Search results for: asymptotic normality

Authors: Özgür Bahadir, Meltem Kurtuncu

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The study was designed as quasi-experimental and conducted to determine the effect of music therapy on anxiety, fear and pain management in 6-12-year-old children undergoing surgery. The present study was carried out between 01.01.2016 and 19.08.2016 in BEU. Application and Research Center. The children aged 6 -12 who applied for surgery between the mentioned dates constituted the universe of the study. In the quasi-experimental study that was conducted in the clinics where children received operational treatment, two groups were formed: experimental group (the children who received musical therapy before the surgery) and control group (the children who were administered surveys and the surgery service routines only). Each group consisted of 30 children, and the participants of the study were 60 children in total. Necessary permissions were obtained from the parents of the children hospitalized before the beginning of the implementation. The data was collected through Child Anxiety Sensitivity Index (CASI), “Fear In Medical Treatment Scale”, Face, Legs, Activity, Cry, Consolability Scale (FLACC), Visual Analog Scale (VAS) and Participant Information Form. In the analysis of the data, Kolmogorov-Smirnov distribution scale was used to examine the normality of the distribution along with descriptive statistics methods (Frequency, Percentage, Mean, Standard Deviation). Data was presented in the tables in numbers and percentages. Means were demonstrated along with the standard deviations. The research compared children received; case and control groups include socio-demographic perspective, non-significant difference statistically among similar groups are intertwined. The general level of fear regarding the medical processes before returning to service after the operation and 30 minutes before getting discharged was found to be significantly low in the experimental group compared to control group (p<0.05). No statistically significant difference was found between experimental and control groups in terms of general level of fear regarding the medical processes before the operation, during the operation day and in the recovery room after the operation (p>0.05). Total CASI AD (anxiety sensitivity) levels before the operation, day of the operation and 30 minutes before the discharge for patients in experimental group was found to be significantly higher than the control group (p>0.05). There was no statistically significant difference between the experimental and control groups in the total CASI AD levels for the post-operative recovery room and for returning to the service room after the operation (p>0.05). VAS levels for patients in the experimental group in the post-operative recovery room was significantly higher than the control group (p>0.05). There was no statistically significant difference between the groups in terms of VAS findings in returning to service room after the operation and in 30 minutes before the discharge (p>0.05). As a result of the research; applied children music therapy in the experimental group anxiety, fear, and pain of the scales, their scores average, is lower than the control group children in this situation an increase in the satisfaction of children and parents was observed. In line with this, music therapy preoperative anxiety, fear, and can be used as an effective method of decreasing postoperative pain clinics is suggested.

Keywords: anxiety, children, fear, music therapy, pain

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Authors: Bamikole J. Adeyemi, Prashant Jadhawar, Lateef Akanji

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Liquid-liquid interfacial flow is an important process that has applications across many spheres. One such applications are residual oil mobilization, where crude oil and low salinity water are emulsified due to lowered interfacial tension under the condition of low shear rates. The amphiphilic components (asphaltenes and resins) in crude oil are considered to assemble at the interface between the two immiscible liquids. To justify emulsification, drag and snap-off suppression as the main effects of low salinity water, mobilization of residual oil is visualized as thickening and slip of the wetting phase at the brine/crude oil interface which results in the squeezing and drag of the non-wetting phase to the pressure sinks. Meanwhile, defining the boundary conditions for such a system can be very challenging since the interfacial dynamics do not only depend on interfacial tension but also the flow rate. Hence, understanding the flow boundary condition at the brine/crude oil interface is an important step towards defining the influence of low salinity water composition on residual oil mobilization. This work presents a numerical evaluation of three slip boundary conditions that may apply at liquid-liquid interfaces. A mathematical model was developed to describe the evolution of a viscoelastic interfacial thin liquid film. The base model is developed by the asymptotic expansion of the full Navier-Stokes equations for fluid motion due to gradients of surface tension. This model was upscaled to describe the dynamics of the film surface deformation. Subsequently, Jeffrey’s model was integrated into the formulations to account for viscoelastic stress within a long wave approximation of the Navier-Stokes equations. To study the fluid response to a prescribed disturbance, a linear stability analysis (LSA) was performed. The dispersion relation and the corresponding characteristic equation for the growth rate were obtained. Three slip (slip, 1; locking, -1; and no-slip, 0) boundary conditions were examined using the resulted characteristic equation. Also, the dynamics of the evolved interfacial thin liquid film were numerically evaluated by considering the influence of the boundary conditions. The linear stability analysis shows that the boundary conditions of such systems are greatly impacted by the presence of amphiphilic molecules when three different values of interfacial tension were tested. The results for slip and locking conditions are consistent with the fundamental solution representation of the diffusion equation where there is film decay. The interfacial films at both boundary conditions respond to exposure time in a similar manner with increasing growth rate which resulted in the formation of more droplets with time. Contrarily, no-slip boundary condition yielded an unbounded growth and it is not affected by interfacial tension.

