bluuebunny/crossref_metadata_2025_split huggingface dataset:
H9N2 avian influenza infection altered expression pattern of Sphiogosine-1-phosphate Receptor 1 in BALB/c mice
Authors: Tong Shuang , Tian Jin , Wang Heng , Huang Zhiqiang , Yu Meng , Sun Lingshuang , Liu Rongchang , Liao Ming , Ning Zhangyong 
Published: September 2013

Abstract

Background
The pathological damage inflicted by virulent AIV strains is often caused by inducing a positive feedback loop of cytokines in immune cells that cause excessive inflammation. Previous research has shown that a G protein-coupled receptor, sphingosine-1-phosphate receptor 1 (S1PR1), plays a crucial role in the development of excessive inflammation in influenza virus infection (Cell 146:861–862, 2011; Cell 146:980–991, 2011). BALB/c mice are common laboratory animals used in research of influenza virus; however the effects of influenza infections on expression patterns of S1PR1 in mice are unknown.

Methods
We investigated the expression patterns of S1PR1 in normal BALB/c mice and those infected by two distinct H9N2 AIV strains, one (A/chicken/Guangdong/V/2008,V) highly pathogenic, and the other (A/chicken/Guangdong/Ts/2004,Ts), non-pathogenic in mice, using quantitative PCR and immunohistochemistry (IHC) to detect S1PR1 mRNA and protein, respectively.

Results
S1PR1 mRNA was ubiquitously expressed in all the tissues examined, and significant differences were seen in mRNA expression between infected Ts, V and control mice in detected tissues, heart, liver, spleen, kidney and brain. S1PR1 protein was expressed in the cytoplasm and also demonstrated quantitative changes in expression in the various tissues between mice infected with the two strains of AIV.

Conclusions
Our results provided the first look at differences in S1PR1 expression patterns in BALB/c mice infected by non-pathogenic and highly pathogenic H9N2 influenza viruses. This information will not only be helpful in designing experiments to better understand the role of S1PR1 in virus-host interactions but also in developing novel anti-influenza agents to minimize the mortality and morbidity associated with highly virulent strains in avian and human populations.
A case of acute myeloid leukemia (AML) with an unreported combination of chromosomal abnormalities: gain of isochromosome 5p, tetrasomy 8 and unbalanced translocation der(19)t(17;19)(q23;p13)
Authors: Paar Christian , Herber Gabriele , Voskova Daniela , Fridrik Michael , Stekel Herbert , Berg Jörg 
Published: September 2013

Abstract

Background
Acute myeloid leukemia (AML) comprises a spectrum of myeloid malignancies which are often associated with distinct chromosomal abnormalities, and the analysis of such abnormalities provides us with important information for disease classification, treatment selection and prognosis. Some chromosomal abnormalities albeit recurrent are rare such as tetrasomy 8 or isochromosome 5p. In addition, erratic chromosomal rearrangements may occur in AML, sometimes unbalanced and also accompanied by other abnormalities. Knowledge on the contribution of rare abnormalities to AML disease, progression and prognosis is limited.
Here we report a unique case of acute monoblastic leukemia with gain of i(5)(p10), tetrasomy 8, an unbalanced translocation der(19)t(17;19)(q23;p13.3) and mutated NPM1.

Results
Bone marrow cells were examined by conventional karyotyping, fluorescence in situ hybridization (FISH) and mutation analysis at diagnosis and follow-up. At diagnosis we detected trisomy 8, an unbalanced translocation der(19)t(17;19)(q23;p13.3) and mutated NPM1. During the course of the disease we observed clonal evolution with gain of i(5)(p10), tetrasomy 8 and eventually duplication of der(19)t(17;19)(q23;p13.3). By using the der(19)t(17;19) as clonal marker, we found that i(5)(p10) and tetrasomy 8 were secondary genetic events and that tetrasomy 8 had clonally evolved from trisomy 8.

