (e.g., every 6 months) following radiotherapy, to further understand the mechanism of late radiation toxicity and its relation to dose.
Oxidative stress and genetic markers of suboptimal antioxidant defense in the aging brain: a theoretical review
Authors: Salminen Lauren E. , Paul Robert H. 
Published: August 2014

AbstractNormal aging involves a gradual breakdown of physiological processes that leads to a decline in cognitive functions and brain integrity, yet the onset and progression of decline are variable among older individuals. While many biological changes may contribute to this degree of variability, oxidative stress is a key mechanism of the aging process that can cause direct damage to cellular architecture within the brain. Oligodendrocytes are at a high risk for oxidative damage due to their role in myelin maintenance and production and limited repair mechanisms, suggesting that white matter may be particularly vulnerable to oxidative activity. Antioxidant defense enzymes within the brain, such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and glutathione-S-transferase (GST), are crucial for breaking down the harmful end products of oxidative phosphorylation. Previous studies have revealed that allele variations of polymorphisms that encode these antioxidants are associated with abnormalities in SOD, CAT, GPx, and GST activity in the central nervous system. This review will focus on the role of oxidative stress in the aging brain and the impact of decreased antioxidant defense on brain integrity and cognitive function. Directions for future research investigations of antioxidant defense genes will also be discussed.
The effects of monetary policy regime shifts on the term structure of interest rates
Authors: Abdymomunov Azamat , Kang Kyu Ho 
Published: August 2014

AbstractWe investigate how the entire term structure of interest rates is influenced by changes in monetary policy regimes. To do so, we develop and estimate an arbitrage-free dynamic term-structure model which accounts for regime shifts in monetary policy and price of risk. Our results for US data from 1985 through 2008 indicate that (
Melatonin as a Candidate Therapeutic Drug for Protecting Bone Cells From Chlorhexidine‐Induced Damage
Authors: Proksch Susanne , Strobel Sabrina Lydia , Vach Kirstin , Abouassi Thaer , Tomakidi Pascal , Ratka‐Krüger Petra , Hellwig Elmar 
Published: August 2014

Background: Melatonin was proposed for use in periodontitis and peri‐implantitis therapy due to its bone‐supportive effects. This issue is of interest because standard adjuvant antiseptics, namely chlorhexidine (CHX), prove damaging for osteoblasts. Thus, the aim of this study is to investigate if melatonin is suitable as an auxiliary agent for protecting osteoblasts from CHX damage.Methods: MC3T3 osteoblast response was determined following administration of various CHX concentrations in the absence or presence of melatonin. Osteoblast morphology was evaluated, total reactive oxygen species (ROS) and superoxide levels were quantified, ratios of apoptotic and necrotic cells were identified by flow cytometry, metabolic activity of remaining cells was assessed, and effects were calculated with repeated measures analysis and post hoc P value adjustment.Results: CHX led to poor morphology, increased total ROS and superoxide levels, and rigorously diminished the number of vital and metabolic active osteoblasts in a concentration‐dependent manner. However, simultaneous melatonin supply supported cell morphogenesis and growth, reduced ROS and superoxide generation, shifted the percentage of CHX‐damaged cells from necrotic/late to early apoptotic events, and modulated metabolic activity in osteoblasts.Conclusion: These data reveal that melatonin protects osteoblasts in the CHX context, thereby implicating melatonin as a promising drug in periodontitis and peri‐implantitis treatment.
An Engineered Approach to Address the Need for Long Term Integrity in Cement Subject to Critical Stress Cycles in Deepwater Production Fields
Authors: Rojas R. Giron , Millan A. , Leon S. Gonzalez , Hernández J. Torres , Pando F. Salas 
Published: August 2014

Abstract
The life cycle of a well is not static; throughout the stages, several changes in downhole conditions occur that can affect the integrity of the well. Common activities performed during the construction of the well (e.g. changes in density of the drilling fluids or an increase in temperature while drilling) may have an impact on the achieved cement isolation. During completion activities including stimulation and fracture treatments and even during abandonment activities, the well is exposed to diverse stresses that can damage the hydraulic isolation achieved with the cementing jobs. This document reflects the main steps for a general design process to achieve long-term isolation developed for deepwater development fields in the Gulf of Mexico, specifically at the production stages. This study includes an interdisciplinary study of geomechanics data from the formations, current drilling techniques, and data from downhole sensors at exploratory wells in the area that allowed for better understanding of how the resulting stresses can affect the interaction between formation, cement sheath, and casing, and provides information to design the required cement systems for the development fields.
Improved Drilling Performance in Carbonates Build-Up Section with Innovative Aggressive PDC Bit Design
Authors: Agawani Waleed , Al-Khaldy Meshal Dawood , Taha Mohammed , Al-Failakawi Khaled A , Omar Marwa Gamal , Al Saadi Dhari Mohammed , Abdelhamid Atef , Al-Osaimi Mohammad K 
Published: August 2014

