bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two biochemically distinct lipophosphoglycans from Leishmania braziliensis and Leishmania infantum trigger different innate immune responses in murine macrophages
Authors: Ibraim Izabela Coimbra , de Assis Rafael Ramiro , Pessoa Natália Lima , Campos Marco Antônio , Melo Maria Norma , Turco Salvatore Joseph , Soares Rodrigo Pedro 
Published: March 2013

AbstractBackgroundThe dominant, cell surface lipophosphoglycan (LPG) ofLeishmaniais a multifunctional molecule involved in the interaction with vertebrate and invertebrate hosts. Although the role of LPG on infection has been extensively studied, it is not known if LPG interspecies variations contribute to the different immunopathologies of leishmaniases. To investigate the issue of interspecies polymorphisms, twoLeishmaniaspecies from the New World that express structural variations of side chains of LPG repeat units were examined. In this context, the procyclic form ofL. braziliensisLPG (strain M2903), is devoid of side chains, while theL. infantumLPG (strain BH46) has up to three glucoses residues in the repeat units.MethodsMice peritoneal macrophages from Balb/c, C57BL/6 and knock-out (TLR2−/−, TLR4−/−) were primed with IFN-γ and stimulated with purified LPG from both species. Nitric oxide and cytokine production, MAPKs (ERK, p38 and JNK) and NF-kB activation were evaluated.ResultsMacrophages stimulated withL. braziliensisLPG, had a higher TNF-α, IL-1β, IL-6 and NO production than those stimulated with that ofL. infantum. Furthermore, the LPGs from the two species resulted in differential kinetics of signaling via MAPK activation.L. infantumLPG exhibited a gradual activation profile, whereasL. braziliensisLPG showed a sharp but transient activation.L. braziliensisLPG was able to activate NF-kB.ConclusionThese data suggest that two biochemically distinct LPGs were able to differentially modulate macrophage functions.
Antioxidant capacity of calendula officinalis flowers extract and prevention of radiation induced oropharyngeal mucositis in patients with head and neck cancers: a randomized controlled clinical study
Authors: Babaee Neda , Moslemi Dariush , Khalilpour Mohammad , Vejdani Fatemeh , Moghadamnia Yasaman , Bijani Ali , Baradaran Mahmoud , Kazemi Mohammad Taghi , Khalilpour Asieh , Pouramir Mahdi , Moghadamnia Ali Akbar 
Published: March 2013

Abstract
This study was designed to determine the effect of Calendula officinalis flowers extract mouthwash as oral gel on radiation-induced oropharyngeal mucositis (OM) in patients with head-and-neck cancer. Forty patients with neck and head cancers under radiotherapy or concurrent chemoradiotherapy protocols were randomly assigned to receive either 2% calendula extract mouthwash or placebo (20 patients in each group). Patients were treated with telecobalt radiotherapy at conventional fractionation (200 cGy/fraction, five fractions weekly, 30–35 fractions within 4–7 weeks). The oropharyngeal mucositis was evaluated by two clinical investigators (a radiation oncologist and a dentist), using the oral mucositis assessment scale (OMAS). Trying to find out the possible mechanism of action of the treatment, total antioxidant, polyphenol and flavonoid contents, and quercetin concentration of the mouth wash were measured. Calendula mouthwash significantly decreased the intensity of OM compared to placebo at week 2 (score: 5.5 vs. 6.8, p = 0.019), week 3 (score: 8.25 vs. 10.95, p < 0.0001) and week 6 (score: 11.4 vs. 13.35, p = 0.031). Total antioxidant, polyphenol and flavonoid contents and quercetin concentration of the 2% extract were 2353.4 ± 56.5 μM, 313.40 ± 6.52 mg/g, 76.66 ± 23.24 mg/g, and 19.41 ± 4.34 mg/l, respectively. Calendula extract gel could be effective on decreasing the intensity of radiotherapy- induced OM during the treatment and antioxidant capacity may be partly responsible for the effect.
The care process of diabetic foot ulcer patients: a qualitative study in Iran
Authors: Aliasgharpour Mansooreh , Nayeri Nahid Dehghan 
Published: March 2013

Abstract
Background
The Purpose of this study is to clarify the care process for Iranian diabetic patients with diabetic foot ulcer condition.

