Large Deformation Diffeomorphic Metric Mapping Provides New Insights into the Link Between Human Ear Morphology and the Head-Related Transfer Functions

The research findings presented in this thesis is composed of four sections. In the first section of this thesis, it is shown how LDDMM can be applied to deforming head and ear shapes in the context of morphoacoustic study. Further, tools are developed to measure differences in 3D shapes using the framework of currents and also to compare and measure the differences between the acoustic responses obtained from BEM simulations for two ear shapes. Finally this section introduces the multi-scale approach for mapping ear shapes using LDDMM. The second section of the thesis estimates a template ear, head and torso shape from the shapes available in the SYMARE database. This part of the thesis explains a new procedure for developing the template ear shape. The template ear and head shapes were are verified by comparing the features in the template shapes to corresponding features in the CIPIC and SYMARE database population. The third section of the thesis examines the quality of the deformations from the template ear shape to target ears in SYMARE from both an acoustic and morphological standpoint. As a result of this investigation, it was identified that ear shapes can be studied more accurately by the use of two physical scales and that scales at which the ear shapes were studied were dependent on the parameters chosen when mapping ears in the LDDMM framework. Finally, this section concludes by noting how shape distances vary with the acoustic distances using the developed tools. In the final part of this thesis, the variations in the morphology of ears are examined using the Kernel Principle Component Analysis (KPCA) and the changes in the corresponding acoustics are studied using the standard principle component analysis (PCA). These examinations involved identifying the number of kernel principle components that are required in order to model ear shapes with an acceptable level of accuracy, both morphologically and acoustically

Antiphospholipid Antibodies in Women with Recurrent Urinary Tract Infection

Background: A variety of infections, including acute and recurrent urinary tract infections (UTIs), can trigger production of antiphospholipid antibodies (aPL).  These antibodies in women can lead to recurrent pregnancy loss. The aim of this study was to evaluate the prevalence of aPL in recurrent UTI patients.Materials and Methods: A total 52 subjects who had positive urine culture and 50 healthy individuals as controls were evaluated for presence of lupus anticoagulant (LA), anticardiolipin, anti-β2 GPI(anti-2-glycoprotein I) autoantibodies  IgM and IgG and Interleukin-8 levels. Determination of lupus anticoagulant was done by Activated Partial Thromboplastin Time (aPTT). Anticardiolipin and anti-β2 GPI autoantibodies were evaluated by ELISA method. Interleukin-8 values were also evaluated using ELISA method. Results: Escherichia coli (86.61%) and Proteus mirabilis (1.92%) had the highest and lowest frequency respectively. The prevalence of anti- β2 GPI IgG and IgM isotypes and anticardiolipin IgG and IgM isotypes or LA in UTI patients and healthy controls was 0.0%. There was significant association between neutrophil counts and IL-8 levels at the p < 0.01.Conclusion: Our results showed that in the UTI group and controls evaluated antiphospholipid antibodies were not present. The production of antiphospholipid antibodies is influenced by various genetic and environmental factors and chronic urinary tract infection alone is not the cause. This can affect the prevalence of antiphospholipid antibodies in various populations. However, other factors, such as the type of antiphospholipid antibody, sampling season and methodology can affect the results

Large Deformation Diffeomorphic Metric Mapping And Fast-Multipole Boundary Element Method Provide New Insights For Binaural Acoustics

This paper describes how Large Deformation Diffeomorphic Metric Mapping (LDDMM) can be coupled with a Fast Multipole (FM) Boundary Element Method (BEM) to investigate the relationship between morphological changes in the head, torso, and outer ears and their acoustic filtering (described by Head Related Transfer Functions, HRTFs). The LDDMM technique provides the ability to study and implement morphological changes in ear, head and torso shapes. The FM-BEM technique provides numerical simulations of the acoustic properties of an individual's head, torso, and outer ears. This paper describes the first application of LDDMM to the study of the relationship between a listener's morphology and a listener's HRTFs. To demonstrate some of the new capabilities provided by the coupling of these powerful tools, we examine the classical question of what it means to ``listen through another individual's outer ears.'' This work utilizes the data provided by the Sydney York Morphological and Acoustic Recordings of Ears (SYMARE) database.Comment: Submitted as a conference paper to IEEE ICASSP 201

Numerical Simulation of Reactive Transport Problems in Porous Media Using Global Implicit Approach