Keywords: boundary conditions, liquid-liquid interfaces, low salinity water, residual oil mobilization

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Authors: Golson Mohamed, Yasmine Gamasy, Khaled EL-Khatib, Anas Al-Natour, Shady Fadel, Haytham Rashwan, Haytham Badawy, Nadia Farghaly

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Introduction: Wilm's tumor is the most common malignant renal tumor in children. Much progress has been made in the management of patients with this malignancy over the last 3 decades. Today treatments are based on several trials and studies conducted by the International Society of Pediatric Oncology (SIOP) in Europe and National Wilm's Tumor Study Group (NWTS) in the USA. It is necessary for us to understand why do we follow either of the protocols, NWTS which follows the upfront surgery principle or the SIOP which follows the upfront chemotherapy principle in all stages of the disease. Objective: The aim of is to assess outcome in patients treated with preoperative chemotherapy and patients treated with upfront surgery to compare their effect on overall survival. Study design: to decide which protocol to follow, study was carried out on records for patients aged 1 day to 18 years old suffering from Wilm's tumor who were admitted to Alexandria University Hospital, pediatric oncology, pediatric urology and pediatric surgery departments, with a retrospective survey records from 2010 to 2015, Design and editing of the transfer sheet with a (PRISMA flow study) Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Data were fed to the computer and analyzed using IBM SPSS software package version 20.0. (11) Qualitative data were described using number and percent. Quantitative data were described using Range (minimum and maximum), mean, standard deviation and median. Comparison between different groups regarding categorical variables was tested using Chi-square test. When more than 20% of the cells have expected count less than 5, correction for chi-square was conducted using Fisher’s Exact test or Monte Carlo correction. The distributions of quantitative variables were tested for normality using Kolmogorov-Smirnov test, Shapiro-Wilk test, and D'Agstino test, if it reveals normal data distribution, parametric tests were applied. If the data were abnormally distributed, non-parametric tests were used. For normally distributed data, a comparison between two independent populations was done using independent t-test. For abnormally distributed data, comparison between two independent populations was done using Mann-Whitney test. Significance of the obtained results was judged at the 5% level. Results: A significantly statistical difference was observed for survival between the two studied groups favoring the upfront chemotherapy(86.4%)as compared to the upfront surgery group (59.3%) where P=0.009. As regard complication, 20 cases (74.1%) out of 27 were complicated in the group of patients treated with upfront surgery. Meanwhile, 30 cases (68.2%) out of 44 had complications in patients treated with upfront chemotherapy. Also, the incidence of intraoperative complication (rupture) was less in upfront chemotherapy group as compared to upfront surgery group. Conclusion: Upfront chemotherapy has superiority over upfront surgery.As the patient who started with upfront chemotherapy shown, higher survival rate, less percent in complication, less percent needed for radiotherapy, and less rate in recurrence.

