Search results for: transition pathways

Authors: Ankan Roy, Niharika, Samir Kumar Patra

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Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

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Authors: Lateefat Amao, Misagh Faezipour

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Implementing electronic health records (EHR) in healthcare is a pivotal transition aimed at digitizing and optimizing patient health information management. The expectations associated with this transition are high, even towards other health information systems (HIS) and health technology. This multifaceted process involves careful planning and execution to improve the quality and efficiency of patient care, especially as healthcare technology is a sensitive niche. Key considerations include a thorough needs assessment, judicious vendor selection, robust infrastructure development, and training and adaptation of healthcare professionals. Comprehensive training programs, data migration from legacy systems and models, interoperability, as well as security and regulatory compliance are imperative for healthcare staff to navigate EHR systems adeptly. The purpose of this work is to offer a comprehensive review of the literature on EHR implementation. It explores the impact of this health technology on health practices, highlights challenges and barriers to its successful utility, and offers practical strategies that can impact its success in healthcare. This paper provides a thorough review of studies on the adoption of EHRs, emphasizing the wide range of experiences and results connected to EHR use in the medical field, especially across different types of healthcare organizations.

Keywords: healthcare, electronic health records, EHR implementation, patient care, interoperability

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Authors: Chao Wu

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Thioredoxin reductase 2 is a mitochondrial enzyme that belongs to the cellular defense against oxidative stress. We deleted mitochondrial Txnrd2 in a KrasG12D-driven pancreatic tumor model. Despite an initial increase in precursor lesions, tumor incidence decreased significantly. We isolated cancer cell lines from these genetically engineered mice and observed an impaired proliferation and colony formation. Reactive Oxygen Species, as determined by DCF fluorescence, were increased. We detected a higher mitochondrial copy number in Txnrd2-deficient cells (KTP). However, measurement of mitochondrial bioenergetics showed no impairment of mitochondrial function and comparable O₂-consumption and extracellular acidification rates. In addition, the mitochondrial complex composition was affected in Txnrd2 deleted cell lines. To gain better insight into the role of Txnrd2, we deleted Txnrd2 in clones from parental KrasG12D cell lines using Crispr/Cas9 technology. The deletion was confirmed by western blot and activity assay. Interestingly, and in line with previous RNA expression analysis, we saw changes in EMT markers in Txnrd2 deleted cell lines and control cell lines. This might help us explain the reduced tumor incidence in KrasG12D; Txnrd2∆panc mice.

Keywords: PDAC, TXNRD2, epithelial-to-mesenchymal-transition, ROS

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Authors: Sunil Kumar, Sandip Dhole, Deepak Salunke, Chung-ming Sun

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Heterocycles bearing nitrogen, oxygen, and selenium are present in innumerable biologically active compounds. For instance, coumarin containing dicoumarol acts as naturally occurring anticoagulant. 2-Acylamido selenazole works as Store-Operated Calcium (SOC) channel regulator. Therefore, due to biologically significance of selenazole and coumarin and our quest to develop efficient methodologies for the synthesis of complex heterocycles, the trisubstituted angular isocoumarinoselenazole synthesis was proposed and achieved by starting from nitrobenzoic acid derivative, available commercially. Synthetic procedure involves three steps: i) the construction of 2-aminobenzoselenazoles, ii) their regioselective N-alkylation at position-2 and iii) alkyne insertion via Ru catalyzed C-H activation. Transition metal free synthesis of benzoselenazoles was successfully brought about by the addition/elimination reaction via intramolecular C-Se bond formation. In the next step, N-alkylation of selenazole furnished two regioisomers. Both the isomers exhibited different reactivity towards [4+2] alkyne annulation reaction. The fusion of α-pyrone ring on the benzo[1,3-d]selenazole skeleton was achieved via Ru(II)-catalyzed C-H activation and alkyne insertion. As evident from mechanism, the selenazole 'N' plays an important role for the experiential selectivity.

Keywords: alkylation, alkyne insertion, coumarin, selenazole

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Authors: Zeynep Yazicioglu

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Project development is a complex process where many stakeholders work together. Employers and main contractors are the base stakeholders, whereas designers, engineers, sub-contractors, suppliers, supervisors, and consultants are other stakeholders. A combination of the complexity of the building process with a large number of stakeholders often leads to time and cost overruns and irregular resource utilization. Failure to comply with the work schedule and inefficient use of resources in the construction processes indicate that it is necessary to accelerate production and increase productivity. The development of computer software called Building Information Modeling, abbreviated as BIM, is a major technological breakthrough in this area. The use of BIM enables architectural, structural, mechanical, and electrical projects to be drawn in coordination. BIM is a tool that should be considered by every stakeholder with the opportunities it offers, such as minimizing construction errors, reducing construction time, forecasting, and determination of the final construction cost. It is a process spreading over the years, enabling all stakeholders associated with the project and construction to use it. The main goal of this paper is to explore the problems associated with the adoption of BIM in multi-stakeholder projects. The paper is a conceptual study, summarizing the author’s practical experience with design offices and construction firms working with BIM. In the transition period to BIM, three of the challenges will be examined in this paper: 1. The compatibility of supplier companies with BIM, 2. The need for two-dimensional drawings, 3. Contractual issues related to BIM. The paper reviews the literature on BIM usage and reviews the challenges in the transition stage to BIM. Even on an international scale, the supplier that can work in harmony with BIM is not very common, which means that BIM's transition is continuing. In parallel, employers, local approval authorities, and material suppliers still need a 2-D drawing. In the BIM environment, different stakeholders can work on the same project simultaneously, giving rise to design ownership issues. Practical applications and problems encountered are also discussed, providing a number of suggestions for the future.

