Search results for: special molecular configuration of thorium di-iodide ThI₂
Commenced in January 2007
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Edition: International
Paper Count: 5245

Search results for: special molecular configuration of thorium di-iodide ThI₂

5005 Inhibition of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase from Mycobacterium Tuberculosis Using High Throughput Virtual Screening and Molecular Dynamics Studies

Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

Abstract:

Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

Procedia PDF Downloads 150
5004 Sesame (Sesamum Indicum L.): Molecular Breeding and Transformation

Authors: Micheale Yifter Weldemichael, Stefaan Werbrouck, Hailay Mehari Gebremedhn

Abstract:

Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: molecular breeding, oil, sesame, shattering

Procedia PDF Downloads 43
5003 Amyloid-β Fibrils Remodeling by an Organic Molecule: Insight from All-Atomic Molecular Dynamics Simulations

Authors: Nikhil Agrawal, Adam A. Skelton

Abstract:

Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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5002 Impact of Self-Efficacy, Resilience and Social Support on Vicarious Trauma among Clinical Psychologists, Counselors and Teachers of Special Schools

Authors: Hamna Hamid, Kashmala Zaman

Abstract:

The aim of this study was to evaluate the relationship between self-efficacy, resilience and social support among clinical psychologists, counselors and teachers of special schools. The study also assesses the gender differences on self-efficacy, resilience, social support and vicarious trauma and also vicarious trauma differences among three professions i.e. clinical psychologists, counselors and teachers of special schools. A sample of 150 women and 97 men were handed out a set questionnaire to complete: General Self-Efficacy Scale, Brief Resilience Scale, Multidimensional Scale of Perceived Social Support and Vicarious Trauma Scale. Results showed that there is significant negative correlation between self-efficacy, resilience and vicarious trauma. Women experiences higher levels of vicarious trauma as compared to men. While clinical psychologists and counselors experience higher levels of vicarious trauma as compared to teachers of special schools. Moderation effect of social support is not significant towards resilience and vicarious trauma.

Keywords: self-efficacy, resilience, vicarious trauma, social-support

Procedia PDF Downloads 41
5001 Evaluation of Newly Synthesized Steroid Derivatives Using In silico Molecular Descriptors and Chemometric Techniques

Authors: Milica Ž. Karadžić, Lidija R. Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Z. Kovačević, Anamarija I. Mandić, Katarina Penov-Gaši, Andrea R. Nikolić, Aleksandar M. Oklješa

Abstract:

This study considered selection of the in silico molecular descriptors and the models for newly synthesized steroid derivatives description and their characterization using chemometric techniques. Multiple linear regression (MLR) models were established and gave the best molecular descriptors for quantitative structure-retention relationship (QSRR) modeling of the retention of the investigated molecules. MLR models were without multicollinearity among the selected molecular descriptors according to the variance inflation factor (VIF) values. Used molecular descriptors were ranked using generalized pair correlation method (GPCM). In this method, the significant difference between independent variables can be noticed regardless almost equal correlation between dependent variable. Generated MLR models were statistically and cross-validated and the best models were kept. Models were ranked using sum of ranking differences (SRD) method. According to this method, the most consistent QSRR model can be found and similarity or dissimilarity between the models could be noticed. In this study, SRD was performed using average values of experimentally observed data as a golden standard. Chemometric analysis was conducted in order to characterize newly synthesized steroid derivatives for further investigation regarding their potential biological activity and further synthesis. This article is based upon work from COST Action (CM1105), supported by COST (European Cooperation in Science and Technology).

Keywords: generalized pair correlation method, molecular descriptors, regression analysis, steroids, sum of ranking differences

Procedia PDF Downloads 313
5000 Preventing Neurodegenerative Diseases by Stabilization of Superoxide Dismutase by Natural Polyphenolic Compounds

Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

Abstract:

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

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4999 Trauma and Its High Influence on Special Education

Authors: Athena Johnson

Abstract:

Special education is an important field but often under-researched, particularly for the cause of learning deficiencies. Often times special education looks at the symptoms rather than the cause, and this can lead to many misdiagnoses. Student trauma, as measured by the Adverse Childhood Experiences (ACE) test, is extremely common, often resulting in Post Traumatic Stress Disorder (PTSD). PTSD affects the brain's ability to learn properly, making students have a much more difficult time with auditory learning and memory due to always being in flight or fight mode, and due to this, students with PTSD are often misdiagnosed with Attention Deficit and Hyperactivity Disorder (ADHD). This can lead to them getting the wrong support, with PTSD students needing more counseling than anything else. Through these research papers' methodologies, a literature review on article research from the perspectives of students who were misdiagnosed, and imperial research, the major findings of this study were the importance of trauma-informed care in schools. Trauma-informed care in the school system is crucial for helping the many students who experience traumatic life events and struggle in school due to it. It is important to support students with PTSD so that they are able to integrate and learn better in society and school with trauma-informed school care.

Keywords: ACE test, ADHD, misdiagnoses, special education, trauma, trauma-informed care, PTSD

Procedia PDF Downloads 80
4998 Microarrays: Wide Clinical Utilities and Advances in Healthcare

Authors: Salma M. Wakil

Abstract:

Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance.

Keywords: microarrays, molecular karyotyping, developmental delay, genetics

Procedia PDF Downloads 425
4997 Molecular Dynamics Analysis onI mpact Behaviour of Carbon Nanotubes and Graphene Sheets

Authors: Sajjad Seifoori

Abstract:

Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: impact, molecular dynamic, graphene, spring mass

Procedia PDF Downloads 302
4996 An Historical Revision of Change and Configuration Management Process

Authors: Expedito Pinto De Paula Junior

Abstract:

Current systems such as artificial satellites, airplanes, automobiles, turbines, power systems and air traffic controls are becoming increasingly more complex and/or highly integrated as defined in SAE-ARP-4754A (Society Automotive Engineering - Certification considerations for highly-integrated or complex aircraft systems standard). Among other processes, the development of such systems requires careful Change and Configuration Management (CCM) to establish and maintain product integrity. Understand the maturity of CCM process based in historical approach is crucial for better implementation in hardware and software lifecycle. The sense of work organization, in all fields of development is directly related to the order and interrelation of the parties, changes in time, and record of these changes. Generally, is observed that engineers, administrators and managers invest more time in technical activities than in organization of work. More these professionals are focused in solving complex problems with a purely technical bias. CCM process is fundamental for development, production and operation of new products specially in the safety critical systems. The objective of this paper is open a discussion about the historical revision based in standards focus of CCM around the world in order to understand and reflect the importance across the years, the contribution of this process for technology evolution, to understand the mature of organizations in the system lifecycle project and the benefits of CCM to avoid errors and mistakes during the Lifecycle Product.

Keywords: changes, configuration management, historical, revision

Procedia PDF Downloads 177
4995 Creating an Inclusive Classroom: Country Case Studies Analysis on Mainstream Teachers' Teaching-Efficacy and Attitudes towards Inclusive Education in Japan and Singapore

Authors: Yei Mian Adrian Yap

Abstract:

This study aims to assess the Japanese and Singaporean mainstream teachers’ attitudes and teaching-efficacy towards the inclusion of students with special needs in the regular classrooms by investigating what kind of key variables influence their attitudes and teaching-efficacy. It also further investigates how they strategize to address their challenges to include their students with special needs in their regular classrooms. In order to understand the nature of teachers’ attitudes and teaching-efficacy towards the inclusive education, a mixed-method research methodology was carried out in Japan and Singapore; it involved an explanatory sequential method of employing quantitative research first before qualitative research. In the quantitative research, 189 Japanese and 183 Singaporean teachers were invited to participate in the questionnaires and out of these participants, 38 Japanese and 15 Singaporean teachers shared their views during their semi-structured interviews. Based on the empirical findings, Japanese teachers’ attitudes and teaching-efficacy were more likely to be influenced by their experiences in teaching students with special needs, knowledge about disability legislation, presence of their disabled family members and level of confidence to teach students with special needs. On the other hand, Singaporean teachers’ attitudes and teaching-efficacy were affected by gender, educational level, received trainings in special needs education, knowledge about disability legislation and level of confidence to teach students with special needs. Both country results also demonstrated that there was a positive correlation between their teaching-efficacy and attitude. Narrative findings further expanded the reasons behind these quantitative factors that shaped teachers’ attitudes and teaching-efficacy. Also, it discussed the various problems faced by Japanese and Singaporean teachers and how they identified their coping strategies to circumvent their challenges in including their students with special needs in their regular classrooms. The significance of this research manifests in necessary educational reforms in both countries especially in the context of inclusive education. These findings may not be as definitive as expected but it is believed that it could provide useful information on the current situation about teachers’ concerns towards the inclusive education. In conclusion, this research could potentially make its positive contribution to the body of literature on teachers’ attitudes and teaching-efficacy in the context of Asian developed countries. Further, these findings could posit that regular teachers’ positive attitudes and strong sense of teaching self-efficacy could directly improve the success rate of inclusion of students with special needs in the regular classrooms.

