Search results for: fragment molecular orbital theory

Authors: Seoi Lee, Dongjoo Chin, Heewon Kim

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Gamification refers to a technique that applies game elements to non-gaming elements, such as education and exercise, to make people more engaged in these behaviors. The purpose of this study was to identify effective elements in gamification for changing human behaviors. In order to accomplish this purpose, a survey based on learning theory was developed, especially for assessing antecedents and consequences of behaviors, and 8 popular and 8 unpopular games were selected for comparison. A total of 407 adult males and females were recruited via crowdsourcing Internet marketplace and completed the survey, which consisted of 19 questions for antecedent and 14 questions for consequences. Results showed no significant differences in consequence questions between popular and unpopular games. For antecedent questions, popular games are superior to unpopular games in character customization, play type selection, a sense of belonging, patch update cycle, and influence or dominance. This study is significant in that it reveals the elements of gamification based on learning theory. Future studies need to empirically validate whether these factors affect behavioral change.

Keywords: gamification, learning theory, antecedent, consequence, behavior change, behaviorism

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Authors: Mohammad Abdullah-Al-Wadud

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In the current era of automation and artificial intelligence, different systems have been increasingly keeping on depending on decision-making capabilities of machines. Such systems/applications may range from simple classifiers to sophisticated surveillance systems based on traditional sensors and related equipment which are becoming more common in the internet of things (IoT) paradigm. However, the available data for such problems are usually imprecise and incomplete, which leads to uncertainty in decisions made based on traditional probability-based classifiers. This requires a robust fusion framework to combine the available information sources with some degree of certainty. The theory of evidence can provide with such a method for combining evidence from different (may be unreliable) sources/observers. This talk will address the employment of the Dempster-Shafer Theory of evidence in some practical applications.

Keywords: decision making, dempster-shafer theory, evidence fusion, incomplete data, uncertainty

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Authors: Mudassar Iqbal, Riaz Hussain, Khalid Mehmood, Farah Ali, Fazal Mahmood, Abdul Ghaffar

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Corynebacterium pseudotuberculosis is an important cause of caseous lymphadenitis (CL), a complex, chronic devastating and destructive disease of small ruminants. In present study, postmortem examination of Chinkara deer (n=25) was conducted in year 2014. Pus samples suggestive of CL were collected from the superficial lymph nodes, liver, spleen and lungs during necropsy and subjected to standard microbiological procedures for isolation and molecular analysis of bacterial pathogens. Pus samples collected from carcasses (25) presenting clinical lesions of C. pseudotuberculosis infection was identified in 19 (76%) carcasses on the basis of culture characteristics. The frequency of C. pseudotuberculosis bacterium was higher in older animals as compared to young animals. Grossly, multiple tubercles of variable size having caseous material were observed in liver, lungs, spleen and lymph nodes. Histopathologically, tissue sections from all the visceral organs were extensively plugged with abscess. In present study specific prolineiminopeptidase (PIP) gene of the C. pseudotuberculosis was amplified by the Polymerase chain reaction technique (PCR) in 17(25) cases. The efficient and reliable molecular analysis along with necropsy findings in present study can be used as valuable approach for diagnosis of caseous lymphadenitis in small ruminants.

Keywords: Chinkara deer, Corynebacterium pseudotuberculosis, Caseous lymphadenitis, PCR

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Authors: Ritesh K. Shukla

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Degradation of biological samples in terms of macromolecules (DNA, RNA, and protein) are the major challenges in the forensic investigation which misleads the result interpretation. Currently, there are no precise methods available to circumvent this problem. Therefore, at the preliminary level, some methods are urgently needed to solve this issue. In this order, Comet assay is one of the most versatile, rapid and sensitive molecular biology technique to assess the DNA degradation. This technique helps to assess DNA degradation even at very low amount of sample. Moreover, the expedient part of this method does not require any additional process of DNA extraction and isolation during DNA degradation assessment. Samples directly embedded on agarose pre-coated microscopic slide and electrophoresis perform on the same slide after lysis step. After electrophoresis microscopic slide stained by DNA binding dye and observed under fluorescent microscope equipped with Komet software. With the help of this technique extent of DNA degradation can be assessed which can help to screen the sample before DNA fingerprinting, whether it is appropriate for DNA analysis or not. This technique not only helps to assess degradation of DNA but many other challenges in forensic investigation such as time since deposition estimation of biological fluids, repair of genetic material from degraded biological sample and early time since death estimation could also be resolved. With the help of this study, an attempt was made to explore the application of well-known molecular biology technique that is Comet assay in the field of forensic science. This assay will open avenue in the field of forensic research and development.