Conclusions
This case of acute monoblastic leukemia presents a combination of rare chromosomal abnormalities including the unbalanced translocation der(19)t(17;19)(q23;p13.3), hitherto un-reported in AML. In addition, our case supports the hypothesis of a step-wise clonal evolution from trisomy 8 to tetrasomy 8 in AML. Reporting and collecting data of rare chromosomal abnormalities will add information to AML disease, progression and prognosis, and may eventually translate to improved patient management.
Cdc42 overexpression induces hyperbranching in the developing mammary gland by enhancing cell migration
Authors: Bray Kristi , Gillette Melissa , Young Jeanette , Loughran Elizabeth , Hwang Melissa , Sears James Cooper , Vargo-Gogola Tracy 
Published: September 2013

Abstract
Introduction
The Rho GTPase Cdc42 is overexpressed and hyperactivated in breast tumors compared to normal breast tissue. Cdc42 regulates key processes that are critical for mammary gland morphogenesis and become disrupted during the development, progression, and metastasis of breast cancer. However, the contribution of Cdc42 to normal and neoplastic mammary gland development in vivo remains poorly understood. We were therefore interested in investigating the effects of Cdc42 overexpression on mammary gland morphogenesis as a first step toward understanding how its overexpression may contribute to mammary tumorigenesis.

Methods
We developed a tetracycline-regulatable Cdc42 overexpression mouse model in which Cdc42 can be inducibly overexpressed in the developing mammary gland. The effects of Cdc42 overexpression during postnatal mammary gland development were investigated using in vivo and in vitro approaches, including morphometric analysis of wholemounted mammary glands, quantification of histological markers, and primary mammary epithelial cell (MEC) functional and biochemical assays.

Results
Analysis of Cdc42-overexpressing mammary glands revealed abnormal terminal end bud (TEB) morphologies, characterized by hyperbudding and trifurcation, and increased side branching within the ductal tree. Quantification of markers of proliferation and apoptosis suggested that these phenotypes were not due to increased cell proliferation or survival. Rather, Cdc42 overexpressing MECs were more migratory and contractile and formed dysmorphic, invasive acini in three-dimensional cultures. Cdc42 and RhoA activities, phosphorylated myosin light chain, and MAPK signaling, which contribute to migration and invasion, were markedly elevated in Cdc42 overexpressing MECs. Interestingly, Cdc42 overexpressing mammary glands displayed several features associated with altered epithelial-stromal interactions, which are known to regulate branching morphogenesis. These included increased stromal thickness and collagen deposition, and stromal cells isolated from Cdc42 overexpressing mammary glands exhibited elevated mRNA expression of extracellular matrix proteins and remodeling enzymes.

Conclusions
These data suggest that Cdc42 overexpression disrupts mammary gland branching morphogenesis by altering Rho GTPase and MAPK signaling, leading to increased MEC contractility and migration in association with stromal alterations. Our studies provide insight into how aberrant Cdc42 expression may contribute to mammary tumorigenesis.
Muscle group dependent responses to stimuli in a grasshopper model for tonic immobility
Authors: Miriyala Ashwin , Dutta-Gupta Aparna , Joseph Joby 
Published: September 2013

Summary
Tonic Immobility (TI) is a prolonged immobile condition exhibited by a variety of animals when exposed to certain stimuli, and is thought to be associated with a specific state of arousal. In our study, we characterize this state by using the reliably inducible TI state of the grasshopper (Hieroglyphus banian) and by monitoring abdominal pulsations and body movements in response to visual and auditory stimuli. These pulsations are present during the TI and ‘awake’, standing states, but not in the CO2 anesthetized state. In response to the stimuli, animals exhibited a suppression in pulsation and a startle response. The suppression of pulsation lasted longer than the duration of stimulus application. During TI, the suppression of pulsation does not habituate over time, whereas the startle response does. In response to the translating visual stimulus, the pulsations are suppressed at a certain phase independent of the time of stimulus application. Thus, we describe TI in Hieroglyphus banian as a state more similar to an ‘awake’ state than to an anesthetized state. During TI, the circuitry to the muscle outputs controlling the abdomen pulsation and the startle response are, at least in some part, different. The central pattern generators that maintain the abdomen pulsation receive inputs from visual and auditory pathways.
Case Article—Keeping Logistics Under Wraps
Authors: Drake Matthew J. , Griffin Paul M. , Swann Julie L. 
Published: September 2013