Keywords: attitudes, inclusive education, special education, teaching-efficacy

Procedia PDF Downloads 296
4994 Comparative Studies of Distributed and Aggregated Energy Storage Configurations in Direct Current Microgrids

Authors: Frimpong Kyeremeh, Albert Y. Appiah, Ben B. K. Ayawli

Abstract:

Energy storage system (ESS) is an essential part of a microgrid (MG) because of its immense benefits to the economics and the stability of MG. For a direct current (DC) MG (DCMG) in which the generating units are mostly variable renewable energy generators, DC bus voltage fluctuation is inevitable; hence ESS is vital in managing the mismatch between load demand and generation. Besides, to accrue the maximum benefits of ESS in the microgrid, there is the need for proper sizing and location of the ESSs. In this paper, a performance comparison is made between two configurations of ESS; distributed battery energy storage system (D-BESS) and an aggregated (centralized) battery energy storage system (A-BESS), on the basis of stability and operational cost for a DCMG. The configuration consists of four households with rooftop PV panels and a wind turbine. The objective is to evaluate and analyze the technical efficiencies, cost effectiveness as well as controllability of each configuration. The MG is first modelled with MATLAB Simulink then, a mathematical model is used to determine the optimal size of the BESS that minimizes the total operational cost of the MG. The performance of the two configurations would be tested with simulations. The two configurations are expected to reduce DC bus voltage fluctuations, but in the cases of voltage stability and optimal cost, the best configuration performance will be determined at the end of the research. The work is in progress, and the result would help MG designers and operators to make the best decision on the use of BESS for DCMG configurations.

Keywords: aggregated energy storage system, DC bus voltage, DC microgrid, distributed battery energy storage, stability

Procedia PDF Downloads 132
4993 Oat βeta Glucan Attenuates the Development of Atherosclerosis and Improves the Intestinal Barrier Function by Reducing Bacterial Endotoxin Translocation in APOE-/- MICE

Authors: Dalal Alghawas, Jetty Lee, Kaisa Poutanen, Hani El-Nezami

Abstract:

Oat β-glucan a water soluble non starch linear polysaccharide has been approved as a cholesterol lowering agent by various food safety administrations and is commonly used to reduce the risk of heart disease. The molecular weight of oat β-glucan can vary depending on the extraction and fractionation methods. It is not clear whether the molecular weight has a significant impact at reducing the acceleration of atherosclerosis. The aim of this study was to investigate three different oat β-glucan fractionations on the development of atherosclerosis in vivo. With special focus on plaque stability and the intestinal barrier function. To test this, ApoE-/- female mice were fed a high fat diet supplemented with oat bran, high molecular weight (HMW) oat β-glucan fractionate and low molecular weight (LMW) oat β-glucan fractionate for 16 weeks. Atherosclerosis risk markers were measured in the plasma, heart and aortic tree. Plaque size was measured in the aortic root and aortic tree. ICAM-1, VCAM-1, E-Selectin, P-Selectin, protein levels were assessed from the aortic tree to determine plaque stability at 16 weeks. The expression of p22phox at the aortic root was evaluated to study the NADPH oxidase complex involved in nitric oxide bioavailability and vascular elasticity. The tight junction proteins E-cadherin and beta-catenin from western blot analyses were analysed as an intestinal barrier function test. Plasma LPS, intestinal D-lactate levels and hepatic FMO gene expression were carried out to confirm whether the compromised intestinal barrier lead to endotoxemia. The oat bran and HMW oat β-glucan diet groups were more effective than the LMW β-glucan diet group at reducing the plaque size and showed marked improvements in plaque stability. The intestinal barrier was compromised for all the experimental groups however the endotoxemia levels were higher in the LMW β-glucan diet group. The oat bran and HMW oat β-glucan diet groups were more effective at attenuating the development of atherosclerosis. Reasons for this could be due to the LMW oat β-glucan diet group’s low viscosity in the gut and the inability to block the reabsorption of cholesterol. Furthermore the low viscosity may allow more bacterial endotoxin translocation through the impaired intestinal barrier. In future food technologists should carefully consider how to incorporate LMW oat β-glucan as a health promoting food.