Keywords: comet assay, DNA degradation, forensic, molecular biology

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Authors: Sizwe Dlamini

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There seems to be little that has been done to investigate cartoons from a literary criticism point of view. Cartoons have been given attention mostly in semiotics as compared to other scholarly perspectives. The aim of this article is to attempt to bridge this gap by observing cartoons through the post-colonial approach as a literary theory. Even though the post-colonial approach has been previously adopted to critique the prose genre and other genres in the African indigenous languages of South Africa, there seems to be no study that has used this approach to analyse the cartoon genre. This study is thus believed to be valuable to scientific knowledge in this sense. The study adopts textual analysis as a qualitative research technique since cartoons are the primary sources of data collection. Through the application of the post-colonial theory, the findings of the study demonstrate that there are depicted socio-cultural, socio-economic, and political issues in Mngadi’s editorial cartoons. These include.

Keywords: editorial cartoons, post-colonial theory, literary criticism, turmoil

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Authors: M. Al Azri, M. Elzain, K. Bouziane, S. M. Chérif

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The electronic and magnetic properties of 6H-SiC with Mn impurities have been calculated using ab-initio calculations. Various configurations of Mn sites and Si and C vacancies were considered. The magnetic coupling between the two Mn atoms at substitutional and interstitials sites with and without vacancies is studied as a function of Mn atoms interatomic distance. It was found that the magnetic interaction energy decreases with increasing distance between the magnetic atoms. The energy levels appearing in the band gap due to vacancies and due to Mn impurities are determined. The calculated DOS’s are used to analyze the nature of the exchange interaction between the impurities. The band coupling model based on the p-d and d-d level repulsions between Mn and SiC has been used to describe the magnetism observed in each configuration. Furthermore, the impacts of applying U to Mn-d orbital on the magnetic moment have also been investigated. The results are used to understand the experimental data obtained on Mn- 6H-SiC (as-implanted and as –annealed) for various Mn concentration (CMn = 0.7%, 1.6%, 7%).

Keywords: ab-initio calculations, diluted magnetic semiconductors, magnetic properties, silicon carbide

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Authors: Eveline Muika Kabongo, Peter Delobelle, Ferdinand Mukumbang, Edward Nicol

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Introduction: Studies have been conducted to establish the effect of the MomConnect program in South Africa, but these studies did not focus on the stakeholders' and implementers' perspectives and the underlying program theory of the MomConnect initiative program. We strived to obtain stakeholders’ perspectives and assumptions on the MomConnect program and develop an initial program theory (IPT) of how the MomConnect initiative was expected to work. Methods: A realist-informed explanatory design used. The interviewer was performed with 10 key informants selected purposively among MomConnect key informants at the a national level of NDoH South Africa. The interview was done via zoom and lasted for 30 to 60 minutes. Introduction and abduction inferencing approaches were applied. The deductive and inductive approaches were performed during the analysis. ICAMO hereustic framework was used to analysed the data in order to get key informants expectations on how the MomConnect will work or not. Results: We developed three folk’s theories illustrating how the key informants’ expected the MomConnect to work. These theories showed that the MomConnect intended to provide users with health information and education that will empower and motivate them with knowledge which will allow the improvement of health services delivery among HCPs and improvement of the uptake of MCH services among pregnant women and mothers and decrease the rate of maternal and child mortality in the country. The lack of an updated mechanism to link women to the outcome was an issue. Another problem enlightened was the introduction of the WhatsApp program instead of SMS messaging, which was free of charge to women. Conclusion: The Folk’s theory developed from this study provided an insight into how the MomConnect was expected to work and what did not work. The folk’s theory will be merged with information from candidate theories on synthesis review and document review to develop our initial program theory of the MomConnect initiative.

