bluuebunny/crossref_metadata_2025_split huggingface dataset:
An overview of control strategy and diagnostic technology for foot-and-mouth disease in China
Authors: Ding Yao-Zhong , Chen Hao-Tai , Zhang Jie , Zhou Jian-Hua , Ma Li-Na , Zhang Liang , Gu Yuanxin , Liu Yong-Sheng 
Published: March 2013

Abstract
Foot-and-mouth disease (FMD) is one of most contagious animal diseases. It affects millions of cloven-hoofed animals and causes huge economic losses in many countries of the world. There are seven serotypes of which three (O, A and Asia 1) are endemic in China. Efficient control of FMD in China is crucial for the prevention and control of FMD in Asia and throughout the world. For the control of FMD, a powerful veterinary administration, a well-trained veterinary staff, a system of rapid and accurate diagnostic procedures and, in many countries, compulsory vaccination of susceptible animals are indispensable. This article strives to outline the Chinese animal disease control and prevention system, in particular for FMD, with the emphasis on diagnostic procedures applied in Chinese laboratories. In addition, new technologies for FMD diagnosis, which are currently in the phase of development or in the process of validation in Chinese laboratories, are described, such as lateral flow devices (LFD), Mab-based ELISAs, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and gold nanopariticle immuno-PCR (GNP-IPCR).
Transcriptome exploration of the sex pheromone gland of Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae)
Authors: González-Caballero Natalia , Valenzuela Jesus G , Ribeiro José MC , Cuervo Patricia , Brazil Reginaldo P 
Published: March 2013

AbstractBackgroundMolecules involved in pheromone biosynthesis may represent alternative targets for insect population control. This may be particularly useful in managing the reproduction ofLutzomyia longipalpis, the main vector of the protozoan parasiteLeishmania infantumin Latin America. Besides the chemical identity of the major components of theL. longipalpissex pheromone, there is no information regarding the molecular biology behind its production. To understand this process, obtaining information on which genes are expressed in the pheromone gland is essential.MethodsIn this study we used a transcriptomic approach to explore the pheromone gland and adjacent abdominal tergites in order to obtain substantial general sequence information. We used a laboratory-rearedL. longipalpis(one spot, 9-Methyl GermacreneB) population, captured in Lapinha Cave, state of Minas Gerais, Brazil for this analysis.ResultsFrom a total of 3,547 cDNA clones, 2,502 high quality sequences from the pheromone gland and adjacent tissues were obtained and assembled into 1,387 contigs. Through blast searches of public databases, a group of transcripts encoding proteins potentially involved in the production of terpenoid precursors were identified in the 4thabdominal tergite, the segment containing the pheromone gland. Among them, protein-coding transcripts for four enzymes of the mevalonate pathway such as 3-hydroxyl-3-methyl glutaryl CoA reductase, phosphomevalonate kinase, diphosphomevalonate descarboxylase, and isopentenyl pyrophosphate isomerase were identified. Moreover, transcripts coding for farnesyl diphosphate synthase and NADP+dependent farnesol dehydrogenase were also found in the same tergite. Additionally, genes potentially involved in pheromone transportation were identified from the three abdominal tergites analyzed.ConclusionThis study constitutes the first transcriptomic analysis exploring the repertoire of genes expressed in the tissue containing theL. longipalpispheromone gland as well as the flanking tissues. Using a comparative approach, a set of molecules potentially present in the mevalonate pathway emerge as interesting subjects for further study regarding their association to pheromone biosynthesis. The sequences presented here may be used as a reference set for future research on pheromone production or other characteristics of pheromone communication in this insect. Moreover, some matches for transcripts of unknown function may provide fertile ground of an in-depth study of pheromone-gland specific molecules.
Decrease of survivin, p53 and Bcl-2 expression in chemorefractory colorectal liver metastases may be predictive of radiosensivity after radioembolization with yttrium-90 resin microspheres
Authors: Melucci Elisa , Cosimelli Maurizio , Carpanese Livio , Pizzi Giuseppe , Izzo Francesco , Fiore Francesco , Golfieri Rita , Giampalma Emanuela , Sperduti Isabella , Ercolani Cristiana , Sciuto Rosa , Mancini Raffaello , Garufi Carlo , Diodoro Maria Grazia , Mottolese Marcella ,   Italian Society of Locoregional Therapies in Oncology (S.I.T.I.L.O.)
Published: March 2013