Keywords: Atherosclerosis, beta glucan, endotoxemia, intestinal barrier function

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4992 Numerical Investigation of a Supersonic Ejector for Refrigeration System

Authors: Karima Megdouli, Bourhan Taschtouch

Abstract:

Supersonic ejectors have many applications in refrigeration systems. And improving ejector performance is the key to improve the efficiency of these systems. One of the main advantages of the ejector is its geometric simplicity and the absence of moving parts. This paper presents a theoretical model for evaluating the performance of a new supersonic ejector configuration for refrigeration system applications. The relationship between the flow field and the key parameters of the new configuration has been illustrated by analyzing the Mach number and flow velocity contours. The method of characteristics (MOC) is used to design the supersonic nozzle of the ejector. The results obtained are compared with those obtained by CFD. The ejector is optimized by minimizing exergy destruction due to irreversibility and shock waves. The optimization converges to an efficient optimum solution, ensuring improved and stable performance over the whole considered range of uncertain operating conditions.

Keywords: supersonic ejector, theoretical model, CFD, optimization, performance

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4991 In-Vitro Dextran Synthesis and Characterization of an Intracellular Glucosyltransferase from Leuconostoc Mesenteroides AA1

Authors: Afsheen Aman, Shah Ali Ul Qader

Abstract:

Dextransucrase [EC 2.4.1.5] is a glucosyltransferase that catalysis the biosynthesis of a natural biopolymer called dextran. It can catalyze the transfer of D-glucopyranosyl residues from sucrose to the main chain of dextran. This unique biopolymer has multiple applications in several industries and the key utilization of dextran lies on its molecular weight and the type of branching. Extracellular dextransucrase from Leuconostoc mesenteroides is most extensively studied and characterized. Limited data is available regarding cell-bound or intracellular dextransucrase and on the characterization of dextran produced by in-vitro reaction of intracellular dextransucrase. L. mesenteroides AA1 is reported to produce extracellular dextransucrase that catalyzes biosynthesis of a high molecular weight dextran with only α-(1→6) linkage. Current study deals with the characterization of an intracellular dextransucrase and in vitro biosynthesis of low molecular weight dextran from L. mesenteroides AA1. Intracellular dextransucrase was extracted from cytoplasm and purified to homogeneity for characterization. Kinetic constants, molecular weight and N-terminal sequence analysis of intracellular dextransucrase reveal unique variation with previously reported extracellular dextransucrase from the same strain. In vitro synthesized biopolymer was characterized using NMR spectroscopic techniques. Intracellular dextransucrase exhibited Vmax and Km values of 130.8 DSU ml-1 hr-1 and 221.3 mM, respectively. Optimum catalytic activity was detected at 35°C in 0.15 M citrate phosphate buffer (pH-5.5) in 05 minutes. Molecular mass of purified intracellular dextransucrase is approximately 220.0 kDa on SDS-PAGE. N-terminal sequence of the intracellular enzyme is: GLPGYFGVN that showed no homology with previously reported sequence for the extracellular dextransucrase. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions. This intracellular dextransucrase is capable of in vitro synthesis of dextran under specific conditions and this biopolymer can be hydrolyzed into different molecular weight fractions for various applications.