This paper describes a teaching case that integrates logistics network design with an ethical decision-making process. The ethical issues center on a proposed network design strategy for parcel transportation known as zone skipping, whose implementation in this setting would require the disguising of the identity of freight. The paper describes the case, discusses its pedagogical goals and provides some recommendations for using the case successfully in a logistics or optimization course. Case Teaching Note: Interested Instructors please see the Instructor Materials page for access to the restricted materials. To maintain the integrity and usefulness of cases published in ITE, unapproved distribution of the case teaching notes and other restricted materials to any other party is prohibited.
Rock Classification in the Haynesville Shale-Gas Formation Based on Petrophysical and Elastic Rock Properties Estimated from Well Logs
Authors: Saneifar Mehrnoosh , Aranibar Alvaro , Heidari Zoya 
Published: September 2013

Abstract
Rock classification can enhance fracture treatment design for successful field development in organic-shale reservoirs. Rock brittleness and elastic properties are important parameters to be considered in selection of the best candidate zones for fracture treatment. However, characterization of the rapid variation of petrophysical, compositional, and rock elastic properties in organic-shale reservoirs is challenging. Well logs can be applied for real-time assessment of these formation properties at relatively high resolution compared to core measurements. In this paper, we introduce a rock classification technique in shale-gas reservoirs that takes into account well-log-based estimates of rock elastic properties as well as mineralogy, kerogen porosity, and organic-richness.
We first conduct a joint interpretation of well logs and core measurements to estimate depth-by-depth petrophysical and compositional properties of the shale-gas reservoir. The self-consistent approximation model is applied to estimate rock elastic properties. This model enables the assessment of elastic properties based on the estimated mineralogy and the inclusion shapes. We then calculate rock brittleness index from the estimated elastic properties. Rock classes are determined using estimated rock brittleness, mineralogy, total organic content. Finally, kerogen porosity is incorporated in the rock classification to further improve the identified rock types.
We applied the introduced rock classification technique in the Haynesville shale-gas formation. The identified rock classes were cross-validated with the existing core images. Unlike core-based rock classification techniques in organic-shale reservoirs, the introduced method in this paper is mainly based on well logs and can provide reliable rock classes without requiring a large core database. An efficient well-log-based rock classification technique can potentially enhance fracture treatment and production from complex organic-shale reservoirs through (a) detecting the best candidate zones for fracture treatment and (b) optimizing the number of required fracture stages.
A Heavy Oil Mobility Quicklook Using Dielectric Measurements at Four Depths of Investigation
Authors: Grayson Stephen , Hemingway James 
Published: September 2013