Keywords: mHealth, MomConnect program, realist evaluation, maternal and child health, maternal and child health services, introduction, theory-driven

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Authors: Libo Jiang, Huan Li, Rongling Wu

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Ordinary differentiation equations (ODE) have proven to be powerful for reconstructing precise and informative gene regulatory networks (GRNs) from dynamic gene expression data. However, joint modeling and analysis of all genes, essential for the systematical characterization of genetic interactions, are challenging due to high dimensionality and a complex pattern of genetic regulation including activation, repression, and antitermination. Here, we address these challenges by unifying variable selection and game theory through ODE. Each gene within a GRN is co-expressed with its partner genes in a way like a game of multiple players, each of which tends to choose an optimal strategy to maximize its “fitness” across the whole network. Based on this unifying theory, we designed and conducted a real experiment to infer salt tolerance-related GRNs for Euphrates poplar, a hero tree that can grow in the saline desert. The pattern and magnitude of interactions between several hub genes within these GRNs were found to determine the capacity of Euphrates poplar to resist to saline stress.

Keywords: gene regulatory network, ordinary differential equation, game theory, LASSO, saline resistance

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Authors: Tracey Estriplet-Adams

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This paper focuses on the influence of maternal-fetal bonding by examining attachment theory, psycho-social-cultural influences/adaptations, and maternal well-being. A systematic review methodology was used to synthesize research results to summarize current evidence that can contribute to evidence-based practices. It explores the relationship between attachment styles, prenatal attachment, and perceptions of maternal-infant bonding/attachment six weeks postpartum. It also examines the protective factors of maternal-fetal attachment development. The research explores Bowlby's attachment theory and its relevance to maternal-fetal bonding with a Black Feminist Theory lens. Additionally, it discusses the impact of perceived stress, social support, and ecological models on maternal-fetal attachment. The relationship between maternal well-being, maternal-fetal attachment, and early postpartum bonding is reviewed. Moreover, the paper specifically addresses black mothers and maternal-fetal bonding, exploring the intersectionality of race, ethnicity, class, geographic location, cultural identities, and immigration status. It considers the role of familial and partner support, as well as the relationship between maternal attachment style and maternal-fetal bonding, within the framework of attachment theory and black feminist theory. Therefore, it is imperative to center Black women's voices in research, policy, and healthcare practices. Black women are experts in their own experiences and advocate for their autonomy in decision-making regarding maternal-fetal health. By amplifying their voices, we can ensure that interventions are grounded in their lived experiences.

Keywords: maternal-fetal bonding, infant well-being, maternal-infant attachment, black mothers

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Authors: Dennis Caasi

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This study analyzed four knowledge-building elements of channel expansion theory namely: communication media, communication content, communication partner, and communication influence vis-à- vis media richness dimensions among parents working overseas and their left-behind children in the Philippines. Results reveal that both parents and children consumed four out of six mediated communications tested in this research, spent one to four days a week connecting, between 30 minutes to 3 hours per engagement, and media consumption is dependent on the message content and media literacy of parents. Family, academic, household, and health were the common communication topics and parents dictate which channel to use. All six medium tested received high ratings based on the media richness constructs.

Keywords: channel expansion theory, computer-mediated communication, media richness theory, overseas Filipino worker

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Authors: Abu Salim Mustafa

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Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing

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Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Evagelos Korobilis-Magas, Adekunle Oke

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The constantly increasing tendency towards a global economy and the subsequent increase in exporting, as a result, has inevitably led to a growing interest in the topic of export success as well. Numerous studies, particularly in the past three decades, have examined a plethora of determinants to export performance. However, to the authors' best knowledge, no study up to date has ever considered decision quality as a potential antecedent to export success by attempting to test the relationship between decision quality and export performance. This is a surprising deficiency given that the export marketing literature has long ago suggested that quality decisions are regarded as the crucial intervening variable between sound decision–making and export performance. This study integrates the different definitions of decision quality proposed in the literature and the key themes incorporated therein and adapts it to an export context. Apart from laying the conceptual foundations for the delineation of this elusive but very important construct, this study is the first ever to test the relationship between decision quality and export performance. Based on survey data from a sample of 189 British export decision-makers and within a contingency theory framework, the results reveal that there is a direct, positive link between decision quality and export performance. This finding opens significant future research avenues and has very important implications for both theory and practice.