Keywords: BIM opportunities, collaboration, contract issues about BIM, stakeholders of project

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Authors: S. U. Khan, T. Ayub, N. Shafiq

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The properties of locally produced metakaolin (MK) as cement replacing material and the comparison of reactivity with commercially available micro-silica have been investigated. Compressive strength, splitting tensile strength, and load-deflection behaviour under bending are the properties that have been studied. The amorphous phase of MK with micro-silica was compared through X-ray diffraction (XRD) pattern. Further, interfacial transition zone of concrete with micro-silica and MK was observed through Field Emission Scanning Electron Microscopy (FESEM). Three mixes of concrete were prepared. One of the mix is without cement replacement as control mix, and the remaining two mixes are 10% cement replacement with micro-silica and MK. It has been found that MK, due to its irregular structure and amorphous phase, has high reactivity with portlandite in concrete. The compressive strength at early age is higher with MK as compared to micro-silica. MK concrete showed higher splitting tensile strength and higher load carrying capacity as compared to control and micro-silica concrete at all ages respectively.

Keywords: metakaolin, compressive strength, splitting tensile strength, load deflection, interfacial transition zone

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Authors: Ayesha Waqar Khan, Mariam Altaf, Jamil Ahmad, Shaheen Shahzad

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Kidney fibrosis is an anticipated outcome of possibly all types of progressive chronic kidney disease (CKD). Epithelial-mesenchymal transition (EMT) signaling pathway is responsible for production of matrix-producing fibroblasts and myofibroblasts in diseased kidney. In this study, a discrete model of TGF-beta (transforming growth factor) and CTGF (connective tissue growth factor) was constructed using Rene Thomas formalism to investigate renal fibrosis turn over. The kinetic logic proposed by Rene Thomas is a renowned approach for modeling of Biological Regulatory Networks (BRNs). This modeling approach uses a set of constraints which represents the dynamics of the BRN thus analyzing the pathway and predicting critical trajectories that lead to a normal or diseased state. The molecular connection between TGF-beta, Smad 2/3 (transcription factor) phosphorylation and CTGF is modeled using GenoTech. The order of BRN is CTGF, TGF-B, and SMAD3 respectively. The predicted cycle depicts activation of TGF-B (TGF-β) via cleavage of its own pro-domain (0,1,0) and presentation to TGFR-II receptor phosphorylating SMAD3 (Smad2/3) in the state (0,1,1). Later TGF-B is turned off (0,0,1) thereby activating SMAD3 that further stimulates the expression of CTGF in the state (1,0,1) and itself turns off in (1,0,0). Elevated CTGF expression reactivates TGF-B (1,1,0) and the cycle continues. The predicted model has generated one cycle and two steady states. Cyclic behavior in this study represents the diseased state in which all three proteins contribute to renal fibrosis. The proposed model is in accordance with the experimental findings of the existing diseased state. Extended cycle results in enhanced CTGF expression through Smad2/3 and Smad4 translocation in the nucleus. The results suggest that the system converges towards organ fibrogenesis if CTGF remains constructively active along with Smad2/3 and Smad 4 that plays an important role in kidney fibrosis. Therefore, modeling regulatory pathways of kidney fibrosis will escort to the progress of therapeutic tools and real-world useful applications such as predictive and preventive medicine.

Keywords: CTGF, renal fibrosis signaling pathway, system biology, qualitative modeling

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Authors: Mohammad Altaf Hossain

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A growing body of literature in urban studies has presented that urban precarity has been a lived experience for low-income groups of people in the cities of the Global South. It does not necessarily mean that cities in the Global North, where advanced capitalist economies exist, avoided the adverse realities of urban precarity. As a multifaceted condition, it creates other associated precariousness in lives -for example, economic deprivation, mental stress, and housing precarity. The interrelations between urbanity and precarity have been ubiquitous regardless of the developed and developing countries. People, mainly manual labourers with low incomes, go through uncertainties in every aspect of life. By analysing qualitative data and embracing structure-agency interaction, this paper intends to present how Bangladeshi migrants experience housing precarity in Dublin. Continued population growth and political economy factors such as labour market inequality, financialisation of the private rental sector, and the impact of cuts to government funding for social housing provision are combined to produce a housing supply crisis, affordability, and access in the city. As a result, low-income people practice informality in securing jobs and housing. The macro-structural components of this analysis include the Irish housing policy, the European labour market, the immigration policy, and the financialised housing market. The micro-structural components of South Asian communities’ experiences include social networks and social class. Access to social networks and practices of informality play a significant role in enabling them to negotiate urban precarity, including housing crises and income insecurity. In some cases, the collective agency of ethnic diaspora communities plays a vital role in negotiating with structural constraints.

Keywords: housing precarity, housing pathways, migration, agency, Dublin

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Authors: Ozlem Oral, Seval Kilic, Ozlem Yedier, Serap Dokmeci, Devrim Gozuacik

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Autophagy is a degradation pathway, activating under stress conditions. It digests macromolecules, such as abnormal proteins and long-lived organelles by engulfing them and by subsequent delivery of the cargo to lysosomes. The members of the phospholipid-dependent serine/threonine kinases, involved in many signaling pathways, which are necessary for the regulation of cellular metabolic activation. Previous studies implicate that, serine/threonine kinases have crucial roles in the mechanism of many diseases depend on the activated and/or inactivated signaling pathway. Data indicates, the signaling pathways activated by serine/threonine kinases are also involved in activation of autophagy mechanism. However, the information about the effect of serine/threonine kinases on autophagy mechanism and the roles of these effects in disease formation is limited. In this study, we investigated the effect of activated serine/threonine kinases on autophagic pathway. We performed a commonly used autophagy technique, GFP-LC3 dot formation and by using microscopy analyses, we evaluated promotion and/or inhibition of autophagy in serine/threonine kinase-overexpressed fibroblasts as well as cancer cells. In addition, we carried out confocal microscopy analyses and examined autophagic flux by utilizing the differential pH sensitivities of RFP and GFP in mRFP-GFP-LC3 probe. Based on the shRNA-library based screening, we identified autophagy-related proteins affected by serine/threonine kinases. We further studied the involvement of serine/threonine kinases on the molecular mechanism of newly identified autophagy proteins and found that, autophagic pathway is indirectly controlled by serine/threonine kinases via specific autophagic proteins. Our data indicate the molecular connection between two critical cellular mechanisms, which have important roles in the formation of many disease pathologies, particularly cancer. This project is supported by TUBITAK-1001-Scientific and Technological Research Projects Funding Program, Project No: 114Z836.