AbstractIn a prospective multicenter phase II trial of radioembolization with yttrium-90 (90Y-RE) in chemorefractory liver-dominant metastatic colorectal cancer (mCRC), we showed that median survival was 12.6 months (95% CI 7.0–18.3) with 48% of 50 patients achieving disease control. In this extension retrospective study, we analyzed whether a panel of biomarkers, known to be associated to an adverse clinical outcome, underwent variations in CRC liver metastases pre and post90Y-RE.Of the 50 patients included in the study, 29 pre-90Y-RE therapy and 15 post-90Y-RE had liver biopsy specimens available. In these series we investigated survivin, p53, Bcl-2 and Ki-67 expression pre- and post-90Y-RE by immuhistochemistry (IHC). Our findings evidenced a decrease of survivin (77% vs 33%), p53 (93% vs 73%), Bcl-2 (37% vs 26%) expression as well as of Ki-67 proliferation index (62.5% vs 40%) on liver biopsies collected post-90Y-RE as compared to pre-90Y-RE. In the subset of 13 matched liver metastases we further confirmed the reduction of survivin (92.3% vs 53.8%; p = 0.06), p53 (100% vs 69.2%; p = 0.05) and Bcl-2 (69.2% vs 53.8%; p = 0.05) expression post-90Y-RE. This biomarker modulation was accompanied by morphological changes as steatohepatitis, hepatocyte necrosis, collagen deposition, proliferating and/or bile duct ectasia, focal sinusoidal dilatation and fibrosis.Although our analysis was conducted in a very limited number cases, these changes appear strictly related to the response to90Y-RE therapy and may deserve further investigation on a larger series of patients.
Endometrial stromal tumors: immunohistochemical and molecular analysis of potential targets of tyrosine kinase inhibitors
Authors: Sardinha Ruth , Hernández Teresa , Fraile Susana , Tresserra Francesc , Vidal August , Gómez Maria Carmén , Astudillo Aurora , Hernández Nieves , Saenz de Santamaría Javier , Ordi Jaume , Gonçalves Luis , Ramos Rafael , Balañá Carmen , de Álava Enrique 
Published: March 2013

Abstract

Background
The systemic treatment of malignant endometrial stromal tumors (EST) is not well established. A few reports describe objective responses to imatinib, which suggest a novel therapeutic strategy for these tumors. Due to these facts, we aimed to perform a retrospective analysis of possible molecular targets of tyrosine kinase inhibitors (TKI) in EST: KIT, PDGFRA and EGFR.

Methods
52 endometrial stromal sarcomas and 13 undifferentiated endometrial sarcomas were examined and reviewed. Mutational analysis were performed for exons 9, 11, 13, and 17 of the KIT gene, exons 12 and 18 of the PDGFRA gene and exons 18, 19, 20 and 21 of the EGFR gene. The incidence and distribution of the KIT, PDGFRA, and EGFR expression were examined by immunohistochemistry, and EGFR amplification was assessed by fluorescence in situ hybridization.

Results
No mutations in KIT, PDGFRA and EGFR genes were detected. Overexpression of KIT, PDGFRA, EGFR, was detected in 2 (3%), 23 (35.4%), 7 (10.8%) cases respectively, whereas amplification of EGFR gene was not found.