This thesis focuses on solutions of reactive transport problems in porous media. The principle mechanisms of flow and reactive mass transport in porous media are investigated. Global implicit approach (GIA), where transport and reaction are fully coupled, and sequential noniterative approach (SNIA) are implemented into the software OpenGeoSys (OGS6) to couple chemical reaction and mass transport. The reduction scheme proposed by Kräutle is used in GIA to reduce the number of coupled nonlinear differential equations. The reduction scheme takes linear combinations within mobile species and immobile species and effectively separates the reaction-independent linear differential equations from coupled nonlinear ones (i.e. reducing the number of primary variables in the nonlinear system). A chemical solver is implemented using semi-smooth Newton iteration which employs complementarity condition to solve for equilibrium mineral reactions. The results of three benchmarks are used for code verification. Based on the solutions of these benchmarks, it is shown that GIA with the reduction scheme is faster (ca. 6.7 times) than SNIA in simulating homogeneous equilibrium reactions and (ca. 24 times) in simulating kinetic reaction. In simulating heterogeneous equilibrium mineral reactions, SNIA outperforms GIA with the reduction scheme by 4.7 times.:Declaration of Authorship iii Acknowledgements iv Abstract v List of Figures viii Symbols ix 1 Introduction 1 1.1 State of the Art 1 1.2 Thesis Objectives 3 1.3 Thesis Outline 4 2 Mathematical Models 5 2.1 Introduction 5 2.2 Mass Balance Equations 5 2.2.1 Groundwater Flow 6 2.2.2 Mass Transport 7 2.2.3 Chemical Reaction 8 2.2.3.1 Equilibrium Reaction 8 2.2.3.2 Kinetic Reaction 10 2.3 Reactive Mass Transport 10 2.4 Initial and Boundary Conditions 11 3 Numerical Solutions 12 3.1 Introduction 12 3.2 Coupling Schemes 12 3.2.1 Operator Splitting 13 3.2.2 Global Implicit 13 3.2.2.1 Standard Reduction Schemes 14 3.2.2.2 Kräutle’s Reduction Scheme 14 3.2.2.3 Local Chemical Solver 21 3.3 Space and Time Discretization 23 3.3.1 Finite Element Method 23 3.3.2 Time Discretization 25 3.3.3 Jacobian Matrix 26 3.4 Code Implementation 29 4 Benchmarks 30 4.1 Introduction 30 4.2 Cation Exchange 30 4.3 Dissolution and Precipitation 32 4.4 Mixing Controlled Biodegradation 33 5 Conclusions and Outlooks 38 5.1 Conclusions 38 5.2 Outlooks 39Diese Arbeit konzentriert sich auf die numerische Berechnung reaktiver Transportprobleme in porösen Medien. Es werden prinzipielle Mechanismen von Fluidströmung und reaktive Stofftransport in porösen Medien untersucht. Um chemische Reaktionen und Stofftransport zu koppeln, wurden die Ansätze Global Implicit Approach (GIA) sowie Sequential Non-Iterative Approach (SNIA) in die Software OpenGeoSys (OGS6) implementiert. Das von Kräutle vorgeschlagene Reduzierungsschema wird in GIA verwendet, um die Anzahl der gekoppelten nichtlinearen Differentialgleichungen zu reduzieren. Das Reduzierungsschema verwendet Linearkombinationen von mobilen und immobile Spezies und trennt die reaktionsunabhngigen linearen Differentialgleichungen von den gekoppelten nichtlinearen Gleichungen (dh Verringerung der Anzahl der Primärvariablen des nicht-linearen Gleichungssystems). Um die Gleichgewichtsreaktionen der Mineralien zu berechnen, wurde ein chemischer Gleichungslaser auf Basis von ”semi-smooth Newton-Iterations” implementiert. Ergebnisse von drei Benchmarks wurden zur Code-Verifikation verwendet. Diese Ergebnisse zeigen, dass die Simulation homogener Equilibriumreaktionen mit GIA 6,7 mal schneller und bei kinetischen Reaktionen 24 mal schneller als SNIA sind. Bei Simulationen heterogener Equilibriumreaktionen ist SNIA 4,7 mal schneller als der GIA Ansatz.:Declaration of Authorship iii Acknowledgements iv Abstract v List of Figures viii Symbols ix 1 Introduction 1 1.1 State of the Art 1 1.2 Thesis Objectives 3 1.3 Thesis Outline 4 2 Mathematical Models 5 2.1 Introduction 5 2.2 Mass Balance Equations 5 2.2.1 Groundwater Flow 6 2.2.2 Mass Transport 7 2.2.3 Chemical Reaction 8 2.2.3.1 Equilibrium Reaction 8 2.2.3.2 Kinetic Reaction 10 2.3 Reactive Mass Transport 10 2.4 Initial and Boundary Conditions 11 3 Numerical Solutions 12 3.1 Introduction 12 3.2 Coupling Schemes 12 3.2.1 Operator Splitting 13 3.2.2 Global Implicit 13 3.2.2.1 Standard Reduction Schemes 14 3.2.2.2 Kräutle’s Reduction Scheme 14 3.2.2.3 Local Chemical Solver 21 3.3 Space and Time Discretization 23 3.3.1 Finite Element Method 23 3.3.2 Time Discretization 25 3.3.3 Jacobian Matrix 26 3.4 Code Implementation 29 4 Benchmarks 30 4.1 Introduction 30 4.2 Cation Exchange 30 4.3 Dissolution and Precipitation 32 4.4 Mixing Controlled Biodegradation 33 5 Conclusions and Outlooks 38 5.1 Conclusions 38 5.2 Outlooks 3