Keywords: Wilm's tumor, renal tumor, chemotherapy, surgery

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Authors: Samuele Viaro, Pierre Ricco

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Görtler instabilities generate in boundary layers from an unbalance between pressure and centrifugal forces caused by concave surfaces. Their spatial streamwise evolution influences transition to turbulence. It is therefore important to understand even the early stages where perturbations, still small, grow linearly and could be controlled more easily. This work presents a rigorous theoretical framework for compressible flows using the linearized unsteady boundary region equations, where only the streamwise pressure gradient and streamwise diffusion terms are neglected from the full governing equations of fluid motion. Boundary and initial conditions are imposed through an asymptotic analysis in order to account for the interaction of the boundary layer with free-stream turbulence. The resulting parabolic system is discretize with a second-order finite difference scheme. Realistic flow parameters are chosen from wind tunnel studies performed at supersonic and subsonic conditions. The Mach number ranges from 0.5 to 8, with two different radii of curvature, 5 m and 10 m, frequencies up to 2000 Hz, and vortex spanwise wavelengths from 5 mm to 20 mm. The evolution of the perturbation flow is shown through velocity, temperature, pressure profiles relatively close to the leading edge, where non-linear effects can still be neglected, and growth rate. Results show that a global stabilizing effect exists with the increase of Mach number, frequency, spanwise wavenumber and radius of curvature. In particular, at high Mach numbers curvature effects are less pronounced and thermal streaks become stronger than velocity streaks. This increase of temperature perturbations saturates at approximately Mach 4 flows, and is limited in the early stage of growth, near the leading edge. In general, Görtler vortices evolve closer to the surface with respect to a flat plate scenario but their location shifts toward the edge of the boundary layer as the Mach number increases. In fact, a jet-like behavior appears for steady vortices having small spanwise wavelengths (less than 10 mm) at Mach 8, creating a region of unperturbed flow close to the wall. A similar response is also found at the highest frequency considered for a Mach 3 flow. Larger vortices are found to have a higher growth rate but are less influenced by the Mach number. An eigenvalue approach is also employed to study the amplification of the perturbations sufficiently downstream from the leading edge. These eigenvalue results are compared with the ones obtained through the initial value approach with inhomogeneous free-stream boundary conditions. All of the parameters here studied have a significant influence on the evolution of the instabilities for the Görtler problem which is indeed highly dependent on initial conditions.

Keywords: compressible boundary layers, Görtler instabilities, receptivity, turbulence transition

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Authors: Sergey A. Lurie, Yury O. Solyaev, Dmitry B. Volkov-Bogorodsky, Alexander V. Volkov

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The media with voids is considered and the method of the analytical estimation of the effective mechanical properties in the theory of elastic materials with voids is proposed. The variational model of the porous media is discussed, which is based on the model of the media with fields of conserved dislocations. It is shown that this model is fully consistent with the known model of the linear elastic materials with voids. In the present work, the generalized model of the porous media is proposed in which the specific surface properties are associated with the field of defects-pores in the volume of the deformed body. Unlike typical surface elasticity model, the strain energy density of the considered model includes the special part of the surface energy with the quadratic form of the free distortion tensor. In the result, the non-classical boundary conditions take modified form of the balance equations of volume and surface stresses. The analytical approach is proposed in the present work which allows to receive the simple enough engineering estimations for effective characteristics of the media with free dilatation. In particular, the effective flexural modulus and Poisson's ratio are determined for the problem of a beam pure bending. Here, the known voids elasticity solution was expanded on the generalized model with the surface effects. Received results allow us to compare the deformed state of the porous beam with the equivalent classic beam to introduce effective bending rigidity. Obtained analytical expressions for the effective properties depend on the thickness of the beam as a parameter. It is shown that the flexural modulus of the porous beam is decreased with an increasing of its thickness and the effective Poisson's ratio of the porous beams can take negative values for the certain values of the model parameters. On the other hand, the effective shear modulus is constant under variation of all values of the non-classical model parameters. Solutions received for a beam pure bending and the hydrostatic loading of the porous media are compared. It is shown that an analytical estimation for the bulk modulus of the porous material under hydrostatic compression gives an asymptotic value for the effective bulk modulus of the porous beam in the case of beam thickness increasing. Additionally, it is shown that the scale effects appear due to the surface properties of the porous media. Obtained results allow us to offer the procedure of an experimental identification of the non-classical parameters in the theory of the linear elastic materials with voids based on the bending tests for samples with different thickness. Finally, the problem of implementation of the Saint-Venant hypothesis for the transverse stresses in the porous beam are discussed. These stresses are different from zero in the solution of the voids elasticity theory, but satisfy the integral equilibrium equations. In this work, the exact value of the introduced surface parameter was found, which provides the vanishing of the transverse stresses on the free surfaces of a beam.