Keywords: export performance, decision quality, mixed methods, contingency theory

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Authors: Ali Ahmad AlGassim

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The objective of this study is to explore the local community perceptions toward the impact of tourism from the COR theory perspective. The current study used qualitative methods and purposive sampling to engage informants. Data was collected using an online survey with closed-ended and open-ended questions from 57 informants living in Al-Jufa Village, and then data was analysed using content analysis. The findings showed that COR theory help explains the residents’ perception of the threat and stress of losing resources. The findings showed the residents feel stressed about losing resources, such as lands, houses, heritage, sociocultural and Islamic values, as well as job and investment opportunities if the village is developed for tourism. Findings also present that one group of residents declared rejections and aiming to resist the development if it takes place, and they will not allowing foreigners to come and live in the village. The findings also show that this stress and strain can be alleviated by allowing residents to participate in the development. Finally, the residents of Al-Juhfa showed a high level of feeling of ownership towards their resources.

Keywords: perception of threat, effect of tourism, COR theory, local community, impact of tourism, Saudi Arabia

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Authors: Hao-Wen Chang, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang

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All-solid-state lithium batteries (ASSLBs) are increasingly recognized as a safer and more reliable alternative to conventional lithium-ion batteries due to their non-flammable nature and enhanced safety performance. ASSLBs utilize a range of solid-state electrolytes, including solid polymer electrolytes (SPEs), inorganic solid electrolytes (ISEs), and composite polymer electrolytes (CPEs). SPEs are particularly valued for their flexibility, ease of processing, and excellent interfacial compatibility with electrodes, though their ionic conductivity remains a significant limitation. ISEs, on the other hand, provide high ionic conductivity, broad electrochemical windows, and strong mechanical properties but often face poor interfacial contact with electrodes, impeding performance. CPEs, which merge the strengths of SPEs and ISEs, represent a compelling solution for next-generation ASSLBs by addressing both electrochemical and mechanical challenges. Despite their potential, the mechanisms governing lithium-ion transport within these systems remain insufficiently understood. In this study, we designed CPEs based on argyrodite-type Li₆PS₅Cl (LPSC) combined with two distinct polymer matrices: poly(ethylene oxide) (PEO) with 24.5 wt% lithium bis(trifluoromethane)sulfonimide (LiTFSI) and polycaprolactone (PCL) with 25.7 wt% LiTFSI. Through density functional theory (DFT) calculations, we investigated the interfacial chemistry of these materials, revealing critical insights into their stability and interactions. Additionally, ab initio molecular dynamics (AIMD) simulations of lithium electrodes interfaced with LPSC layers containing polymers and LiTFSI demonstrated that the polymer matrix significantly mitigates LPSC decomposition, compared to systems with only a lithium electrode and LPSC layers. These findings underscore the pivotal role of CPEs in improving the performance and longevity of ASSLBs, offering a promising path forward for next-generation energy storage technologies.

Keywords: all-solid-state lithium-ion batteries, composite solid electrolytes, DFT calculations, Li-ion transport

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: Zareen Khan

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Islamic Banking has experienced high growth in Pakistan in recent years and has successfully survived the economic downturn of 2009-2011. Despite the increase in branch network and expansion of services, it is unclear if Islamic banks are truly following the theory and practical application of Shariah Law. This paper explores the theological basis of Islamic finance and examines the discrepancies between the theory and practice of Islamic banking using Pakistan as a case study. It discusses areas where Islamic banks lack proper Shariah compliance and analyzes the financial weaknesses of Islamic banks in terms of the services offered. Furthermore, the paper offers plausible explanations for the clientele of Islamic banks. The case study has three major findings. Firstly, most of the employees of Islamic banks come from conventional banking backgrounds and the banks have to invest in additional trainings to specialize employees in Islamic Banking. Secondly despite the efforts of State Bank of Pakistan, there is a lack of accounting and auditing standards tailored for Islamic Banking. Thirdly, majority of the clients of Islamic banks in Pakistan are accustomed to conventional banking causing the bankers to “speak the conventional banking language.” Combined, these three factors can create gaps in the practical application of Islamic finance in Islamic banks in Pakistan.