Conclusions
Absence of significant expression, amplification and activating mutations on these tyrosine kinase receptors suggest that it is unlikely that EST can benefit from therapies such as TKI on the systemic setting.
Integrin α1 subunit is up-regulated in colorectal cancer
Authors: Boudjadi Salah , Carrier Julie C , Beaulieu Jean-François 
Published: March 2013

Abstract

Background
Colorectal cancer remains one of the leading causes of death from cancer in industrialized countries. Integrins are a family of heterodimeric glycoproteins involved in bidirectional cell signaling and participate in the regulation of cell shape, adhesion, migration, differentiation, gene transcription, survival and proliferation. The α1 subunit is known to be involved in RAS/ERK proliferative pathway activation and plays an important role in mammary carcinoma cell proliferation and migration. In the small intestine, α1 is present in the crypt proliferative compartment and absent in the villus, but nothing is known about its expression in the colon mucosa, or in colorectal cancer.

Results
In the present study, we demonstrated that in the colon mucosa, α1 is present in the basolateral domain of the proliferative cells of the crypt, and in the surrounding myofibroblasts. We found higher levels of α1 mRNA in 86% of tumours compared to their corresponding matched margin tissues. Immunohistochemical analysis showed that α1 staining was moderate to high in 65% of tumour cells and 97% of the reactive cells surrounding the tumour cells vs 23% of normal epithelial cells.

Conclusion
Our findings suggest an active role for the α1β1 integrin in colorectal cancer progression.
Establishment and Validation of Analytical Reference Panels for the Standardization of Quantitative BCR-ABL1 Measurements on the International Scale
Authors: White Helen E , Hedges John , Bendit Israel , Branford Susan , Colomer Dolors , Hochhaus Andreas , Hughes Timothy , Kamel-Reid Suzanne , Kim Dong-Wook , Modur Vijay , Müller Martin C , Pagnano Katia B , Pane Fabrizio , Radich Jerry , Cross Nicholas CP , Labourier Emmanuel 
Published: March 2013

BACKGROUND
Current guidelines for managing Philadelphia-positive chronic myeloid leukemia include monitoring the expression of the BCR-ABL1 (breakpoint cluster region/c-abl oncogene 1, non-receptor tyrosine kinase) fusion gene by quantitative reverse-transcription PCR (RT-qPCR). Our goal was to establish and validate reference panels to mitigate the interlaboratory imprecision of quantitative BCR-ABL1 measurements and to facilitate global standardization on the international scale (IS).

METHODS
Four-level secondary reference panels were manufactured under controlled and validated processes with synthetic Armored RNA Quant molecules (Asuragen) calibrated to reference standards from the WHO and the NIST. Performance was evaluated in IS reference laboratories and with non–IS-standardized RT-qPCR methods.

RESULTS
For most methods, percent ratios for BCR-ABL1 e13a2 and e14a2 relative to ABL1 or BCR were robust at 4 different levels and linear over 3 logarithms, from 10% to 0.01% on the IS. The intraassay and interassay imprecision was &lt;2-fold overall. Performance was stable across 3 consecutive lots, in multiple laboratories, and over a period of 18 months to date. International field trials demonstrated the commutability of the reagents and their accurate alignment to the IS within the intra- and interlaboratory imprecision of IS-standardized methods.

CONCLUSIONS
The synthetic calibrator panels are robust, reproducibly manufactured, analytically calibrated to the WHO primary standards, and compatible with most BCR-ABL1 RT-qPCR assay designs. The broad availability of secondary reference reagents will further facilitate interlaboratory comparative studies and independent quality assessment programs, which are of paramount importance for worldwide standardization of BCR-ABL1 monitoring results and the optimization of current and new therapeutic approaches for chronic myeloid leukemia.
Modeling Gas Solubility in Water for Foam Propagation in Porous Media
Authors: Beni Ali Naderi , Varavei Abdoljalil , Delshad Mojdeh , Farajzadeh Rouhollah 
Published: March 2013