Keywords: autophagy, GFP-LC3 dot formation assay, serine/threonine kinases, shRNA-library screening

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Authors: Sulalit Bandyopadhyay, Muhammad Awais Ashfaq Alvi, Anuvansh Sharma, Wilhelm R. Glomm

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Release of drugs from nanogels and nanogel-based systems can occur under the influence of external stimuli like temperature, pH, magnetic fields and so on. pNIPAm-AAc nanogels respond to the combined action of both temperature and pH, the former being mostly determined by hydrophilic-to-hydrophobic transitions above the volume phase transition temperature (VPTT), while the latter is controlled by the degree of protonation of the carboxylic acid groups. These nanogels based systems are promising candidates in the field of drug delivery. Combining nanogels with magneto-plasmonic nanoparticles (NPs) introduce imaging and targeting modalities along with stimuli-response in one hybrid system, thereby incorporating multifunctionality. Fe@Au core-shell NPs possess optical signature in the visible spectrum owing to localized surface plasmon resonance (LSPR) of the Au shell, and superparamagnetic properties stemming from the Fe core. Although there exist several synthesis methods to control the size and physico-chemical properties of pNIPAm-AAc nanogels, yet, there is no comprehensive study that highlights the dependence of incorporation of one or more layers of NPs to these nanogels. In addition, effective determination of volume phase transition temperature (VPTT) of the nanogels is a challenge which complicates their uses in biological applications. Here, we have modified the swelling-collapse properties of pNIPAm-AAc nanogels, by combining with Fe@Au NPs using different solution based methods. The hydrophilic-hydrophobic transition of the nanogels above the VPTT has been confirmed to be reversible. Further, an analytical method has been developed to deduce the average VPTT which is found to be 37.3°C for the nanogels and 39.3°C for nanogel coated Fe@Au NPs. An opposite swelling –collapse behaviour is observed for the latter where the Fe@Au NPs act as bridge molecules pulling together the gelling units. Thereafter, Cyt C, a model protein drug and L-Dopa, a drug used in the clinical treatment of Parkinson’s disease were loaded separately into the nanogels and nanogel coated Fe@Au NPs, using a modified breathing-in mechanism. This gave high loading and encapsulation efficiencies (L Dopa: ~9% and 70µg/mg of nanogels, Cyt C: ~30% and 10µg/mg of nanogels respectively for both the drugs. The release kinetics of L-Dopa, monitored using UV-vis spectrophotometry was observed to be rather slow (over several hours) with highest release happening under a combination of high temperature (above VPTT) and acidic conditions. However, the release of L-Dopa from nanogel coated Fe@Au NPs was the fastest, accounting for release of almost 87% of the initially loaded drug in ~30 hours. The chemical structure of the drug, drug incorporation method, location of the drug and presence of Fe@Au NPs largely alter the drug release mechanism and the kinetics of these nanogels and Fe@Au NPs coated with nanogels.

Keywords: controlled release, nanogels, volume phase transition temperature, l-dopa

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Authors: Raheleh Hajilou

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In this study, we report the synthesis and characterization of YBa2Cu3O7-δ (YBCO) high-temperature superconductor prepared by solid-state method and doped with Sm in different weight percentages, 0, 0.01, 0.02 and 0.05 wt. The result of X-ray diffraction (XRD) analysis conforms to the formation of an orthorhombic phase of superconductivity in our samples. This is an important finding and indicates that the samples may exhibit superconductivity properties at certain conditions. Our results unequivocally point to a different structural order or disorder in SM/Y samples as compared to Sm based samples. We suggest that different site preferences of oxygen vacancies, predominantly created in CuO2 planes (CuO chains) of Y and Sm-based samples, might be responsible for the observed difference in the behavior. This contention is supported by a host of other considerations and experimental observations. The study investigated the effects of Sm doping on the YBCO system on various properties such as structural, critical temperature (Tc), scanning electron microscope (SEM), irresistibility line(IL), critical current density, jc, and flux line pinning force. It Seems the sample x=0.05 undergoes an insulator transition, which suppresses its superconducting transition temperature (Tc). Additionally, magnetization was measured as a function of temperature (M-T) and magnetic loops (M-H) at constant temperatures of 10. 20, 30, 40, 50 and 60K up to 10KG.

Keywords: high-Tc superconductors, Scanning electron microscopy, X-ray scattering, Irreversibility line

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Authors: Mohd Mudasir Shafi, Zafrul Hasan, Talat Saleem

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Information and communication Technology (ICT) services have been defined as a route to good governance. Introduction of ICT into Governance has given rise to the idea of e-governance which helps in enhancing transparency, generating accountability and responsiveness in the system in order to provide faster and quality service to the citizen. Advancement in ICT has provided governments all over the world to speed up the delivery of information and services to citizens and businesses and increase their participation in governance. There has been varying degree of success over the past decade into providing services to the citizens using internet and different web services. These e-government initiatives have been extensively researched. Our research is aimed at the transition from electronic government to mobile government (m-government) initiatives implementing the mobile services and concerned to understand the major factors which will aid to adoption and distribution of these services. There must be some amount of research done in the integration process between e-government and m-government. There must also be enough amount of investigation done all the factors that could affect the transition process. Such factors differ between different places and the advancement in information and technology available there. In this paper, we have discussed why mobile communication system can be used for effective e-governance and the areas where m-governance can be implemented. The paper will examine some of the reasons as well as the main opportunities for improving effective governance through mobile phones.