Association of IFN-γ and P2X7 Receptor Gene Polymorphisms in Susceptibility to Tuberculosis Among Iranian Patients

Interferon-gamma (IFN-γ) and P2X7 receptor are crucial for host defence against mycobacterial infections. Recent studies have indicated that IFN-γ, IFN-γ receptor 1 (IFN-γR1) andP2X7 gene polymorphisms are associated with susceptibility to pulmonary tuberculosis (TB). However, the relationship between IFN-γ and P2X7 polymorphism and TB susceptibility remains inconclusive in Iranian population. For this reason, single nucleotide polymorphisms (SNPs) in IFN-γ (G+2109A), IFN-γR1 (G-611A) and P2X7 genes (at –762, 1513 position) in patients (n = 100) were assessed using PCR-RFLP. Data were analysed with SPSS version 18. For the 2109 loci of IFN-γ gene, the frequency of mutant alleles between patients and controls were not statistically significant. However, there was a significant difference between the TB patient and controls for –611 alleles of IFN-γR1 (P = 0.01). Additionally, the frequency of P2X7 gene polymorphisms (SNP-762 and 1513) between patients and controls was statistically significant. In conclusions, our study revealed a significant association of IFN-γR1 and P2X7 genes polymorphisms with risk of developing TB in Iranian population

The Association between Interleukin-10 Gene Polymorphisms and Hepatitis B Virus: Evidence in Iran

Background and Aim: Hepatitis B virus (HBV) is a human carcinogenesis agent. Interleukin 10 (IL-10) is a key anti-inflammatory cytokine, and single nucleotide polymorphisms in IL-10 gene promoter are correlated with infections caused by HBV. This research intended to assess the prevalence and genotype of HBV as well as the association between the polymorphisms of -819 and -1082 in the IL-10 gene with HBV in individuals with HBV infection in Qom Province, Iran Methods: In this cross-sectional research, 360 individuals with chronic HBV infection and control group were involved between July 2018 and March 2019. HBV diagnosis was evaluated using ELISA and nested PCR assays. To determine polymorphisms in the IL-10 gene promoter in HBV positive and control samples, an allele-specific polymerase chain reaction technique was employed. Results: The constructed phylogenetic trees for the HBsAg gene revealed that all sequences under study belong to genotype D and also, the majority of HBV samples presented similar sequences to the Iranian samples. Genotype frequencies of TT, TC and CC (polymorphism -819) were 82.2%, 11.6% and 6.1% for patients and 85%, 10.5% and 4.4% in control groups, respectively. Also, frequency of genotypes of AA, AG and GG (polymorphism -1082) were 45%, 43.8% and 11.1% for patients and 42.2%, 46.1% and 11.6% in control groups, respectively. Conclusion: Here, we found no association among IL-10 gene polymorphisms in control and HBV-infected groups. However, more studies about the frequency of chronic HBV infection are necessary to be conducted. *Corresponding Author: Mohsen Zargar; Email: [email protected] Interleukins-10 Gene Polymorphism and Hepatitis B Virus: Evidence in Iran. Arch Med Lab Sci. 2021;7:1-7 (e7). https://doi.org/10.22037/amls.v7.3355