Abstract
Heavy oil sands around the world contain vast quantities of hydrocarbons. Evaluation of heavy oil sands is often complicated by low-salinity formation waters, reducing the contrast between oil- and water-bearing sands. Dielectric permittivity measurements are an excellent solution to this issue because they provide a water-filled porosity to compare with total porosity from density-neutron logs. In water sands, total and water-filled porosities read the same. But in oil zones, a difference is observed which is proportional to the oil saturation in the near-wellbore region. This yields an "oil crossover" indicator at the wellsite, allowing for easy identification of pay versus water sands, regardless of formation water salinity.
New dielectric measurements are available that offer an enhancement to heavy oil evaluation. A new dielectric tool has been developed that scans the reservoir with various receiver spacings, frequencies, and polarizations to provide a vast array of measurements. A novel application of a subset of these measurements makes it possible to evaluate heavy oil mobility in a wellsite quicklook presentation. This quicklook uses dielectric porosity measurements at four depths of investigation (DOI) in the region from 1-in. to 4-in. into the formation. If oil has moved owing to invasion, the four curves will show separation indicative of the movement. In a recent case study, the new dielectric tool was run in combination with triple-combo measurements on a number of wells in California, USA, containing heavy oil sands with varying oil mobility. In the immobile oil sands, the expected oil crossover was observed, with the four dielectric curves overlaying each other. In the mobile oil sands, each of the four curves showed variations in the oil crossover. Validation of the oil mobility interpretation was provided by a nuclear magnetic resonance (NMR) log run in one of the wells. The NMR porosity showed the well-known porosity deficit, resulting from the short T2 response of heavy oil, in the immobile oil zones. The deficit diminished where the quicklook showed higher oil mobility, confirming the interpretation. The quicklook allowed well-to-well and sand-to-sand mobility comparisons in the field. Nonlinear gradations were observed within the study area. The dielectric mobility quicklook also provides more effective use of oil saturations obtained from sidewall core samples by identifying flushing seen in high-mobility zones, where core saturations can be affected. This novel wellsite quicklook method for identification of oil mobility allows operators to adapt the completion technique and hardware to their advantage and optimize exploitation of the reservoir.
Acoustic Mapping and Characterization of Organic Matter in Shales
Authors: Bocangel Wara , Sondergeld Carl , Rai Chandra 
Published: September 2013

Abstract
The quantity and kind of hydrocarbon produced by organic rich shales is determined by the type, amount, distribution, and connectivity of the organics within the rock. The present study applies a new technique for mapping the distribution of organics using impedance contrast in Scanning Acoustic Microscope (SAM) images. Both SAM and SEM images were used to observe key features such as organic size, concentration, natural fractures, and organic lamination parallel to bedding. Complementary petrophysical and topological analyses were conducted with focus on the Wolfcamp shale formation.
The low density and compressional velocity of organic matter resulted in lower impedances with respect to the matrix. This impedance contrast made the SAM a suitable instrument to map organics. With a transducer frequency of 100 MHz, we resolved organic features that were larger than 10 µm. Fine core sampling of the Wolfcamp formation exhibited cyclic variation of TOC content that correlated positively with total porosity and connected porosity. Microstructural studies revealed connected organic networks, organic porosity, and microfractures, especially in high TOC samples. NMR wettability studies showed that samples with low TOC tend to be water wet whereas high TOC samples imbibed more dodecane, indicating oil wettability. The topological study on the organics showed that organic particle size distribution is skewed to finer particle areas (average 3.6 ×106 µm2). The organic roundness analysis indicated that most of the particles are circular or elliptical with specific minor to major axis ratios of 0.5 to 0.7.
Further topological studies of organics distributed parallel and perpendicular to the bedding plane will be key in elastic modeling. Microstructural studies with SEM and optical microscopes have been constrained to small areas at high resolution. This study indicates that acoustic microscopy can be used to analyze larger areas and provide a better understanding on the role of organic matter in shales at a larger scale.
Interpreting Distributed-Temperature Measurements Gathered in Deepwater Gas-Well Testing
Authors: Kabir C. S. , Yi X. , Jakymec M. , Hasan A. R. 
Published: September 2013

Abstract
In typical drill-stem testing (DST), transient pressures are gathered downhole while rate measurements occur at the surface. Adverse effects of heat transfer upon pressure, particularly during a buildup test in a gas well necessitate the close proximity of pressure measurements to the point of fluid entry. While pressure measurements are reliable with sufficient resolution in most settings, rate measurements often lack synergy with pressure due to the sensor resolution and frequency of monitoring. This lack of pressure/rate harmony may precipitate significant uncertainty in transient-test interpretations.
This paper presents a case study for a deepwater asset in Western Australia, where temperatures were recorded at various depth stations in four wells, each in a different reservoir, before, during, and after transient testing, in addition to the traditional downhole pressure and surface rate measurements. This temperature data allowed estimation of gas flow rates. The flow rate accuracy increased at shallower depths because increased heat transfer enhanced the fidelity of measurements. Overall, the distributed temperature data allowed the estimation of both the static geothermal and the dynamic flow temperature gradients.
An Experimental Study of Cyclic Gas Injection to Improve Shale Oil Recovery
Authors: Gamadi T. D. , Sheng J. J. , Soliman M. Y 
Published: September 2013