Keywords: effective properties, scale effects, surface defects, voids elasticity

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Authors: M. Skibinska, A. Rajewska-Rager, M. Dmitrzak-Weglarz, N. Lepczynska, P. Sibilski, P. Kapelski, J. Pawlak, J. Twarowska-Hauser

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Introduction: Neurotrophic factors have been implicated in neuropsychiatric disorders. Brain-Derived Neurotrophic Factor (BDNF) influences neuron differentiation in development as well as synaptic plasticity and neuron survival in adulthood. BDNF is widely studied in mood disorders and has been proposed as a biomarker for depression. BDNF is synthesized as precursor protein – proBDNF. Both forms are biologically active and exert opposite effects on neurons. Aim: The aim of the study was to examine the serum levels of BDNF and proBDNF in unipolar and bipolar young patients below 24 years old during hypo/manic, depressive episodes and in remission compared to healthy control group. Methods: In a prospective 2 years follow-up study, we investigated alterations in levels of BDNF and proBDNF in 79 patients (23 males, mean age 19.08, SD 3.3 and 56 females, mean age 18.39, SD 3.28) diagnosed with mood disorders: unipolar and bipolar disorder compared with 35 healthy control subjects (7 males, mean age 20.43, SD 4.23 and 28 females, mean age 21.25, SD 2.11). Clinical characteristics including mood, comorbidity, family history, and treatment, were evaluated during control visits and clinical symptoms were rated using the Hamilton Depression Rating Scale and Young Mania Rating Scale. Serum BDNF and proBDNF concentrations were determined by Enzyme-Linked Immunosorbent Assays (ELISA) method. Serum BDNF and proBDNF levels were analysed with covariates: sex, age, age > 18 and < 18 years old, family history of affective disorders, drug-free vs. medicated status. Normality of the data was tested using Shapiro-Wilk test. Levene’s test was used to calculate homogeneity of variance. Non-parametric Tests: Mann-Whitney U test, Kruskal-Wallis ANOVA, Friedman’s ANOVA, Wilcoxon signed rank test, Spearman correlation coefficient were applied in analyses The statistical significance level was set at p < 0.05. Results: BDNF and proBDNF serum levels did not differ between patients at baseline and controls as well as comparing patients in acute episode of depression/hypo/mania at baseline and euthymia (at month 3 or 6). Comparing BDNF and proBDNF levels between patients in euthymia and control group no differences have been found. Increased BDNF level in women compared to men at baseline (p=0.01) have been observed. BDNF level at baseline was negatively correlated with depression and mania occurence at 24 month (p=0.04). BDNF level at 12 month was negatively correlated with depression and mania occurence at 12 month (p=0.01). Correlation of BDNF level with sex have been detected (p=0.01). proBDNF levels at month 3, 6 and 12 negatively correlated with disease status (p=0.02, p=0.008, p=0.009, respectively). No other correlations of BDNF and proBDNF levels with clinical and demographical variables have been detected. Discussion: Our results did not show any differences in BDNF and proBDNF levels between depression, mania, euthymia, and controls. Imbalance in BDNF/proBDNF signalling may be involved in pathogenesis of mood disorders. Further studies on larger groups are recommended. Grant was founded by National Science Center in Poland no 2011/03/D/NZ5/06146.