Keywords: islamic finance, comparing theory with practice, islamic banking, Pakistan

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Authors: Akarsh Verma, Avinash Parashar

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The aim of this article is to study the effects of hydroxyl functional group on the mechanical strength and fracture toughness of graphene. This functional group forms the backbone of intrinsic atomic structure of graphene oxide (GO). Molecular dynamics-based simulations were performed in conjunction with reactive force field (ReaxFF) parameters to capture the mode-I fracture toughness of hydroxyl functionalised graphene. Moreover, these simulations helped in concluding that spatial distribution and concentration of hydroxyl functional group significantly affects the fracture morphology of graphene nanosheet. In contrast to literature investigations, atomistic simulations predicted a transition in the failure morphology of hydroxyl functionalised graphene from brittle to ductile as a function of its spatial distribution on graphene sheet.

Keywords: graphene, graphene oxide, ReaxFF, molecular dynamics

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Authors: Hailang Yang

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To ensure the confidentiality and integrity of speech signals in communication transmission, this paper proposes a voice signal encryption scheme based on chaotic theory. Firstly, the scheme utilizes chaotic mapping to generate a key stream and then employs the key stream to perform bitwise exclusive OR (XOR) operations for encrypting the speech signal. Additionally, the scheme utilizes a chaotic hash function to generate a Message Authentication Code (MAC), which is appended to the encrypted data to verify the integrity of the data. Subsequently, we analyze the security performance and encryption efficiency of the scheme, comparing and optimizing it against existing solutions. Finally, experimental results demonstrate that the proposed scheme can resist common attacks, achieving high-quality encryption and speed.

Keywords: chaotic theory, XOR encryption, chaotic hash function, Message Authentication Code (MAC)

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Rasha Al-Saedi, Anthony Meijer

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The progress of new porous materials has increased rapidly over the past decade for use in applications such as catalysis, gas storage and removal of environmentally unfriendly species due to their high surface area and high thermal stability. In this work, a theoretical study of the zirconium-based metal organic framework (MOFs) were examined in order to determine their potential for gas adsorption of various guest molecules: CO2, N2, CH4 and H2. The zirconium cluster consists of an inner Zr6O4(OH)4 core in which the triangular faces of the Zr6- octahedron are alternatively capped by O and OH groups which bound to nine formate groups and three benzoate groups linkers. General formula is [Zr(μ-O)4(μ-OH)4(HCOO)9((phyO2C)3X))] where X= CH2OH, CH2NH2, CH2CONH2, n(NH2); (n = 1-3). Three types of adsorption sites on the Zr metal center have been studied, named according to capped chemical groups as the ‘−O site’; the H of (μ-OH) site removed and added to (μ-O) site, ‘–OH site’; (μ-OH) site removed, the ‘void site’ where H2O molecule removed; (μ-OH) from one site and H from other (μ-OH) site, in addition to no defect versions. A series of investigations have been performed aiming to address this important issue. First, density functional theory DFT-B3LYP method with 6-311G(d,p) basis set was employed using Gaussian 09 package in order to evaluate the gas adsorption performance of missing-linker defects in zirconium cluster. Next, study the gas adsorption behaviour on different functionalised zirconium clusters. Those functional groups as mentioned above include: amines, alcohol, amide, in comparison with non-substitution clusters. Then, dispersion-corrected density functional theory (DFT-D) calculations were performed to further understand the enhanced gas binding on zirconium clusters. Finally, study the water effect on CO2 and N2 adsorption. The small functionalized Zr clusters were found to result in good CO2 adsorption over N2, CH4, and H2 due to the quadrupole moment of CO2 while N2, CH4 and H2 weakly polar or non-polar. The adsorption efficiency was determined using the dispersion method where the adsorption binding improved as most of the interactions, for example, van der Waals interactions are missing with the conventional DFT method. The calculated gas binding strengths on the no defect site are higher than those on the −O site, −OH site and the void site, this difference is especially notable for CO2. It has been stated that the enhanced affinity of CO2 of no defect versions is most likely due to the electrostatic interactions between the negatively charged O of CO2 and the positively charged H of (μ-OH) metal site. The uptake of the gas molecule does not enhance in presence of water as the latter binds to Zr clusters more strongly than gas species which attributed to the competition on adsorption sites.