Abstract
The gas solubility in water is one of the important influencing factors for foam rheology in porous media in foam flood processes for enhanced oil recovery (EOR). With regard to the application, numerical simulation plays a critical role in integrating geological, geophysical, and hydrological lab or field observations. In other words, validation of such processes can be based on lab analogues. Therefore, this type of exercise is necessary before making decision for permitting of foam flood projects.
In this study, fluid flow components of foam injection process are identified and quantified using well-constrained coreflood experimental data. The method allows estimating the foam evolution within complex numerical models. In particular, solubility features associated with injected gas at room temperature were first determined experimentally using a coreflood and X-ray tomography. Then, this problem is modeled with our in-house compositional reservoir simulator employing different foam models with varying complexity. These include local-equilibrium approximation considerations based on population balance and a table-look-up approach modeling of the fully coupled fluid flow and mass transport equations on different grid systems. A three-phase flash cubic equation of state (EOS) is used to allow for mutual solubilities of water, oil, and gas in all three phases. Also, the finite-difference structured and un-structured grids and the finite-difference approximation of the pressure and component molar-balance equations are used in the simulator employing an implicit pressure and explicit phase saturations and compositions (IMPES) solution scheme.
We obtained a fairly good match between the experimental and the simulation results confirming that we can use the simulator to predict the physical and chemical behavior of Foam-Assisted-EOR systems. With respect to the oil recovery, the simulation results indicate that unlike CO2, N2 foam produces more oil. It is also shown that the key parameters in model development include compositional EOS, the choice of solver and solution algorithm, grid discretization, and fluid flow characteristic curves.
This method is particularly important since it allows for the easy identification and evolution of the spread of foam plume. Further, this framework offers a guide for inclusion of existing knowledge on foam into practical numerical simulator.
Highly Optimized Phase Equilibrium Calculations
Authors: Haugen Kjetil B. , Beckner Bret L. 
Published: March 2013

Abstract
Phase equilibrium calculations can consume a significant fraction of total CPU time in compositional reservoir simulations. Thus, reducing the number calculations based on information from previous time steps is a common practice. Nevertheless, each time step requires a certain number of phase equilibrium calculations, and their computational cost ultimately depends on the speed at which the individual calculation is performed. The non-linear nature of phase equilibrium calculations requires an iterative solution procedure. A common approach is to combine successive substitutions and Newton iterations. However, accelerated successive substitutions, quasi-Newton methods, and reduced methods can reduce the number of iterations or the computational cost per iteration. Unfortunately, the importance of code optimization is rarely discussed in the literature. This paper investigates the impact of a handful of optimization techniques on the execution speeds of phase equilibrium algorithms. A series of benchmarks indicates that improving the instruction level parallelism in dense linear algebra operations and in the evaluation of transcendental functions leads to a 2X speed-up. An additional 3X performance improvement is achieved by a combination of SIMD vectorization and mixed precision implementations.
CO2 Mobility and Transitions between Co-Current and Counter-Current Flows
Authors: Javaheri Mohammad , Jessen Kristian 
Published: March 2013

Abstract
In this work, we study the modeling of CO2 migration/mobility in two-phase displacements of relevance to sequestration processes in saline aquifers. The main focus of this paper is on accurate modeling and robust numerical implementation of transitions between co-current and counter-current flows in fully implicit simulation of multiphase flow.
Several experimental and modeling studies have demonstrated that relative permeability decreases when multiphase flow transitions from co-current to counter-current settings in strongly water-wet porous materials. However, the associated implications in the context of CO2 sequestration design and optimization have not yet been studied or implemented in commonly available reservoir simulation tools.
In this study, the relative permeability of each phase is considered to be flow dependent, and a continuous transition between co-current and counter-current relative permeability functions (including hysteresis) has been implemented and tested in a fully implicit reservoir simulator. The transition is represented as a scanning loop between the bounding co- and counter-current relative permeability functions. This allows us to gauge the impact of transitions from co-current to counter-current flow on the vertical movement of CO2 and its impact on sweep efficiency, plume migration and entrapment in sequestration process.
Our formulation/implementation of flow dependent relative permeability functions is demonstrated to maintain the numerical stability of conventional fully implicit schemes. However, the total simulation time increases slightly because of the decrease in the vertical mobility and the associated increased travel distance prior to full phase segregation. Furthermore, the footprint of CO2 in the top layers of a reservoir, as predicted by traditional and by our new approach, is shown to be quite different. The results and analysis presented in this paper demonstrate that it is necessary to consider/integrate this effect in numerical calculations whenever transitions between co-current and counter-current flow may occur.
A Comparison of Analytic and Segmented Heat and Quality Loss in Thermal Steam Injection Wells
Authors: Stone Terry W. , Li Gary , Pallister Ian 
Published: March 2013