Keywords: e-governance, mobile phones, information technology, m-government

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Authors: Matúš Mihalik, Martin Vavra, Kornel Csach, Marián Mihalik

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GdMnO₃ belongs to orthorhombically distorted, GdFeO₃-type family of perovskite compounds. These compounds are naturally vacant and the amount of vacancies depend on the sample preparation conditions. Our GdMnO₃ samples were prepared by float zone method and the vacancies were controlled using an air, Ar and O₂ preparation atmosphere. The highest amount of vacancies was found for sample prepared in Ar atmosphere, while the sample prepared in O₂ was observed to be almost vacancy-free. The magnetic measurements indicate that the preparation atmosphere has no impact on Néel temperature (TN ~ 42 K), however, it has strong impact on the incommensurate antiferromagnetic (IC) to canted A-type weak ferromagnetic (AWF) phase transition at T1: T1 = 23.4 K; 18 K and 6.7 K for samples prepared in Ar; air and O₂ atmosphere; respectively. The hysteresis loop measured at 2 K has a butterfly-type shape with the remnant magnetization (Mr) of 0.6 µB/f.u. for Ar and air sample, while Mr = 0.3 µB/f.u. for O₂ sample. The shape of the hysteresis loop depends on the preparation atmosphere in magnetic fields up to 1.5 T, but is independent for higher magnetic fields. The coercive field of less than 0.06 T and the maximum magnetic moment of 6 µB/f.u. at magnetic field µ0H = 7 T do not depend on the preparation atmosphere. All these findings indicate that only AWF phase of GdMnO₃ compound is directly affected by the vacancies in the system, while IC phase and the field induced ferroelectric phase are not affected.

Keywords: magnetism, perovskites, sample preparation, magnetic phase transition

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Authors: J. Belovickis, V. Samulionis, J. Banys, M. V. Silibin, A. V. Solnyshkin, A. V. Sysa

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Ferroelectric polymers exhibit good flexibility, processability and low cost of production. Doping of ferroelectric polymers with nanofillers may modify its dielectric, elastic or piezoelectric properties. Carbon nanotubes are one of the ingredients that can improve the mechanical properties of polymer based composites. In this work, we report on both the ultrasonic and the dielectric properties of the copolymer polyvinylidene fluoride/tetrafluoroethylene (P(VDF-TrFE)) of the composition 70/30 mol% with various concentrations of carbon nanotubes (CNT). Experimental study of ultrasonic wave attenuation and velocity in these composites has been performed over wide temperature range (100 K – 410 K) using an ultrasonic automatic pulse-echo tecnique. The temperature dependences of ultrasonic velocity and attenuation showed anomalies attributed to the glass transition and paraelectric-ferroelectric phase transition. Our investigations showed mechanical losses to be dependent on the volume fraction of the CNTs within the composites. The existence of broad hysteresis of the ultrasonic wave attenuation and velocity within the nanocomposites is presented between cooling and heating cycles. By the means of dielectric spectroscopy, it is shown that the dielectric properties may be tuned by varying the volume fraction of the CNT fillers.

Keywords: carbon nanotubes, polymer composites, PVDF-TrFE, ultrasonic spectroscopy

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Authors: Huimin Liu, Li Xiang, Yue Liu, Jing Wang

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Background: As one of typical case for the developing countries who are stepping into the aging times globally, more and more older people in China might face the problem of which they could not maintain normal life due to the functional disability. While the government take efforts to build long-term care system and further carry out related policies for the core concept, there is still lack of strong evidence to evaluating the profile of disability states in the elderly population and its transition rate. It has been proved that disability is a dynamic condition of the person rather than irreversible so it means possible to intervene timely on them who might be in a risk of severe disability. Objective: The aim of this study was to depict the picture of the disability transferring status of the older people in China, and then find out individual characteristics that change the state of disability to provide theory basis for disability prevention and early intervention among elderly people. Methods: Data for this study came from the 2011 baseline survey and the 2013 follow-up survey of the China Health and Retirement Longitudinal Study (CHARLS). Normal ADL function, 1~2 ADLs disability,3 or above ADLs disability and death were defined from state 1 to state 4. Multi-state Markov model was applied and the four-state homogeneous model with discrete states and discrete times from two visits follow-up data was constructed to explore factors for various progressive stages. We modeled the effect of explanatory variables on the rates of transition by using a proportional intensities model with covariate, such as gender. Result: In the total sample, state 2 constituent ratio is nearly about 17.0%, while state 3 proportion is blow the former, accounting for 8.5%. Moreover, ADL disability statistics difference is not obvious between two years. About half of the state 2 in 2011 improved to become normal in 2013 even though they get elder. However, state 3 transferred into the proportion of death increased obviously, closed to the proportion back to state 2 or normal functions. From the estimated intensities, we see the older people are eleven times as likely to develop at 1~2 ADLs disability than dying. After disability onset (state 2), progression to state 3 is 30% more likely than recovery. Once in state 3, a mean of 0.76 years is spent before death or recovery. In this model, a typical person in state 2 has a probability of 0.5 of disability-free one year from now while the moderate disabled or above has a probability of 0.14 being dead. Conclusion: On the long-term care cost considerations, preventive programs for delay the disability progression of the elderly could be adopted based on the current disabled state and main factors of each stage. And in general terms, those focusing elderly individuals who are moderate or above disabled should go first.