Keywords: density functional theory, gas adsorption, metal- organic frameworks, molecular simulation, porous materials, theoretical chemistry

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Authors: Mahdi Jalili

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Functional connectivity in the human brain can be represented as a network using electroencephalography (EEG) signals. Network representation of EEG time series can be an efficient vehicle to understand the underlying mechanisms of brain function. Brain functional networks – whose nodes are brain regions and edges correspond to functional links between them – are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which graph theory metrics are sex dependent. To this end, EEGs from 24 healthy female subjects and 21 healthy male subjects were recorded in eyes-closed resting state conditions. The connectivity matrices were extracted using correlation analysis and were further binarized to obtain binary functional networks. Global and local efficiency measures – as graph theory metrics– were computed for the extracted networks. We found that male brains have a significantly greater global efficiency (i.e., global communicability of the network) across all frequency bands for a wide range of cost values in both hemispheres. Furthermore, for a range of cost values, female brains showed significantly greater right-hemispheric local efficiency (i.e., local connectivity) than male brains.

Keywords: EEG, brain, functional networks, network science, graph theory

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Santi Maneewatchararangsri, Wanpen Chaicumpa, Patcharin Saengjaruk, Urai Chaisri

Abstract:

Leptospirosis is a globally neglected disease that continues to be a significant public health and veterinary burden, with millions of cases reported each year. Early and accurate differential diagnosis of leptospirosis from other febrile illnesses and the development of a broad spectrum of leptospirosis vaccines are needed. The LipL32 outer membrane lipoprotein is a member of Leptospira adhesive matrices and has been found to exert hemolytic activity to erythrocytes in vitro. Therefore, LipL32 is regarded as a potential target for diagnosis, broad-spectrum leptospirosis vaccines, and for passive immunotherapy. In this study, we established LipL32-specific mouse monoclonal antibodies, mAbLPF1 and mAbLPF2, and their respective mouse- and humanized-engineered single chain variable fragment (ScFv). Their antibodies’ neutralizing activities against Leptospira-mediated hemolysis in vitro, and the therapeutic efficacy of mAbs against heterologous Leptospira infected hamsters were demonstrated. The epitope peptide of mAb LPF1 was mapped to a non-contiguous carboxy-terminal β-turn and amphipathic α-helix of LipL32 structure contributing to phospholipid/host cell adhesion and membrane insertion. We found that the mAbLPF2 epitope was located on the interacting loop of peptide binding groove of the LipL32 molecule responsible for interactions with host constituents. Epitope sequences are highly conserved among Leptospira spp. and are absent from the LipL32 superfamily of other microorganisms. Both epitopes are surface-exposed, readily accessible by mAbs, and immunogenic. However, they are less dominant when revealed by LipL32-specific immunoglobulins from leptospirosis-patient sera and rabbit hyperimmune serum raised by whole Leptospira. Our study also demonstrated an adhesion inhibitory activity of LipL32 protein to host membrane components and cells mediated by mAbs as well as an anti-hemolytic activity of the respective antibodies. The therapeutic antibodies, particularly the humanized-ScFv, have a potential for further development as non-drug therapeutic agent for human leptospirosis, especially in subjects allergic to antibiotics. The epitope peptides recognized by two therapeutic mAbs have potential use as tools for structure-function studies. Finally, protective peptides may be used as a target for epitope-based vaccines for control of leptospirosis.

Keywords: leptospira lipl32-specific antibodies, therapeutic epitopes, epitopes characterization, immunotherapy

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

Abstract:

Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: R. Bennai, M. Nebab, H. Ait Atmane, B. Ayache, H. Fourn

Abstract:

In this work, a study of the stability of a functionally graduated sandwiches beam using a refined theory of hyperbolic shear deformation of a beam was developed. The effects of transverse shear strains and the transverse normal deformation are considered. The constituent materials of the beam are supposed gradually variable depending on the height direction based on a simple power distribution law in terms of the volume fractions of the constituents; the two materials with which we worked are metals and ceramics. In order to examine the present model, illustrative examples are presented to show the effects of changes in different parameters such as the material graduation, the stretching effect of the thickness and thickness ratio –length on the buckling of FGM sandwich beams.

Keywords: FGM materials, refined shear deformation theory, stretching effect, buckling, boundary conditions

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Authors: Richa Mardianingrum, Srie R. N. Endah

Abstract:

In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Khabat Barkhordari

Abstract:

Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

Abstract:

In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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