Methods
The main question of this research was “How is the care process for diabetic foot ulcer patients and how do patients experience it?” This study was within the Grounded Theory method. Data collection was carried out until data saturation was achieved. Saturation was achieved after interviewing 11 patients, 4 physicians, one head nurse and one nurse.

Results
Three main themes emerged from this study, including: “disease management, disease experience and continuity of care”. Each of these themes is consisted of different sub-themes.

Conclusions
This is the first study to describe the care process in Iranian diabetic patients with diabetic foot ulcer disease. Knowing patients’ experience and the manner of dealing with them once faced with foot ulcer condition could facilitate a comprehensive decision making by therapists and better recovery of diabetic patients.
A feasibility study on beef tallow conversion to some esters for biodiesel production
Authors: Ghazavi Mohamad Ali , Fallahipanah Majid , Jeshvaghani Hamed Shahmirzae 
Published: March 2013

Abstract

Background
Nowadays, management and recycling of industrial by-products are one of the most important issues in developing and developed countries. Beef tallow is one of these residues produced in slaughter houses and primarily is utilized in soap production industry. However, when this industry is overloaded, the extra fats are usually incinerated or disposed in a sanitary landfill. However, beef tallow may be consumed in biodiesel production. Therefore, in this work, the process of biodiesel production in a pilot plant has been studied using beef tallow as raw material with methanol and potassium hydroxide as catalyst. The quality of the produced biodiesel is evaluated using Fourier transform infrared spectroscopy (FTIR) method.

Results
FTIR analysis showed that the final product contains ester compositions which can be used as biodiesel fuel in diesel engines. The viscosity of natural beef tallow was very high, and actually, it was solid; however, after transesterification the viscosity of the final product decreased, and it became liquid. The viscosity of the final product measured at 40°C was 5.3 mm2 s−1, and the comparison of this biodiesel with the data of ASTMD-445 standard resulted in the similarity of this product with petroleum diesel (3 to 12 mm2 s−1).

Conclusions
Alkaline transesterification of beef tallow with methanol decreases the viscosity of the final synthesized product and produces a high quality biodiesel for diesel engines. Beef tallow is one of the low cost residual materials available in slaughter houses. Therefore, the slaughter houses can be considered as one of the available sources to produce biodiesel. In this research, the process of biodiesel production from beef tallow was validated, but the economical viability must be improved by recovering methanol and glycerol.
Modeling the heterogeneity in risk of progression to Alzheimer's disease acrosscognitive profiles in mild cognitive impairment
Authors: Tatsuoka Curtis , Tseng Huiyun , Jaeger Judith , Varadi Ferenc , Smith Mark A , Yamada Tomoko , Smyth Kathleen A , Lerner Alan J ,   The Alzheimer's Disease Neuroimaging Initiative
Published: March 2013

Abstract
Introduction
Heterogeneity in risk of conversion to Alzheimer's disease (AD) among individualswith mild cognitive impairment (MCI) is well known. Novel statistical methods thatare based on partially ordered set (poset) models can be used to create modelsthat provide detailed and accurate information about performance with specificcognitive functions. This approach allows for the study of direct links betweenspecific cognitive functions and risk of conversion to AD from MCI. It also allowsfor further delineation of multi-domain amnestic MCI, in relation to specificnon-amnestic cognitive deficits, and the modeling of a range of episodic memoryfunctioning levels.

Methods
From the Alzheimer's Disease Neuroimaging Initiative (ADNI) study, conversion at24 months of 268 MCI subjects was analyzed. It was found that 101 of thosesubjects (37.7%) converted to AD within that time frame. Poset models were thenused to classify cognitive performance for MCI subjects. Respective observedconversion rates to AD were calculated for various cognitive subgroups, and byAPOE e4 allele status. These rates were then compared across subgroups.