Keywords: Markov model, elderly people, disability, transition intensity

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Authors: Tomokazu Shirai, Akihiko Kondo

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Technologies of metabolic engineering or synthetic biology are essential for effective microbial bioproduction. It is especially important to develop an in silico tool for designing a metabolic pathway producing an unnatural and valuable chemical such as fossil materials of fuel or plastics. We here demonstrated two in silico tools for designing novel metabolic pathways: BioProV and HyMeP. Furthermore, we succeeded in creating an artificial metabolic pathway by enzyme engineering.

Keywords: bioinformatics, metabolic engineering, synthetic biology, genome scale model

Procedia PDF Downloads 333

Authors: M. Sasajima, M. Watanabe, T. Yamaguchi Y. Kurosawa, Y. Koike

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In very narrow pathways, the speed of sound propagation and the phase of sound waves change due to the air viscosity. We have developed a new Finite Element Method (FEM) that includes the effects of air viscosity for modeling a narrow sound pathway. This method is developed as an extension of the existing FEM for porous sound-absorbing materials. The numerical calculation results for several three-dimensional slit models using the proposed FEM are validated against existing calculation methods.

Keywords: simulation, FEM, air viscosity, slit

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Authors: Anton G. Akulichev, Avinash Tiwari, Ben Alcock, Andreas Echtermeyer

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Low temperatures are known to pose a major threat for polymers; many are prone to excessive stiffness or even brittleness. There is a technology gap between the properties of existing elastomeric sealing materials and the properties needed for service in extremely cold regions. Moreover, some aspects of low temperature behaviour of rubber are not thoroughly studied and understood. The paper presents results of laboratory testing of a conventional oilfield HNBR (hydrogenated nitrile butadiene rubber) elastomer at low climatic temperatures above and below its glass transition point, as well as the performance of some filled HNBR formulations. Particular emphasis in the experiments is put on rubber viscoelastic characteristics studied by Dynamic Mechanical Analysis (DMA) and quasi-static mechanical testing results at low temperatures. As demonstrated by the stress relaxation and DMA experiments the transition region near Tg of the studied compound has the most striking features, like rapid stress relaxation, as compared to the glassy and rubbery plateau. In addition the quasi-static experiments show that molecular movement below Tg is not completely frozen, but rather evident and manifested in a certain stress decay as well. The effect of temperature and filler additions on typical mechanical and other properties of the materials is also discussed.

Keywords: characterization, filled elastomers, HNBR, low temperature

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Authors: Domenico Carmelo Mongelli, Laura Carnieletto, Michele De Carli, Filippo Busato

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Starting from the current context in which the Russian invasion in Ukraine has highlighted Europe's dependence on natural gas imports for heating buildings, this study proposes solutions to resolve this dependency and evaluates related scenarios in the near future. In the first part of this work the methodologies and results of the economic impact are indicated by simulating a massive replacement of boilers powered by fossil fuels with electrically powered hightemperature air-water heat pumps for heating residential buildings in different European climates, without changing the current energy mix. For each individual European region, the costs for the purchase and installation of heat pumps for all residential buildings have been determined. Again for each individual European region, the economic savings during the operation phase that would be obtained in this future scenario of energy transition from fossil fuels to the electrification of domestic heating were calculated. For the European regions for which the economic savings were identified as positive, the payback times of the economic investments were analysed. In the second part of the work, hypothesizing different scenarios for a possible greater use of renewable energy sources and therefore with different possible future scenarios of the energy mix, the methodologies and results of the simulations on the economic analysis and on the environmental analysis are reported which have allowed us to evaluate the future effects of the energy transition from boilers to heat pumps for each European region. In the third part, assuming a rapid short-term diffusion of cooling for European residential buildings, the penetration shares in the cooling market and future projections of energy needs for cooling for each European region have been identified. A database was created where the results of this research relating to 38 European Nations divided into 179 regions were reported. Other previous works on the topics covered were limited to analyzing individual European nations, without ever going into detail about the individual regions within each nation, while the original contribution of the present work lies in the fact that the results achieved allow a specific numerical analysis and punctual for every single European region.

Keywords: buildings, energy, Europe, future

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Authors: Afsaneh Mohammadnejad, Marianne Nygaard, Jan Baumbach, Shuxia Li, Weilong Li, Jesper Lund, Jacob v. B. Hjelmborg, Lene Christensen, Qihua Tan

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Cognitive impairment in the elderly is a key issue affecting the quality of life. Despite a strong genetic background in cognition, only a limited number of single nucleotide polymorphisms (SNPs) have been found. These explain a small proportion of the genetic component of cognitive function, thus leaving a large proportion unaccounted for. We hypothesize that one reason for this missing heritability is the misspecified modeling in data analysis concerning phenotype distribution as well as the relationship between SNP dosage and the phenotype of interest. In an attempt to overcome these issues, we introduced a model-free method based on the generalized correlation coefficient (GCC) in a genome-wide association study (GWAS) of cognitive function in twin samples and compared its performance with two popular linear regression models. The GCC-based GWAS identified two genome-wide significant (P-value < 5e-8) SNPs; rs2904650 near ZDHHC2 on chromosome 8 and rs111256489 near CD6 on chromosome 11. The kinship model also detected two genome-wide significant SNPs, rs112169253 on chromosome 4 and rs17417920 on chromosome 7, whereas no genome-wide significant SNPs were found by the linear mixed model (LME). Compared to the linear models, more meaningful biological pathways like GABA receptor activation, ion channel transport, neuroactive ligand-receptor interaction, and the renin-angiotensin system were found to be enriched by SNPs from GCC. The GCC model outperformed the linear regression models by identifying more genome-wide significant genetic variants and more meaningful biological pathways related to cognitive function. Moreover, GCC-based GWAS was robust in handling genetically related twin samples, which is an important feature in handling genetic confounding in association studies.