Keywords: bipolar disorder, Brain-Derived Neurotrophic Factor (BDNF), proBDNF, unipolar depression

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Authors: A. C. Facin, M. C. Maronezi , M. P. Menezes, G. L. Montanhim, L. Pavan, M. A. R. Feliciano, R. P. Nociti, R. A. R. Uscategui, P. C. Moraes

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The incidence of brachycephalic syndrome (BS) in the clinical routine of small animals has increased significantly giving the higher proportion of brachycephalic pets in the last years and has been considered as an animal welfare problem. The treatment of BS is surgical and the clinical signs related can be considerably attenuated. Nevertheless, the systemic effects of the BS are still poorly reported and little is known about these when the surgical correction is not performed early. Affected dogs are more likely to develop cardiopulmonary, gastrointestinal and sleep disorders in which the chronic hypoxemia plays a major role. This syndrome is compared with the obstructive sleep apnea (OSA) in humans, both considered as causes of systemic and metabolic dysfunction. Among the several consequences of the BS little is known if the syndrome also affects the hepatic tissue of brachycephalic patients. Elastography is a promising ultrasound technique that evaluates tissue elasticity and has been recently used with the purpose of diagnosis of liver fibrosis. In medicine, it is a growing concern regarding the hepatic injury of patients affected by OSA. This prospective study hypothesizes if there is any consequence of BS in the hepatic parenchyma of brachycephalic dogs that don’t receive any surgical treatment. This study was conducted following the approval of the Animal Ethics and Welfare Committee of the Faculdade de Ciências Agrárias e Veterinárias, UNESP, Campus Jaboticabal, Brazil (protocol no 17944/2017) and funded by Sao Paulo Research Foundation (FAPESP, process no 2017/24809-4). The methodology was based in ARFI elastography using the ACUSON S2000/SIEMENS device, with convex multifrequential transducer and specific software as well as clinical evaluation of the syndrome, in order to determine if they can be used as a prognostic non-invasive tool. On quantitative elastography, it was collected three measures of shear wave velocity (meters per second) and depth in centimeters in the left lateral, left medial, right lateral, right medial and caudate lobe of the liver. The brachycephalic patients, 16 pugs and 30 french bulldogs, were classified using a previously established 4-point functional grading system based on clinical evaluation before and after a 3-minute exercise tolerance test already established and validated. The control group was based on the same features collected in 22 beagles. The software R version 3.3.0 was used for the analysis and the significance level was set at 0.05. The data were analysed for normality of residuals and homogeneity of variances by Shapiro-Wilks test. Comparisons of parametric continuous variables between breeds were performed by using ANOVA with a post hoc test for pair wise comparison. The preliminary results show significant statistic differences between the brachycephalic groups and the control group in all lobes analysed (p ≤ 0,05), with higher values of shear wave velocities in the hepatic tissue of brachycephalic dogs. In this context, the results obtained in this study contributes to the understanding of BS as well as its consequences in our patients, reflecting in evidence that one more systemic consequence of the syndrome may occur in brachycephalic patients, which was not related in the veterinary literature yet.