Results
The observed conversion rate for MCI subjects with a relatively lower functioningwith a high level of episodic memory at baseline was 61.2%. In MCI subjects whoadditionally also had relatively lower perceptual motor speed functioning and atleast one APOE e4 allele, the conversion rate was 84.2%. In contrast, the observedconversion rate was 9.8% for MCI subjects with a relatively higher episodic memoryfunctioning level and no APOE e4 allele. Relatively lower functioning withcognitive flexibility and perceptual motor speed by itself also appears to beassociated with higher conversion rates.

Conclusions
Among MCI subjects, specific baseline cognitive profiles that were derived throughposet modeling methods, are clearly associated with differential rates ofconversion to AD. More precise delineation of MCI by such cognitive functioningprofiles, including notions such as multidomain amnestic MCI, can help in gainingfurther insight into how heterogeneity arises in outcomes. Poset-based modelingmethods may be useful for providing more precise classification of cognitivesubgroups among MCI for imaging and genetics studies, and for developing moreefficient and focused cognitive test batteries.
Comparison of three molecular assays for the detection and molecular characterization of circulating tumor cells in breast cancer
Authors: Strati Areti , Kasimir-Bauer Sabine , Markou Athina , Parisi Cleo , Lianidou Evi S 
Published: March 2013

Abstract
Introduction
Comparison studies between different analytical methodologies for circulating tumor cells (CTC) detection and molecular characterization are urgently needed, since standardization of assays is essential before their use in clinical practice.

Methods
We compared three different CTC molecular assays. To avoid discrepancies due to pre-analytical errors we used the same cDNAs throughout our study. CTC were isolated using anti-EpCAM and anti-MUC1 coated magnetic beads from 2 × 5 ml of peripheral blood of 254 early and 51 metastatic breast cancer patients and 30 healthy individuals. The same cDNAs were analyzed by: a) singleplex RT-qPCR assay for CK-19; b) multiplex RT-qPCR for CK-19, HER-2, MAGE- A3, and PBGD; and c) a commercially available molecular assay (AdnaTest BreastCancer) for GA733-2, MUC-1, HER-2 and beta-actin.

Results
In early breast cancer, CK-19 RT-qPCR, multiplex RT-qPCR and the AdnaTest, were positive for the presence of CTC in 14.2%, 22.8% and 16.5% subjects, respectively. The concordance between the AdnaTest and CK-19 RT-qPCR was 72.4% while between the AdnaTest and multiplex RT-qPCR was 64.6%. In patients with overt metastasis, CK-19 RT-qPCR, multiplex RT-qPCR and the AdnaTest were positive in 41.2%, 39.2% and 54.9% patients, respectively. The concordance between the AdnaTest and CK-19 RT-qPCR was 70.6% while between the AdnaTest and multiplex RT-qPCR was 68.6%.

Conclusions
All CTC assays gave similar results in about 70% of cases. Better agreement was found in the metastatic setting, possibly explained by the higher tumor load in this group. Discordances could be attributed to the different gene transcripts used to evaluate CTC positivity. Our results indicate the importance of CTC heterogeneity for their detection by different analytical methodologies.
Amygdala activation in maltreated children during pre-attentive emotional processing
Authors: McCrory Eamon J. , De Brito Stéphane A. , Kelly Philip A. , Bird Geoffrey , Sebastian Catherine L. , Mechelli Andrea , Samuel Sophie , Viding Essi 
Published: March 2013

BackgroundChildhood adversity is associated with significantly increased risk of psychiatric disorder. To date, functional magnetic resonance imaging (fMRI) studies of children have mainly focused on institutionalisation and investigated conscious processing of affect.AimsTo investigate neural response to pre-attentively presented affect cues in a community sample of children with documented experiences of maltreatment in the home.MethodA masked dot-probe paradigm involving pre-attentive presentation of angry, happy and neutral facial expressions was employed. Eighteen maltreated children were compared with 23 carefully matched non-maltreated peers.ResultsIncreased neural response was observed in the right amygdala for pre-attentively presented angry and happy faces in maltreated v. non-maltreated children. Level of amygdala activation was negatively associated with age at onset for several abuse subtypes.ConclusionsMaltreatment is associated with heightened neural response to positive and negative facial affect, even to stimuli outside awareness. This may represent a latent neural risk factor for future psychiatric disorder.
On the Performance of the Upstream Mobility Scheme Applied to Counter-Current Two-Phase Flow in a Heterogeneous Porous Medium
Authors: Mykkeltvedt Trine S. , Aavatsmark Ivar , Tveit Svenn 
Published: March 2013