Keywords: cognition, generalized correlation coefficient, GWAS, twins

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Authors: Subodh Kumar, Sanjeev Kumar Sharma, Gaurav Kaushik, Pramod Avti, Phulen Sarma, Bikash Medhi, Krishan Lal Khanduja

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Background: It is well known that cigarette smoke is one of the causative factors in various lung diseases especially cancer. Carcinogens and oxidant molecules present in cigarette smoke not only damage the cellular constituents (lipids, proteins, DNA) but may also regulate the molecular pathways involved in inflammation and cancer. Continuous oxidative stress caused by the constituents of cigarette smoke leads to higher PhospholipaseA₂ (PLA₂) activity, resulting in elevated levels of secondary metabolites whose role is well defined in cancer. To reduce the burden of chronic inflammation as well as oxidative stress, and higher levels of secondary metabolites, we checked the curative potential of PLA₂ inhibitor Bromoenol Lactone (BEL) during continuous exposure of cigarette smoke condensate (CSC). Aim: To check the therapeutic potential of Bromoenol Lactone (BEL), an inhibitor of PhospholipaseA₂s, in pathways of CSC-induced changes in type I and type II alveolar epithelial cells. Methods: Effect of BEL on CSC-induced PLA2 activity were checked using colorimetric assay, cellular toxicity using cell viability assay, membrane integrity using fluorescein di-acetate (FDA) uptake assay, reactive oxygen species (ROS) levels and apoptosis markers through flow cytometry, and cellular regulation using MAPKinases levels, in lung epithelium. Results: BEL significantly mimicked CSC-induced PLA₂ activity, ROS levels, apoptosis, and kinases level whereas improved cellular viability and membrane integrity. Conclusions: Current observations revealed that BEL may be a potential therapeutic agent during Cigarette smoke-induced anomalies in lung epithelium.

Keywords: cigarette smoke condensate, phospholipase A₂, oxidative stress, alveolar epithelium, bromoenol lactone

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Authors: Hosein Hamisheh Bahar, Mohammad Hossein Fazel Zarandi, Akbar Esfahanipour

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In this paper, a hybrid expert system is developed by using fuzzy genetic network programming with reinforcement learning (GNP-RL). In this system, the frame-based structure of the system uses the trading rules extracted by GNP. These rules are extracted by using technical indices of the stock prices in the training time period. For developing this system, we applied fuzzy node transition and decision making in both processing and judgment nodes of GNP-RL. Consequently, using these method not only did increase the accuracy of node transition and decision making in GNP's nodes, but also extended the GNP's binary signals to ternary trading signals. In the other words, in our proposed Fuzzy GNP-RL model, a No Trade signal is added to conventional Buy or Sell signals. Finally, the obtained rules are used in a frame-based system implemented in Kappa-PC software. This developed trading system has been used to generate trading signals for ten companies listed in Tehran Stock Exchange (TSE). The simulation results in the testing time period shows that the developed system has more favorable performance in comparison with the Buy and Hold strategy.

Keywords: fuzzy genetic network programming, hybrid expert system, technical trading signal, Tehran stock exchange

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Authors: Diana C. El Assal, Fatima Monteiro, Caroline May, Peter Barbuti, Silvia Bolognin, Averina Nicolae, Hulda Haraldsdottir, Lemmer R. P. El Assal, Swagatika Sahoo, Longfei Mao, Jens Schwamborn, Rejko Kruger, Ines Thiele, Kathrin Marcus, Ronan M. T. Fleming

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Degeneration of substantia nigra pars compacta dopaminergic neurons is one of the hallmarks of Parkinson's disease. These neurons have a highly complex axonal arborisation and a high energy demand, so any reduction in ATP synthesis could lead to an imbalance between supply and demand, thereby impeding normal neuronal bioenergetic requirements. Synaptic mitochondria exhibit increased vulnerability to dysfunction in Parkinson's disease. After biogenesis in and transport from the cell body, synaptic mitochondria become highly dependent upon oxidative phosphorylation. We applied a systems biochemistry approach to identify the metabolic pathways used by neuronal mitochondria for energy generation. The mitochondrial component of an existing manual reconstruction of human metabolism was extended with manual curation of the biochemical literature and specialised using omics data from Parkinson's disease patients and controls, to generate reconstructions of synaptic and somal mitochondrial metabolism. These reconstructions were converted into stoichiometrically- and fluxconsistent constraint-based computational models. These models predict that Parkinson's disease is accompanied by an increase in the rate of glycolysis and a decrease in the rate of oxidative phosphorylation within synaptic mitochondria. This is consistent with independent experimental reports of a compensatory switching of bioenergetic pathways in the putamen of post-mortem Parkinson's disease patients. Ongoing work, in the context of the SysMedPD project is aimed at computational prediction of mitochondrial drug targets to slow the progression of neurodegeneration in the subset of Parkinson's disease patients with overt mitochondrial dysfunction.