Abstract
Striking a balance between aggressiveness and steerability has always been a challenge in engineering new bit designs. The purpose of this paper is to highlight the engineering steps and challenges faced with designing a more aggressive bit that will drill faster while improving directional control and limiting vibrations to suit the application.
North Kuwait's 8.5″ build up section's geology comprises of layered carbonates, shale and sandstone. The section is known to induce vibrations in conventional RSS BHAs and can be challenging for directional work.
As a rule, less blades in a PDC bit makes a more aggressive bit that is therefore harder to steer with. Historically Kuwait's 8.5″ sections are drilled with a 6 bladed bit design. While proving stable, such a medium-set bit design limits performance in these formations.
The engineering process involved:
In depth analysis of current bit designs involved studying wear patterns, comparing designs that drilled faster sections and those that minimized downhole vibrations Analyzing different drive system specific requirements and the designs found most stable. Selecting the most appropriate PDC depth of cut management technology that would allow the bit to sustain higher parameters without generating extensive torque Drilling and hydraulics simulation software to optimize flow and simulate depth of cut management Extensive field trials
The result was the first 5 bladed PDC bit run in Kuwait; which improved drilling rate of penetrations by 24% while minimizing vibrations and maintaining precise steerability on RSS and AKO mud motor BHAs.
By managing the bits aggressiveness, a more aggressive PDC bit design was proposed and trialed on several wells proving consistent performance improvement on field average rate of penetrations while maintaining accurate steerability to successfully land the wells.
7” Multizone Single Trip Gravel Pack Aids in Reducing Costs and Enhances Completion Flexibility in Offshore Indonesia
Authors: Ping Wei , Lavoix Frederic , Muryanto Bonifasius , Nurrachman Firman , Chaloupka Vladimir , Landry Jed , Li Chun Ming 
Published: August 2014

Abstract
Multizone Single Trip Gravel Pack (MZ-STGP) completion has been the mainstay in Mahakam River Delta and North Java Sea in Indonesia since 2007. The system has been used as a sand control solution for its cost efficiency, the ability to complete multiple sands in a single trip and to provide zonal isolation for production selectivity.
Initial completions have used the 9 5/8” system offering large bore and pumping capacity required for deeper zone gravel packing. Additional requirements has driven the need for a use of a smaller system under various scenarios such as cases where 9 5/8” casing cannot reach planned depth, retrofitting gravel pack in existing wells or completing unexpected additional reserves below 9 5/8” casing shoe.
The paper reviews successful history of a 7” MZ-STGP system including its first worldwide installation in 2009. Introduction of the new system has been very smooth including another world's first combined 7” and 9 5/8” multizone gravel pack completion. The paper presents application concerns when considering multizone systems, as well as lessons learnt from the presented cases.
To date, eight wells have been completed successfully using this slimmer system within expected time frame confirming rig time reduction of 8-10 days per well compared to stacked gravel packs. Not only has the 7” MZ-STGP proven to reduce costs for operators, but it has also permited significant flexibility in drilling and completion operations. The system is now considered as a standard contingency for many operators in cases where a 9 5/8” shoe must be set higher than planned or when openhole completion cannot be run inside of an 8 1/2” open hole.
High Compression Expandable Liner Hanger Case History in the Bakken Shale: Pre-job Planning, Real Time Monitoring and Post Job Analysis
Authors: McCormick John , Brown Casey , Walters Gary 
Published: August 2014