Abstract
The upstream mobility scheme is widely used to solve hyperbolic conservation equations numerically. When heterogeneities in the porous medium are introduced, the flux function in these equations attains a spatial discontinuity. In many systems the upstream mobility scheme approximates a solution close to the solution produced by solving the associated Riemann problem, but in the case of a heterogeneous system there exists no convergence analysis.
In this work the upstream mobility scheme is applied to a counter-current flow in a reservoir where discontinuities in the flux function are introduced through the permeability. Examples of such counter-current flow systems in heterogeneous reservoirs are Water-Alternating-Gas (WAG), Steam-Assisted Gravity Drainage (SAGD) and flow of CO2 and brine. The flux functions in these systems involve both advection and gravity segregation components. In this work we show that the upstream mobility scheme may exhibit large errors compared to the physically relevant solution for some combinations of flux functions in such a system. We show that a small perturbation of the relative permeability values can lead to a large difference in the solution produced by the upstream mobility scheme.
We look at the one-dimensional case since the Riemann solutions are mostly unknown for more than one dimension. However, in the multidimensional case, many numerical methods use one-dimensional calculations for the flux in the direction normal to the boundaries of the discretization cell. Not only does the scheme encounter large errors compared to the physically relevant solution, but the solution also lacks entropy consistency. Studies of these errors and the convergence performance of the scheme are important due to the extensive use of the upstream mobility scheme in the reservoir simulation community.
Adjoint-Based History Matching of Structural Models Using Production and Time-Lapse Seismic Data
Authors: Kahrobaei S.. , van Essen G. M. , Van Doren J. F. , Van den Hof P. M. , Jansen J. D. 
Published: March 2013

Abstract
In spite of large uncertainties in the actual reservoir structure, structural parameters of a reservoir model are usually fixed during history matching and only the flow properties of the model are allowed to vary. This often leads to unlikely or even unfeasible property updates and possibly to a poor predictive capability of the model. In those cases it may be expected that updating of the structural parameters will improve the quality of the history match. Preferably such structural updates should be implemented in the static (geological) model, and not just in the dynamic (flow) model. In this paper we use a gradient-based history matching method to update structural properties of the static model. We use an adjoint method to efficiently compute the derivatives of the data mismatch with respect to grid block porosities in the dynamic model and convert the corresponding volume changes to structural updates (layer thicknesses) in the static model. This method is suitable for structural updating of large scale reservoir models using production data and/or time-lapse seismics or other spatially distributed data. The method is tested on a 3D synthetic model, where time-lapse as well as production data have been used to update depth of the reservoir’s bottom horizon. We obtained significant improvements in the history match quality and the predictive capability of the model.
Advanced Strategies of Forward Simulation for Adjoint-Based Optimization
Authors: Volkov O. , Voskov D. V. 
Published: March 2013