Keywords: bioenergetics, mitochondria, Parkinson's disease, systems biochemistry

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Authors: Kuheli Chakrabarty, Animesh Ghosh, Atanu Roy, Gourab Kanti Das

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Aldol reaction is an important class of carbon-carbon bond forming reactions. One of the popular ways to impose asymmetry in aldol reaction is the introduction of chiral auxiliary that binds the approaching reactants and create dissymmetry in the reaction environment, which finally evolves to enantiomeric excess in the aldol products. The last decade witnesses the usage of natural amino acids as chiral auxiliary to control the stereoselectivity in various carbon-carbon bond forming processes. In this context, L-proline was found to be an effective organocatalyst in asymmetric aldol additions. In last few decades the use of water as solvent or co-solvent in asymmetric organocatalytic reaction is increased sharply. Simple amino acids like L-proline does not catalyze asymmetric aldol reaction in aqueous medium not only that, In organic solvent medium high catalytic loading (~30 mol%) is required to achieve moderate to high asymmetric induction. In this context, huge efforts have been made to modify L-proline and 4-hydroxy-L-proline to prepare organocatalyst for aqueous medium asymmetric aldol reaction. Here, we report the result of our DFT calculations on asymmetric aldol reaction of benzaldehyde, p-NO2 benzaldehyde and t-butyraldehyde with a number of ketones using L-proline hydrazide as organocatalyst in wet solvent free condition. Gaussian 09 program package and Gauss View program were used for the present work. Geometry optimizations were performed using B3LYP hybrid functional and 6-31G(d,p) basis set. Transition structures were confirmed by hessian calculation and IRC calculation. As the reactions were carried out in solvent free condition, No solvent effect were studied theoretically. Present study has revealed for the first time, the direct involvement of two water molecules in the aldol transition structures. In the TS, the enamine and the aldehyde is connected through hydrogen bonding by the assistance of two intervening water molecules forming a supramolecular network. Formation of this type of supramolecular assembly is possible due to the presence of protonated -NH2 group in the L-proline hydrazide moiety, which is responsible for the favorable entropy contribution to the aldol reaction. It is also revealed from the present study that, water assisted TS is energetically more favorable than the TS without involving any water molecule. It can be concluded from this study that, insertion of polar group capable of hydrogen bond formation in the L-proline skeleton can lead to a favorable aldol reaction with significantly high enantiomeric excess in wet solvent free condition by reducing the activation barrier of this reaction.

Keywords: aldol reaction, DFT, organocatalysis, transition structure

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Authors: Henry Kelly, Helena Shaw

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This paper will seek how innovative methods from Health Economics and, to a lesser extent, wellbeing analysis can be applied in the Cost-Benefit Analysis (CBA) of transport infrastructure and policy interventions. The context for this will focus on the framework articulated by the UK Treasury (finance department) and the English Department for Transport. Both have well-established methods for undertaking CBA, but there is increased policy interest, particularly at a regional level of exploring broader strategic goals beyond those traditionally associated with transport user benefits, productivity gains, and labour market access. Links to different CBA approaches internationally, such as New Zealand, France, and Wales will be referenced. By exploring a complementary method of accessing the impacts of policies through the quantification of health impacts is a fruitful line to explore. In a previous piece of work, 14 impact pathways were identified, mapping the relationship between transport and health. These are wide-ranging, from improved employment prospects, the stress of unreliable journey times, and air quality to isolation and loneliness. Importantly, we will consider these different measures of health from an intersectional point of view to ensure that the basis that remains in the health industry does not get translated across to this work. The objective is to explore how a CBA based on these pathways may, through quantifying forecast impacts in terms of Quality-Adjusted Life Years may, produce different findings than a standard approach. Of particular interest is how a health-based approach may have different distributional impacts on socio-economic groups and may favour distinct types of interventions. Consideration will be given to the degree this approach may double-count impacts or if it is possible to identify additional benefits to the established CBA approach. The investigation will explore a range of schemes, from a high-speed rail link, highway improvements, rural mobility hubs, and coach services to cycle lanes. The conclusions should aid the progression of methods concerning the assessment of publicly funded infrastructure projects.

Keywords: cost-benefit analysis, health, QALYs transport

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Authors: Chandra Shekhar Maurya, Chiranjit Sarkar

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The transient response of rheological properties of a carbonyl iron (CI)-water-based magnetorheological fluid (MRF) was studied under shear rate, shear stress, and shear strain working mode subjected to step-change in an applied magnetic field. MR fluid is a kind of smart material whose rheological properties change under an applied magnetic field. We prepared an MR fluid comprising of CI 65 weight %, water 35 weight %, and OPTIGEL WX used as an additive by changing the weight %. It was found that the MR effect of the CI/water suspension was enhanced by using an additive. A transient shear stress response was observed by switched on and switched off of the magnetic field to see the stability, relaxation behavior, and resulting change in rheological properties. When the magnetic field is on, a sudden increase in the shear stress was observed due to the fast motion of magnetic structures that describe the transition from the liquidlike state to the solid-like state due to an increase in dipole-dipole interaction of magnetic particles. Simultaneously, the complete reverse transition occurs due to instantaneous breakage of the chain structure once the magnetic field is switched off.

Keywords: magnetorheological fluid, rheological properties, shears stress, shears strain, viscosity

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Authors: A. Cagnacci, D. F. Barattini, E. Casolati, M. Mangrella, E. Piccolo, S. Rosu, L. C. Pătrașcu

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This Triple study aimed to evaluate the efficacy of polycarbophil vaginal gel (PCV) in treating symptoms of vaginal atrophy (VA) in peri- and post-menopausal women. Women in peri- (n=29) and postmenopause (n=54) diagnosed with VA were progressively enrolled and treated once a day for 30 days. Thereafter, those wishing to continue (n=73) received the PCV treatment for an additional 180 days. The vaginal health index (VHI) and vaginal dryness, irritation, and pain at intercourse, along with treatment safety, were evaluated at baseline, 30 days of treatment, and after additional 180 days. At baseline, the VHI (p<0.056) and VAS of vaginal dryness (p=0.0001,) irritation (p=0.002), and pain at intercourse (p=0.0001) were worse in postmenopausal women than in perimenopausal women. VHI and VA symptoms improved in all women, and after 30 days of PCV administration, they were similar between peri-and postmenopausal women. After an additional 180 days of treatment, VHI further increased (p=0.0001), VAS of all symptoms (P=0.0001) and the Global Symptom Score (P=0.0001) further decreased. The treatment was safe. Treatment with PCV improves VA symptoms in both peri- and post-menopausal women. Prolongation of treatment up to 6 months increases the efficacy of treatment with no side effects.