Keywords: characterization, dextran, dextransucrase, leuconostoc mesenteroides

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4990 A Performance Model for Designing Network in Reverse Logistic

Authors: S. Dhib, S. A. Addouche, T. Loukil, A. Elmhamedi

Abstract:

In this paper, a reverse supply chain network is investigated for a decision making. This decision is surrounded by complex flows of returned products, due to the increasing quantity, the type of returned products and the variety of recovery option products (reuse, recycling, and refurbishment). The most important problem in the reverse logistic network (RLN) is to orient returned products to the suitable type of recovery option. However, returned products orientations from collect sources to the recovery disposition have not well considered in performance model. In this study, we propose a performance model for designing a network configuration on reverse logistics. Conceptual and analytical models are developed with taking into account operational, economic and environmental factors on designing network.

Keywords: reverse logistics, network design, performance model, open loop configuration

Procedia PDF Downloads 415
4989 Thrombophilic Mutations in Tunisian Patients with Recurrent Pregnancy Loss

Authors: Frikha Rim, Abdelmoula Bouayed Nouha, Rebai Tarek

Abstract:

Pregnancy is a hypercoagulable state which causing a defective maternal haemostatic response and leading to thrombosis of the uteroplacental vasculature, that might cause pregnancy complications as recurrent pregnancy loss (RPL). Since heritable Thrombophilic defects are associated with increased thrombosis, their prevalence was evaluated in patients with special emphasis on combinations of the above pathologies. Especially, Factor V Leiden (FVL) G1691A, methylene tetra hydro folate reductase (MTHFR) C677T, and factor II (FII) G20210A mutations are three important causes of thrombophilia, which might be related to recurrent pregnancy loss (RPL). In this study we evaluated the presence of these three mutations [factor V Leiden (FVL), prothrombin G20210A (PTG) and methylenetetrahydrofolate reductase (MTHFR) C677T] amongst 35 Tunisian women with more than 2 miscarriages, referred to our genetic counseling. DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of each mutation. Factor V Leiden and Prothrombin mutation were detected respectively in 5.7% and 2.9% of women with particular history of early fetal loss and thrombotic events. Despites the luck of strength of this study, we insist that testing for the most inherited thrombophilia (FVL and FII mutation) should be performed in women with RPL in the context of thrombotic events. Multi-centre collaboration is necessary to clarify the real impact of thrombotic molecular defects on the pregnancy outcome, to ascertain the effect of thrombophilia on recurrent pregnancy loss and then to evaluate the appropriate therapeutic approach.

Keywords: thrombophilia, recurrent pregnancy loss, factor V Leiden, prothrombin G20210A, methylene tetra hydro folate reductase

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4988 Coding Considerations for Standalone Molecular Dynamics Simulations of Atomistic Structures

Authors: R. O. Ocaya, J. J. Terblans

Abstract:

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C language, molecular dynamics, simulation, embedded atom method

Procedia PDF Downloads 273
4987 Unbalanced Cylindrical Magnetron for Accelerating Cavities Coating

Authors: G. Rosaz, V. Semblanet, S. Calatroni, A. Sublet, M. Taborelli

Abstract:

We report in this paper the design and qualification of a cylindrical unbalanced magnetron source. The dedicated magnetic assemblies were simulated using a finite element model. A hall-effect magnetic probe was then used to characterize those assemblies and compared to the theoretical magnetic profiles. These show a good agreement between the expected and actual values. The qualification of the different magnetic assemblies was then performed by measuring the ion flux density reaching the surface of the sample to be coated using a commercial retarding field energy analyzer. The strongest unbalanced configuration shows an increase from 0.016 A.cm-2 to 0.074 A.cm-2 of the ion flux density reaching the sample surface compared to the standard balanced configuration for a pressure 5.10-3 mbar and a plasma source power of 300 W.