Abstract
Adjoint-based simulation is one of the most efficient methods for reservoir simulation optimization. The gradient information of the objective function and constraints is used to generate a sequence of quadratic programming subproblems converging to the extremum of non-linear problem. The adjoint method provides accurate gradients that help to converge to the optimal solution using the least number of iterations, where each iteration is a forward simulation. The quality and stability of the gradients play important roles in the optimization process. In this paper we present analysis of adjoint-gradients based on different aspects of the forward simulation. We demonstrate that in the presence of compressibility, gradients evaluated using bottom hole pressure (BHP) controls are less consistent with respect to time step refinement, and less stable compared with gradients evaluated using rate controls. Using simple examples, we demonstrate that adjoint-based gradients for rate-controls converge with refinement of the time step while gradients for BHP-controls suffer from convergence problem. Another important aspect of our study is the effect of different nonlinear constraints in the optimization process. In forward simulation, nonlinear constraints often introduce additional complexities due to the discontinuous nature of the switching procedure. Switching can occur at control points in time, or between two controls, and depends strongly on the time-stepping strategy and the truncation error. We compare strategies where individual well constraints are applied directly during the forward simulations and as nonlinear constraints in the optimization process. We demonstrate using two practical examples the advantages and disadvantages of both strategies. We also study the effect of time-truncation error and time-stepping strategy on the quality of the adjoint-gradients. For the time scale, we propose coarsening in both simulation time and redundant control time steps. With larger time steps and smaller numbers of control switches, we can improve efficiency of forward simulation by several fold. Next, the optimal controls of coarse time-step simulation are used as the initial guess for forward simulation of finer time-step resolution. We show how all of these issues affect the optimization of a full-field model.
Advanced Wellbore Simulation of Flow Control Devices With Feedback Control for Thermal Operations
Authors: Stone Terry , Damas Carlos Emilio , Woiceshyn Glenn , Law David Hin-Sum , Brown George , Olapade Peter , Bailey William J. 
Published: March 2013

Abstract
Events such as hydraulic gradients in the horizontal completion, geologic and fluid variations in the reservoir and well placement issues can produce very poor steam conformance in the Steam Assisted Gravity Drainage (SAGD) process. Operators have implemented many strategies in an effort to address the issue. Simultaneous injection in inner tubing and annulus space or dual-tubing completions are commonly used in SAGD wells to provide controllable injection and production from the heel and toe regions of the horizontal well pair but this does not guarantee both uniform and efficient performance. This paper presents a study of a hybrid of two technologies to improve both conformance and economics of this thermal process.
Recent work suggests that using Proportional-Integral-Derivative (PID) feedback to control the steam injection can lead to improvements in SAGD performance and conformance. The feedback control is applied to each steam injection point in the horizontal well pair. Injection at these control points is regulated by a PID feedback controller monitoring temperature differences between injected and produced fluids in order to both enforce a specified subcool and to achieve uniform production along the entire length of the producer. PID feedback control can be practically and inexpensively implemented in the field with current technology.
Inflow or injection control devices (ICDs) can also improve SAGD performance. ICDs (or FCDs) can be incorporated in the horizontal completion as restrictive elements to modify the pressure distribution along the length of the wellbore. Among other benefits, properly sized and distributed ICDs can create a more uniform flow profile along the horizontal section of the well, regardless of permeability, formation damage and wellbore location. Furthermore, ICDs on the producer can provide a self-regulating effect to prevent live steam from entering the sand control screen.
This paper examines detailed wellbore simulations of a SAGD process in which wells are equipped with a combination of ICD completions and feedback control in order to (i) determine the physical mechanisms (including the dynamic flow paths inside the well and in the near wellbore region), and (ii) outline practical procedures to determine an improved ICD completion and feedback control design. A novel aspect of this work is the inclusion of a revised flow-regime-independent multiphase flow correlation that can predict the pressure drop in horizontal and near-horizontal wells. Results presented in this paper should aid reservoir simulation engineers in both the design and optimization of steam injection in a SAGD well pair.
Modeling Multiphase Flow With Nonplanar Fractures
Authors: Al-Hinai Omar , Singh Gurpreet , Pencheva Gergina , Almani Tameem , Wheeler Mary F. 
Published: March 2013

Abstract
Modeling flow with fractures can be challenging due to complex fracture geometries, strong variations in length and time scales as well as the need to combine multiple flow models. In this work, we propose a technique for overcoming these challenges based on the mimetic finite difference method (MFD) and the related multipoint flux mixed finite element method (MFMFE). These discretizations can be employed for solving problems over a set of general polyhedral meshes that can capture nonplanar fracture geometry. Our approach defines a physically and mathematically consistent technique for including internal boundary conditions. In our discretizations, flow in the reservoir and flow in the fracture are coupled using different physical models and numerical schemes. The respective flow models are locally conservative and are based on an implicit pressure/explicit saturation formulation and its iterative form.