Keywords: airway obstruction, brachycephalic airway obstructive syndrome, hepatic injury, obstructive sleep apnea

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Authors: Yasmin A. M. Ferreira, Ana C. K. Pelissari, Sofia De C. F. Vicente, Raquel M. Da S. Campos, Deborah C. L. Masquio, Lian Tock, Lila M. Oyama, Flavia C. Corgosinho, Valter T. Boldarine, Ana R. Dâmaso

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The prevalence of overweight and obesity is growing around the world and currently considered a global epidemic. Food and nutrition are essential requirements for promoting health and protecting non-communicable chronic diseases, such as obesity and cardiovascular disease. Specific dietary components may modulate the inflammation and oxidative stress in obese individuals. Few studies have investigated the dietary Inflammation Factor Rating (IFR) in obese adolescents. The IFR was developed to characterize an individual´s diet on anti- to pro-inflammatory score. This evaluation contributes to investigate the effects of inflammatory diet in metabolic profile in several individual conditions. Objectives: The present study aims to investigate the effects of a multidisciplinary weight loss therapy on inflammation factor rating and cardiometabolic risk in obese adolescents. Methods: A total of 26 volunteers (14-19 y.o) were recruited and submitted to 20 weeks interdisciplinary therapy allied to health education website- Ciclo do Emagrecimento®, including clinical, nutritional, psychological counseling and exercise training. The body weight was monitored weekly by self-report and photo. The adolescents answered a test to evaluate the knowledge of the topics covered in the videos. A 24h dietary record was applied at the baseline and after 20 weeks to assess the food intake and to calculate IFR. A negative IFR suggests that diet may have inflammatory effects and a positive IFR indicates an anti-inflammatory effect. Statistical analysis was performed using the program STATISTICA version 12.5 for Windows. The adopted significant value was α ≤ 5 %. Data normality was verified with the Kolmogorov Smirnov test. Data were expressed as mean±SD values. To analyze the effects of intervention it was applied test t. Pearson´s correlations test was performed. Results: After 20 weeks of treatment, body mass index (BMI), body weight, body fat (kg and %), abdominal and waist circumferences decreased significantly. The mean of high-density lipoprotein cholesterol (HDL-c) increased after the therapy. Moreover, it was found an improvement of inflammation factor rating from -427,27±322,47 to -297,15±240,01, suggesting beneficial effects of nutritional counselling. Considering the correlations analysis, it was found that pro-inflammatory diet is associated with increase in the BMI, very low-density lipoprotein cholesterol (VLDL), triglycerides, insulin and insulin resistance index (HOMA-IR); while an anti-inflammatory diet is associated with improvement of HDL-c and insulin sensitivity Check index (QUICKI). Conclusion: The 20-week blended multidisciplinary therapy was effective to reduce body weight, anthropometric circumferences and improve inflammatory markers in obese adolescents. In addition, our results showed that an increase in inflammatory profile diet is associated with cardiometabolic parameters, suggesting the relevance to stimulate anti-inflammatory diet habits as an effective strategy to treat and control of obesity and related comorbidities. Financial Support: FAPESP (2017/07372-1) and CNPq (409943/2016-9)

Keywords: cardiometabolic risk, inflammatory diet, multidisciplinary therapy, obesity

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Authors: Monika Dmitrzak-Weglarz, Aleksandra Rajewska-Rager, Maria Skibinska, Natalia Lepczynska, Piotr Sibilski, Joanna Pawlak, Pawel Kapelski, Joanna Hauser