Abstract
Loss of steam quality and energy in steam injection wells is a key component in the design of steam-based thermal operations. These operations are increasingly employing more sophisticated wells that have longer trajectories with multiple control points. Reservoir simulation of thermal fields requires high accuracy in thermal boundary conditions for all wells, and conductive heat loss often plays a large role in overall energy conservation. Thermal injection wells are usually modelled only in the reservoir where injection enthalpy and steam quality at the bottom hole depth are estimated. In this paper, an examination is made of the benefits of modelling conductive heat and quality loss through the upper formation as part of the overall field simulation.
A comparison is made between the use of analytic models for heat and quality loss through the overburden based on work by Ramey and Satter, and a multisegment thermal well model that is segmented from the surface through the overburden and to the top of the oil-bearing formation. The analytic models of heat and steam quality loss are based on steady-state wellbore flow and conductive heat loss to the overburden. A more detailed representation of wellbore physics and control is available with the multi-segmented steam injection well model, including conductive heat transfer between the wellbore tubular and overburden or reservoir, a user-specified nodal resolution, a multiphase flow model that includes unequal phase flow rates of steam and condensate, the ability to correctly model the phase change of steam vapour to condensate as it flows downward from the surface, and an implicit coupling to the reservoir. Limitations of the analytic and segmented models are discussed including accuracy differences and instances when one or the other models may not be appropriate.
Multiphase Upscaling Using Approximation Techniques
Authors: Yang Yahan , Wang Xiaochen , Wu Xiao-Hui , Bi Linfeng 
Published: March 2013

Abstract
Coarsening and upscaling are common practices in reservoir simulation for reducing model size to improve computational efficiency. As part of the standard simulation workflow, engineers upscale geological models to simulation models to reduce the CPU time and requirement on computational resources. Coarsening is also an attractive approach for reduced order modeling. In that case, aggressive coarsening is carried out to drastically reduce the size of the simulation model, and hence simulation time. In reduced order modeling, a run is expected to take a small fraction of time required for a typical simulation run. Reduced order modeling plays a crucial role in uncertainty quantification, history matching, and other applications where a large number of simulation models need to be evaluated.
This paper proposes a new method for upscaling relative permeability for reduced order modeling and multiphase flow simulation. With this approach, approximations are introduced to eliminate the need for local or global multiphase flow simulations for the purpose of building coarse-scale displacement tables. Instead, the technique is based on global pressure solutions and velocity fields for incompressible two-phase flow. A set of time-of-flight and corresponding saturation solutions are obtained by solving 1st order partial differential equations in space variables using finite difference technique. The partial differential equation for saturations is general and may include gravity effects. Spatial time-of-flight (TOF) and saturation solutions are combined to construct approximate time-dependent saturation functions from which coarse-scale relative permeability functions are generated. To account for mobility differences in the reservoir before and after the reservoir is swept, several coarse relative permeability functions are computed based on a few approximate saturation and velocity distributions. This set of coarse relative permeability functions are then averaged to produce the final coarse permeability functions to be used for coarse-scale flow simulation. The proposed technique has been used to simulate flow on models with challenging horizontal and vertical permeability properties. Test results show that the use of the proposed multiphase upscaling method significantly improves the accuracy of coarse simulation results, while speeding up the run by more than 100 times.