Abstract
Low oil recovery in shale oil reservoirs and vast shale reservoir volumes stimulate our efforts to investigate the application of enhanced oil recovery methods in shale oil reservoirs. A recent numerical study has indicated that cyclic gas injection could be an effective method to increase the oil recovery of shale oil reservoirs, and gas channeling can be mitigated. This paper presents our experimental verification and quantification of the potential to improve oil recovery by cyclic gas injection in shale oil reservoirs. Core plugs of Barnett, Marcos and Eagle Ford shales were used. The oil used was Mineral oil (Soltrol 130) and the gas used was Nitrogen. Unfractured cores were used in the experiments. The effects of cyclic time and injection pressure on oil recovery, among other parameters, were investigated. Our results also showed that cycle gas injection could increase the recovery from 10 to 50% depending on the injection pressure and shale core type. This study shows that one of the important mechanisms of cyclic gas injection is the pressure effect that causes a large pressure drawdown during the production phase. The cyclic gas injection provides an effective and practical method to improve oil recovery in shale reservoirs because the gas needed is available in liquid-rich shale plays.
Optimizing Water Injection in a Mature Chalk Field by Application of Streamline Simulation
Authors: Johansen K. , Jensen L. J. , Marsden C. , Bakshi S. 
Published: September 2013

Abstract
The South Arne field, located in the Danish sector in the North Sea, has been produced since 1999. The field is Operated by Hess with Dong energy and Danoil as partners. Initially, the field was developed with production wells only but water injectors were added after 1½ years which increased the recovery potential of the field significantly. Currently the field is operated with 20 wells (7 injectors and 13 producers). All wells are fitted with sliding sleeve doors that allow zones to be opened or shut. This provides the valuable opportunity (or obligation) to pursue a more efficient recovery of oil by manipulating sliding sleeve doors – both in injecting and producing wells. In order to understand the long term effects from such well interventions a full field streamline simulation model has been built that will allow the injection efficiencies of individual zones to be quantified. Knowing the injection efficiency of zones enables the right zones to be chosen for interventions and to optimize the overall field water injection efficiency. The main goal has been to reduce water recycling and improve the macroscopic sweep by diverting flow from injectors into less swept areas. An associated benefit from reducing water recycling is the reduced need for lift gas, that can then be allocated to other wells.
It will be shown how an existing conventional simulation model was adapted to a streamline simulator and how this model was used to predict future optimal interventions in injection wells to optimize oil recovery. Excluding the positive effect from freeing up lift gas a ∼1% increase in oil recovery is expected from relatively few yearly interventions.
A Project Based Production Engineering Training Course for Improved Job Performance
Authors: Phillips James , Wilkie David , Aggour Tamir 
Published: September 2013

Abstract
A key element of the training strategy of Saudi Aramco's Upstream Professional Development Center is to utilize simulated work environments and project-based learning that is customized to the actual job roles, workflows, tools and data that trainees will encounter on the job. This paper presents details of the design, development and implementation of a project-based training course that serves as the capstone learning event in a program designed to develop new university graduates into independently contributing production engineers. The course provides participants with an opportunity to integrate and practice job-critical skills learned during the four-year program, using real company data, workflows and tools to work through a realistic well surveillance and testing project. The outcome of the course is a plan to optimize and manage a field that includes free flowing wells, artificial lift wells and gas wells. The learned skills are reinforced by having the participants repeat the exercise for an area of their assigned fields upon leaving the course, culminating in a presentation to their local management on their findings and recommendations. Project-based training that reflects actual work environments results in high learner engagement, higher retention levels and improved job performance. The opportunity to immediately practice the learned skills upon returning to work ensures the adoption of learning and adds business value. This work provides a model of training that can be utilized in any technical environment to design, develop and deliver training that improves individual job performance and adds value to the business.