Keywords: ion energy distribution function, magnetron sputtering, niobium, unbalanced, SRF cavities, thin film

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4986 Heat Capacity of a Soluble in Water Protein: Equilibrium Molecular Dynamics Simulation

Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

Abstract:

Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

Procedia PDF Downloads 277
4985 Impact of Self-Efficacy, Resilience, and Social Support on Vicarious Trauma among Clinical Psychologists, Counselors, and Teachers of Special Schools

Authors: Hamna Hamid, Kashmala Zaman

Abstract:

The aim of this study was to evaluate the relationship between self-efficacy, resilience, and social support among clinical psychologists, counselors, and teachers of special schools. The study also assesses the gender differences in self-efficacy, resilience, social support, and vicarious trauma and also vicarious trauma differences among three professions, i.e., clinical psychologists, counselors, and teachers of special schools. A sample of 150 women and 97 men were handed out a set questionnaire to complete: a General Self-Efficacy Scale, Brief Resilience Scale, Multidimensional Scale of Perceived Social Support, and Vicarious Trauma Scale. Results showed that there is a significant negative correlation between self-efficacy, resilience, and vicarious trauma. Women experience higher levels of vicarious trauma as compared to men. At the same time, clinical psychologists and counselors experience higher levels of vicarious trauma as compared to teachers of special schools. The moderation effect of social support is not significant towards resilience and vicarious trauma.

Keywords: self-efficacy, resilience, vicarious-trauma social-support, social support

Procedia PDF Downloads 47
4984 Enhancing Student Success: Parent and Family Are the Main Obstacle to Their Children's Success

Authors: Adel Hashlan

Abstract:

Parent and family engagement plays a crucial role in supporting the success of students with special needs in educational settings. This paper explores the significance of parental involvement in special education, examining its impact on academic achievement, social-emotional development, and overall well-being. Drawing on a review of current literature and empirical research, the paper highlights the benefits of meaningful collaboration between educators, parents, and families in promoting positive outcomes for students with diverse learning needs. The abstract begins by establishing the importance of parent and family engagement in special education, emphasizing its multifaceted impact on student success. It then outlines the key components of effective parent and family involvement initiatives, including communication strategies, collaboration frameworks, and partnership-building approaches. Additionally, the abstract addresses common barriers to parental involvement and explores strategies for overcoming these challenges, such as cultural responsiveness, accessibility, and empowerment. Furthermore, the abstract discusses the implications of parent and family engagement for educational policy and practice, emphasizing the need for systemic support and resource allocation to facilitate meaningful partnerships between schools and families. It concludes by underscoring the importance of ongoing research and professional development efforts to enhance the effectiveness of parent and family engagement initiatives in special education and maximize the potential for student achievement and well-being. Overall, this paper contributes to the growing body of literature on parent and family engagement in special education, providing insights into best practices, challenges, and opportunities for fostering collaborative partnerships that support the diverse needs of students with disabilities.

Keywords: special education, autism, parent, school

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4983 Electrospray Deposition Technique of Dye Molecules in the Vacuum

Authors: Nouf Alharbi

Abstract:

The electrospray deposition technique became an important method that enables fragile, nonvolatile molecules to be deposited in situ in high vacuum environments. Furthermore, it is considered one of the ways to close the gap between basic surface science and molecular engineering, which represents a gradual change in the range of scientist research. Also, this paper talked about one of the most important techniques that have been developed and aimed for helping to further develop and characterize the electrospray by providing data collected using an image charge detection instrument. Image charge detection mass spectrometry (CDMS) is used to measure speed and charge distributions of the molecular ions. As well as, some data has been included using SIMION simulation to simulate the energies and masses of the molecular ions through the system in order to refine the mass-selection process.

Keywords: charge, deposition, electrospray, image, ions, molecules, SIMION

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4982 Deep Groundwater Potential and Chemical Analysis Based on Well Logging Analysis at Kapuk-Cengkareng, West Jakarta, DKI Jakarta, Indonesia

Authors: Josua Sihotang

Abstract:

Jakarta Capital Special Region is the province that densely populated with rapidly growing infrastructure but less attention for the environmental condition. This makes some social problem happened like lack of clean water supply. Shallow groundwater and river water condition that has contaminated make the layer of deep water carrier (aquifer) should be done. This research aims to provide the people insight about deep groundwater potential and to determine the depth, location, and quality where the aquifer can be found in Jakarta’s area, particularly Kapuk-Cengkareng’s people. This research was conducted by geophysical method namely Well Logging Analysis. Well Logging is the geophysical method to know the subsurface lithology with the physical characteristic. The observation in this research area was conducted with several well devices that is Spontaneous Potential Log (SP Log), Resistivity Log, and Gamma Ray Log (GR Log). The first devices well is SP log which is work by comprising the electrical potential difference between the electrodes on the surface with the electrodes that is contained in the borehole and rock formations. The second is Resistivity Log, used to determine both the hydrocarbon and water zone based on their porosity and permeability properties. The last is GR Log, work by identifying radioactivity levels of rocks which is containing elements of thorium, uranium, or potassium. The observation result is curve-shaped which describes the type of lithological coating in subsurface. The result from the research can be interpreted that there are four of the deep groundwater layer zone with different quality. The good groundwater layer can be found in layers with good porosity and permeability. By analyzing the curves, it can be known that most of the layers which were found in this wellbore are clay stone with low resistivity and high gamma radiation. The resistivity value of the clay stone layers is about 2-4 ohm-meter with 65-80 Cps gamma radiation. There are several layers with high resistivity value and low gamma radiation (sand stone) that can be potential for being an aquifer. This is reinforced by the sand layer with a right-leaning SP log curve proving that this layer is permeable. These layers have 4-9 ohm-meter resistivity value with 40-65 Cps gamma radiation. These are mostly found as fresh water aquifer.

Keywords: aquifer, deep groundwater potential, well devices, well logging analysis

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4981 Theoretical Study of Electronic Structure of Erbium (Er), Fermium (Fm), and Nobelium (No)

Authors: Saleh O. Allehabi, V. A. Dzubaa, V. V. Flambaum, Jiguang Li, A. V. Afanasjev, S. E. Agbemava

Abstract:

Recently developed versions of the configuration method for open shells, configuration interaction with perturbation theory (CIPT), and configuration interaction with many-body perturbation theory (CI+MBPT) techniques are used to study the electronic structure of Er, Fm, and No atoms. Excitation energies of odd states connected to the even ground state by electric dipole transitions, the corresponding transition rates, isotope shift, hyperfine structure, ionization potentials, and static scalar polarizabilities are calculated. The way of extracting parameters of nuclear charge distribution beyond nuclear root mean square (RMS) radius, e.g., a parameter of quadrupole deformation β, is demonstrated. In nuclei with spin > 1/2, parameter β is extracted from the quadrupole hyperfine structure. With zero nuclear spin or spin 1/2, it is impossible since quadrupole zero, so a different method was developed. The measurements of at least two atomic transitions are needed to disentangle the contributions of the changes in deformation and nuclear RMS radius into field isotopic shift. This is important for testing nuclear theory and for searching for the hypothetical island of stability. Fm and No are heavy elements approaching the superheavy region, for which the experimental data are very poor, only seven lines for the Fm element and one line for the No element. Since Er and Fm have similar electronic structures, calculations for Er serve as a guide to the accuracy of the calculations. Twenty-eight new levels of Fm atom are reported.

Keywords: atomic spectra, electronic transitions, isotope effect, electron correlation calculations for atoms

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4980 Molecular Identification and Evolutionary Status of Lucilia bufonivora: An Obligate Parasite of Amphibians in Europe

Authors: Gerardo Arias, Richard Wall, Jamie Stevens

Abstract:

Lucilia bufonivora Moniez, is an obligate parasite of toads and frogs widely distributed in Europe. Its sister taxon Lucilia silvarum Meigen behaves mainly as a carrion breeder in Europe, however it has been reported as a facultative parasite of amphibians. These two closely related species are morphologically almost identical, which has led to misidentification, and in fact, it has been suggested that the amphibian myiasis cases by L. silvarum reported in Europe should be attributed to L. bufonivora. Both species remain poorly studied and their taxonomic relationships are still unclear. The identification of the larval specimens involved in amphibian myiasis with molecular tools and phylogenetic analysis of these two closely related species may resolve this problem. In this work seventeen unidentified larval specimens extracted from toad myiasis cases of the UK, the Netherlands and Switzerland were obtained, their COX1 (mtDNA) and EF1-α (Nuclear DNA) gene regions were amplified and then sequenced. The 17 larval samples were identified with both molecular markers as L. bufonivora. Phylogenetic analysis was carried out with 10 other blowfly species, including L. silvarum samples from the UK and USA. Bayesian Inference trees of COX1 and a combined-gene dataset suggested that L. silvarum and L. bufonivora are separate sister species. However, the nuclear gene EF1-α does not appear to resolve their relationships, suggesting that the rates of evolution of the mtDNA are much faster than those of the nuclear DNA. This work provides the molecular evidence for successful identification of L. bufonivora and a molecular analysis of the populations of this obligate parasite from different locations across Europe. The relationships with L. silvarum are discussed.