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Epidermal growth factor (EGF) is a well-known neurotrophic factor that involves in neuronal growth and synaptic plasticity. The proteomic research provided in order to identify novel candidate biological markers for mood disorders focused on elevated EGF serum level in patients during depression episode. However, the EGF association with mood disorder spectrum among adolescents and young adults has not been studied extensively. In this study, we aim to investigate the serum levels of EGF in adolescents and young adults during hypo/manic, depressive episodes and in remission compared to healthy control group. In our study, we involved 80 patients aged 12-24 years in 2-year follow-up study with a primary diagnosis of mood disorder spectrum, and 35 healthy volunteers matched by age and gender. Diagnoses were established according to DSM-IV-TR criteria using structured clinical interviews: K-SADS for child and adolescents, and SCID for young adults. Clinical and biological evaluations were made at baseline and euthymic mood (at 3th or 6th month of treatment and after 1 and 2 years). The Young Mania Rating Scale and Hamilton Rating Scale for Depression were used for assessment. The study protocols were approved by the relevant ethics committee. Serum protein concentration was determined by Enzyme-Linked Immunosorbent Assays (ELISA) method. Human EGF (cat. no DY 236) DuoSet ELISA kit was used (R&D Systems). Serum EGF levels were analysed with following variables: age, age under 18 and above 18 years old, sex, family history of affective disorders, drug-free vs. medicated. Shapiro-Wilk test was used to test the normality of the data. The homogeneity of variance was calculated with Levene’s test. EGF levels showed non-normal distribution and the homogeneity of variance was violated. Non-parametric tests: Mann-Whitney U test, Kruskall-Wallis ANOVA, Friedman’s ANOVA, Wilcoxon signed rank test, Spearman correlation coefficient was applied in the analyses The statistical significance level was set at p<0.05. Elevated EGF level at baseline (p=0.001) and at month 24 (p=0.02) was detected in study subjects compared with controls. Increased EGF level in women at month 12 (p=0.02) compared to men in study group have been observed. Using Wilcoxon signed rank test differences in EGF levels were detected: decrease from baseline to month 3 (p=0.014) and increase comparing: month 3 vs. 24 (p=0.013); month 6 vs. 12 (p=0.021) and vs. 24 (p=0.008). EGF level at baseline was negatively correlated with depression and mania occurrence at 24 months. EGF level at 24 months was positively correlated with depression and mania occurrence at 12 months. No other correlations of EGF levels with clinical and demographical variables have been detected. The findings of the present study indicate that EGF serum level is significantly elevated in the study group of patients compared to the controls. We also observed fluctuations in EGF levels during two years of disease observation. EGF seems to be useful as an early marker for prediction of diagnosis, course of illness and treatment response in young patients during first episode od mood disorders, which requires further investigation. Grant was founded by National Science Center in Poland no 2011/03/D/NZ5/06146.

Keywords: biological marker, epidermal growth factor, mood disorders, prediction

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Authors: Sagar Saroha, Sawan S. Sinha, Sunil Lakshmipathy

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Reynolds averaged Navier-Stokes (RANS) model is the popular computational tool for prediction of turbulent flows. Being computationally less expensive as compared to direct numerical simulation (DNS), RANS has received wide acceptance in industry and research community as well. However, for high Reynolds number flows, the traditional RANS approach based on the Boussinesq hypothesis is incapacitated to capture all the essential flow characteristics, and thus, its performance is restricted in high Reynolds number flows of practical interest. RANS performance turns out to be inadequate in regimes like flow over curved surfaces, flows with rapid changes in the mean strain rate, duct flows involving secondary streamlines and three-dimensional separated flows. In the recent decade, partially averaged Navier-Stokes (PANS) methodology has gained acceptability among seamless bridging methods of turbulence- placed between DNS and RANS. PANS methodology, being a scale resolving bridging method, is inherently more suitable than RANS for simulating turbulent flows. The superior ability of PANS method has been demonstrated for some cases like swirling flows, high-speed mixing environment, and high Reynolds number turbulent flows. In our work, we intend to evaluate PANS in case of separated turbulent flows past bluff bodies -which is of broad aerodynamic research and industrial application. PANS equations, being derived from base RANS, continue to inherit the inadequacies from the parent RANS model based on linear eddy-viscosity model (LEVM) closure. To enhance PANS’ capabilities for simulating separated flows, the shortcomings of the LEVM closure need to be addressed. Inabilities of the LEVMs have inspired the development of non-linear eddy viscosity models (NLEVM). To explore the potential improvement in PANS performance, in our study we evaluate the PANS behavior in conjugation with NLEVM. Our work can be categorized into three significant steps: (i) Extraction of PANS version of NLEVM from RANS model, (ii) testing the model in the homogeneous turbulence environment and (iii) application and evaluation of the model in the canonical case of separated non-homogeneous flow field (flow past prismatic bodies and bodies of revolution at high Reynolds number). PANS version of NLEVM shall be derived and implemented in OpenFOAM -an open source solver. Homogeneous flows evaluation will comprise the study of the influence of the PANS’ filter-width control parameter on the turbulent stresses; the homogeneous analysis performed over typical velocity fields and asymptotic analysis of Reynolds stress tensor. Non-homogeneous flow case will include the study of mean integrated quantities and various instantaneous flow field features including wake structures. Performance of PANS + NLEVM shall be compared against the LEVM based PANS and LEVM based RANS. This assessment will contribute to significant improvement of the predictive ability of the computational fluid dynamics (CFD) tools in massively separated turbulent flows past bluff bodies.