Crushing analysis of the industrial cage mill and the laboratory jaw crusher

Many research studies have been conducted on the liberation of locked minerals using a crusher and comparing this device with the other devices. This paper reviews the liberation of middle coal by different methods of crushing force. In the Tabas coal washing plant, particles of 0.5-50 mm size are processed through the heavy media method (using 3 Tri-flo separators) and particles of 0-0.5 mm size are processed using the flotation method (using 6 column flotation cells). A Tri-flo separator with a diameter of 700 mm and the capacity of 120 tons per hour is used for the cleaning of 6-50 mm raw coal particles. The study was conducted using a laboratory jaw crusher and a cage mill with a specific comminution ratio, both crushing forces were analyzed with the same distribution and mechanism of production of fines. In this study, grading and washability characteristics of a representative sample of middle product were reviewed and the dimensions of the ash were measured for each section. Intermediate product crushing using a laboratory jaw crusher and an industrial cage mill were conducted at up to 5 mm size and 50 percent of final speed. The amount of coal released after each section grading was determined by a sinking and floating test for size +0.5 mm and release analysis and ash testing for smaller dimensions of -0.5, these tests were conducted for each section product dimension. The results indicated that utilizing a cage mill is more effective than a laboratory jaw crusher, resulting in 11-percent more yield with 12 ash. The rate of fines produced through the laboratory jaw crusher is less than the industrial cage mill

Kernal principal component analysis of the ear morphology

This paper describes features in the ear shape that change across a population of ears and explores the corresponding changes in ear acoustics. The statistical analysis conducted over the space of ear shapes uses a kernel principal component analysis (KPCA). Further, it utilizes the framework of large deformation diffeomorphic metric mapping and the vector space that is constructed over the space of initial momentums, which describes the diffeomorphic transformations from the reference template ear shape. The population of ear shapes examined by the KPCA are 124 left and right ear shapes from the SYMARE database that were rigidly aligned to the template (population average) ear. In the work presented here we show the morphological variations captured by the first two kernel principal components, and also show the acoustic transfer functions of the ears which are computed using fast multipole boundary element method simulations

Reduction of vancomycin resistance inVanAand VanBcontainingVancomycin Resistant Enterococci (VRE) isolatesin presence of lactoferrin protein

چکیده زمینه و هدف : پروتئین لاکتوفرین(Lactoferrin(LF)) دارای اثرات ضدمیکروبی اثبات شده ای است. هدف از این مطالعه بررسی تأثیر لاکتوفرین روی حداقل غلظت مهاری) Minimum inhibitory concentration (MIC))وانکومایسین در سویه های انتروکوک مقاوم به وانکومایسین دارای ژنهای مقاومت VanA و VanB بود. ﻣﻮﺍﺩ ﻭ ﺭﻭﺵﻫﺎ: در این مطالعه مقطعی ، پس از جداسازی و تشخیص265 سویه انتروکوک از نمونه های بالینی ، MIC وانکومایسین و تیکوپلانین سویه هابا روش تست اپسیلومتر ( Epsilometer test(Etest)) بدست آمد. نمونه های انتروکوک مقاوم به وانکومایسین Vancomycin Resistance Entrococcus(VRE)) ) ، با روش real time PCR ازلحاظ وجود ژنهای مقاوم به وانکومایسین VanA و VanB بررسی شد و سپس تأثیر لاکتوفرین را بر روی MIC آنتی بیوتیک وانکومایسین سویه های VRE مورد بررسی و بااستفاده از نرم افزارآماری SPSS نسخه 20 (version 20, SPSS Inc., Chicago, IL) و آزمون های آماری رگرسیون خطی و همبستگی پیرسون با سطح معنی داری P-value <0.05 آنالیز گردید. ﻧﺘﺎﻳﺞ: نمونه VanA در غلظت µg/ml) 2048)پروتئین لاکتوفرین MIC وانکومایسین را 85 و 80 برابر به ترتیب در روش تغییر یافته Etest و میکروتیتر کاهش داده و در نمونه VanB در غلظت µg/ml) 512) پروتئین لاکتوفرین MIC وانکومایسین را 10و 10.3 برابر به ترتیب در روش تغییر یافته Etest و میکروتیتر کاهش داده است. شاخص لاکتوفرین ارتباط همبستگی مثبت معنی داری را با کاهش MIC وانکومایسین نشان داد (001/0 Pvalue< و r=0.183 ). نتیجه گیری: غلظت های متفاوت پروتئین لاکتوفرین در شرایط آزمایشگاهی باعث کاهش مقاومت در سویه هایVRE دارای ژن VanA و VanB می شود ،پیشنهاد پتانسیل استفاده از این پروتئین به عنوان یک عامل کمکی به وانکومایسین وجود دارد