Keywords: calliphoridae, molecular evolution, myiasis, obligate parasitism

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4979 Molecular Dynamics Simulation Studies of High-Intensity, Nanosecond Pulsed Electric Fields Induced Membrane Electroporation

Authors: Jiahui Song

Abstract:

The use of high-intensity, nanosecond electric pulses has been a recent development in biomedical. High-intensity (∼100 kV/cm), nanosecond duration-pulsed electric fields have been shown to induce cellular electroporation. This will lead to an increase in transmembrane conductivity and diffusive permeability. These effects will also alter the electrical potential across the membrane. The applications include electrically triggered intracellular calcium release, shrinkage of tumors, and temporary blockage of the action potential in nerves. In this research, the dynamics of pore formation with the presence of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations show pore formation occurs for a pulse with the amplitude of 0.5V/nm at 1ns at temperature 316°K. Also increasing temperatures facilitate pore formation. When the temperature is increased to 323°K, pore forms at 0.75ns with the pulse amplitude of 0.5V/nm. For statistical significance, a total of eight MD simulations are carried out with different starting molecular velocities for each simulation. Also, actual experimental observations are compared against MD simulation results.

Keywords: molecular dynamics, high-intensity, nanosecond, electroporation

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4978 An Investigation into the Role of School Social Workers and Psychologists with Children Experiencing Special Educational Needs in Libya

Authors: Abdelbasit Gadour

Abstract:

This study explores the function of schools’ psychosocial services within Libyan mainstream schools in relation to children’s special educational needs (SEN). This is with the aim to examine the role of school social workers and psychologists in the assessment procedure of children with special educational needs. A semi-structured interview was used in this study, with 21 professionals working in the schools’ psychosocial services, of whom thirteen were school social workers (SSWs) and eight were school psychologists (SPs). The results of the interviews with SSWs and SPs provided insights into how SEN children are identified, assessed, and dealt with by school professionals. It appears from the results that what constitutes a problem has not changed significantly, and the link between learning difficulties and behavioral difficulties is also evident from this study. Children with behavior difficulties are more likely to be referred to school psychosocial services than children with learning difficulties. Yet, it is not clear from the interviews with SSWs and SPs whether children are excluded merely because of their behavior problems. Instead, they would surely be expelled from the school if they failed academically. Furthermore, the interviews with SSWs and SPs yield a rather unusual source accountable for children’s SEN; school-related difficulties were a major factor in which almost all participants attributed children’s learning and behavior problems to teachers’ deficiencies, followed by school lack of resources.

Keywords: psychologist, school, social workers, special education

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4977 Molecular Analysis of Somaclonal Variation in Tissue Culture Derived Bananas Using MSAP and SSR Marker

Authors: Emma K. Sales, Nilda G. Butardo

Abstract:

The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated. Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP). Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest. These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: methylation, MSAP, somaclones, SSR, subculture, 2, 4-D

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4976 Teachers' Perceptions on Teaching Saudi English Special Edition Textbooks in Respect of Culture

Authors: Sumayyah Qaed J. Alsulami

Abstract:

English as a foreign language (EFL) in Saudi Arabia is still new and evolving. Recently, many of the university language centres that provide intensive and mandatory English courses for the preparatory-year students have been working to develop English teaching. These centres emphasise teaching using 'special editions' textbooks for Saudi students. While the government has been working to provide social and economic policies that intend to open up and communicate widely with the world, there is a need to educate Saudi citizens to be aware and understand others in order to promote tolerance and accept others, especially in a conservative culture like Saudi Arabia. In this study, the data will be English teachers’ views on teaching culture using the special edition textbooks that will be conducted by semi-structured interviews. Teachers’ views will manifest to what extent these textbooks are used interculturally to teach the students.

Keywords: EFL, intercultural teaching, teachers' views, textbooks

Procedia PDF Downloads 106