Keywords: bridging methods of turbulence, high Re-CFD, non-linear PANS, separated turbulent flows

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Authors: Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Lucinda Kurzava, Hannah Buvala, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

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Hepatocellular carcinoma (HCC), the most prevalent type of primary liver cancer, is the second leading cause of cancer death worldwide. Late onset of clinical symptoms in HCC results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable early detection biomarkers that can distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed and could increase the cure rate from 5% to 80%. We used Illumina-450K microarray to test whether blood DNA, an easily accessible source of DNA, bear site-specific changes in DNA methylation in response to HCC before diagnosis with conventional tools (pre-diagnostic). Top 11 differentially methylated sites were selected for validation by pyrosequencing. The diagnostic potential of the 11 pyrosequenced probes was tested in blood samples from a prospective cohort of cirrhotic patients. We identified 971 differentially methylated CpG sites in pre-diagnostic HCC cases as compared with healthy controls (P < 0.05, paired Wilcoxon test, ICC ≥ 0.5). Nearly 76% of differentially methylated CpG sites showed lower levels of methylation in cases vs. controls (P = 2.973E-11, Wilcoxon test). Classification of the CpG sites according to their location relative to CpG islands and transcription start site revealed that those hypomethylated loci are located in regulatory regions important for gene transcription such as CpG island shores, promoters, and 5’UTR at higher frequency than hypermethylated sites. Among 735 CpG sites hypomethylated in cases vs. controls, 482 sites were assigned to gene coding regions whereas 236 hypermethylated sites corresponded to 160 genes. Bioinformatics analysis using GO, KEGG and DAVID knowledgebase indicate that differentially methylated CpG sites are located in genes associated with functions that are essential for gene transcription, cell adhesion, cell migration, and regulation of signal transduction pathways. Taking into account the magnitude of the difference, statistical significance, location, and consistency across the majority of matched pairs case-control, we selected 11 CpG loci corresponding to 10 genes for further validation by pyrosequencing. We established that methylation of CpG sites within 5 out of those 10 genes distinguish cirrhotic patients who subsequently developed HCC from those who stayed cancer free (cirrhotic controls), demonstrating potential as biomarkers of early detection in populations at risk. The best predictive value was detected for CpGs located within BARD1 (AUC=0.70, asymptotic significance ˂0.01). Using an additive logistic regression model, we further showed that 9 CpG loci within those 5 genes, that were covered in pyrosequenced probes, constitute a panel with high diagnostic accuracy (AUC=0.887; 95% CI:0.80-0.98). The panel was able to distinguish pre-diagnostic cases from cirrhotic controls free of cancer with 88% sensitivity at 70% specificity. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established biomarker panel has high potential to be developed into a routine clinical test after validation in larger cohorts. This study was supported by Showalter Trust, American Cancer Society (IRG#14-190-56), and Purdue Center for Cancer Research (P30 CA023168) granted to BS.

Keywords: biomarker, DNA methylation, early detection, hepatocellular carcinoma

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