Abstract
Shale plays have become a dominant source for oil and gas production in the United States and in other global areas. There also has been a dramatic increase in the number of horizontal wells being drilled in these plays as well as in the lateral lengths. Unfortunately, horizontal wells can create massive compressive and bending forces that increase the likelihood of damage to downhole tools. Challenges in running completion equipment to the target depths in the Bakken Shale when multi-stage fracturing operations are planned has also been challenging. This paper will discuss the use of expandable liner hangers (ELHs) and how they have been capable of meeting some of the Bakken Shale challenges.
Challenges when completing long horizontals are centered around large compressive loads, including the ability to get the string to bottom and the performance of downhole tools such as liner hangers. Expandable liner hangers have resolved some of these problems, since the ELH systems integrate the liner hanger, packer, and tieback receptacle into a single unit and can provide simpler operations with fewer trips into the hole. The ELH does not rely upon cement above the liner top to provide an efficient seal, since no slips are used to hang the liner. Instead, multiple elastomeric bands support the liner weight and supply redundant gas-tight seals. Although not yet a widely understood technology, high compression ELH completions have increased reliability, safety, and profitability in the Bakken shale, and this has led to the significant increase in its use.
High-compression expandable liner hanger (ELH) runs in the Bakken Shale have shown consistent superior performance, specifically the ability to handle massive loads when pushing strings to TD. This paper disseminates technical information to increase operator awareness of how this technology can improve completions in the still relatively new area of drilling in US shale plays. This paper also discusses how this technology provides needed solutions for safely delivering the completion string to TD and accurately placing completion equipment with flexibility and reliability.
Achievement of Maximum Mud Weights in K-Formate WBM with Micromax and Its Successful Implementations in Deep HPHT Wells
Authors: Al-Muhailan Mohannad , Al-Foudari Saud Jumah , Debroy Amalendu , Rajagopalan Arun 
Published: August 2014

Abstract
The Jurassic reservoirs of deep wells in Kuwait have traditionally been drilled with OBM. Barite is utilized as the weighting material in the OBM resulting damages to these reservoirs, thereby reducing the productivity to a significant extent. The higher oil to water ratio (95/5) of OBM limits the possibilities of identifying the micro fractures in reservoirs due to the limited conductive medium in OBM. Potassium formate WBM, with Manganese Tetraoxide as weighting material was successfully applied in HPHT wells overcoming these limitations.
K-Formate brine was utilized up to maximum density of 12.5 ppg to reduce the impacts of solids in the mud. For the first time, maximum mud weight of 17.8 ppg was achieved operationally using micromax (Mn3O4) in this WBM. Also, for the first time in Kuwait, this kind of fluid was used to drill the section with the inclinations above 60° in deep wells.
As a result of using K-Formate WBM in the reservoir sections, production increased significantly when compared to the wells drilled with OBM and barite. Wells were simulated easily without the presence of barite. Water based conductive medium gave better quality of image logs. Unlike other WBM's, K-formate WBM was stored for long periods, over a year in the mud plants without any damage to the mud properties. Recycling reduced the overall fluid costs in the subsequent wells drilled with K-formate WBM. Environmental damage due to the OBM spills and cuttings were completely avoided; K-formate WBM is highly bio-degradable under atmospheric conditions and is environmentally friendly.
The experience and success gained with its use on the initial wells led to the planned usage of this WBM on all deep exploratory wells. This paper explains the experiences gained and the achievements made over the years with K-formate WBM used for drilling the deep HPHT wells.
ECD Management Solves Lost Circulation Issues in Cementing Narrow Pressure Window: A Case Study
Authors: Isgenderov Islam , Bogaerts Martijn , Osayande Victor , Kurawle Irfan , Kanahuati Alia Iza , Aghaguluyev Javid 
Published: August 2014

Abstract
Zonal isolation in narrow pressure windows has traditionally been challenging. This is due to cement slurry losses or potential fluid flow after cement placement. Accurate pressure data are essential for well control and successful primary cementing. Higher fluid densities and pumping rates can lead to induced fracture and lost circulation. Often, to mitigate the potential for dynamic losses during cement placement, low-density Newtonian fluids (preflush) are pumped ahead of weighted spacers. It is recognized in the industry that Newtonian fluids achieve a turbulent flow regime much easier than non-Newtonian fluids. The impact of Newtonian fluids on the stability of nonaqueous fluid (NAF) systems and weighted spacers are often disregarded during cement job design and testing.
During cement placement, especially in extended reach wells, depending on the volume of preflush needed to maintain adequate wellbore security, a long column of preflush/mud interface may be created. With the Newtonian phase in turbulent flow, the erodability of the mud interface increases significantly. Though preferred for cementing, Newtonian fluids have a detrimental effect on the stability of the fluid interface. Whenever the yield point of the interface falls below the critical value for solids suspension or the slip velocity, weighting material sags out of the mud; this results in hydrostatic imbalance in the fluid column. When the overall hydrostatic pressure falls below the formation pressure at any point in the wellbore, the cement slurry will be invaded by formation fluid influx and a flow pathway created while cement is setting. This channel can become a flow path for hydrocarbons to the surface, leading to sustained casing pressure or a hydrocarbon seep to surface or seabed.
In the Caspian region, an engineering approach was implemented to manage cementing equivalent circulating densities (ECD) when designing cement jobs using lighter and Newtonian fluids ahead of weighted spacers. It has led to successful zonal isolation for recent wells and an evaluation of design considerations for cementing ERD wells.