Keywords: late menopausal transition, postmenopause, polycarbophil, sexuality, vaginal dryness

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Authors: Sohil I. Alqazlan

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Introduction and Objectives: There is limited research focusing on young adults with intellectual disabilities (ID) and their experiences after finishing compulsory education, especially in the Middle Eastern/Arab countries. This paper aims to further understand the lives of young adults with ID in Riyadh [the capital city of Saudi Arabia], particularly as they go on to access Post-Secondary Education [PSE]. As part of this study, it is important to understand the roles of high schools in Riyadh in terms of preparing their students for post-school life. To achieve this, the researcher has asked Saudi Arabia’s Ministry of Education to provide student transition plans (TPs) for post-school opportunities. However, and unfortunately, high schools in Riyadh do not use transition plans for their students. Therefore, the researcher has requested individual education plans (IEPs) for students with ID in their final year at high school to find the type of support the students had regarding both their long- and short-term goals that might help them access PSE or the labour market. Methods: The researcher analysed 10 IEPs of students in their final year at high school. To achieve the aim of the study, the researcher compared these IEPs with expectations set out in the official IEP framework of the MoE in Saudi Arabia, such as collaboration on the IEP sample and the focus on adult life. By analysing the students’ IEPs in terms of various goals, this study attempts to highlight skills that might offer students more independence after finishing compulsory education and going on to PSE. Results: Unfortunately, communication between IEP team members proved persistently absent in the sample. This was clear from the fact that none of the team members, apart from the SEN teachers, had signed any of the IEPs. Thus, none of the daily or weekly goals outlined were sent to parents to review at home. As a result of this, there were no goals in the IEPs that clearly referred to PSE. However, some long-term goals were set which might help those with ID become more independent in their adult life. For example, in the IEPs, which dealt with computer skills, the student had goals related to using Microsoft Word. Finally, just one goal of these IEPs set an important independent skill for the young adults with ID: “the student will learn how to use public transportation”. Conclusions: From analysing the ten IEPs, it was clear that SEN teachers in Riyadh schools were working without any help from other professionals. The students with ID, as well as their families, were not consulted on their views on important goals. Therefore, more work needs to be done with the students regarding their transition to PSE, perhaps by building partnerships between high schools and potential PSE institutions. Finally, more PSE programmes and a higher level of employer awareness could help create a bridge for students transferring from high school to PSE. Schools could also focus their IEP goals towards specific PSE programmes the student might attend, which could increase their chances of success.

Keywords: high school, post-secondary education, PSE, students with intellectual disabilities

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Authors: Rumana Keyani, Haleema Sadia, Asia Nosheen, Rabia Naz, Humaira Yasmin, Sidra Zahoor

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Tomato is a significant crop of the world and is one of the staple foods of Pakistan. A vast number of plant pathogens from simple viruses to complex parasites cause diseases in tomatoes but fungal infection in our country is quite high. Sometimes the symptoms are too harsh destroying the crop altogether. Countries like our own with continuously increasing massive population and limited resources cannot afford such an economic loss. There is an array of morphological, genetic, biochemical and molecular processes involved in plant resistance mechanisms to biotic stress. The study of different metabolic pathways like Jasmonic acid (JA) pathways and most importantly signaling molecules like ROS/RNS and their redoxin enzymes i.e. TRX and NRX is crucial to disease management, contributing to healthy plant growth. So, improving tolerance in crop plants against biotic stresses is a dire need of our country and world as whole. In the current study, fungal pathogenic strains Alternaria solani and Rhizoctonia solani were used to inoculate tomatoes to check the defense responses of tomato plant against these pathogens at molecular as well as phenotypic level with jasmonic acid and spermidine pretreatment. All the growth parameters (root and shoot length, dry and weight root, shoot weight measured 7 days post-inoculation, exhibited that infection drastically declined the growth of the plant whereas jasmonic acid and spermidine assisted the plants to cope up with the infection. Thus, JA and Spermidine treatments maintained comparatively better growth factors. Antioxidant assays and expression analysis through real time quantitative PCR following time course experiment at 24, 48 and 72 hours intervals also exhibited that activation of JA defense genes and a polyamine Spermidine helps in mediating tomato responses against fungal infection when used alone but the two treatments combined mask the effect of each other.

Keywords: fungal infection, jasmonic acid defence, tomato, spermidine

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Authors: Amine.Harbia, Hicham. Moutaabbidb, Yann. Le Godecb, Said. Benmokhtara, Mouhammed. Moutaabbida

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This study explores the structural and magnetic characteristics of newly synthesized double perovskite oxides, La₂NiₓCo1-xMnO₆, with x ranging from 0.2 to 0.8. Utilizing X-ray powder diffraction and SQUID magnetometry, we analyzed the compounds that consistently exhibit a monoclinic structure with the P21/n space group at ambient temperature. it findings reveal that as Ni2+ is progressively substituted by Co2+, there is a corresponding decrease in cell parameters, attributable to the smaller ionic radius of Ni2+ (0.69 Å) compared to Co2+ (0.74 Å). The crystal structure features octahedrally coordinated (Co/Ni)2+ and Mn4+ cations with oxygen, forming (Co/Ni)O6 and MnO6 octahedra linked via oxygen atoms along different crystallographic axes. Magnetic characterization conducted over a temperature range of 2 to 300 K in both DC and AC magnetic fields, showed a predominant paramagnetic to ferromagnetic transition between 232 K and 260 K, with the Curie temperature notably increasing with higher x values. Samples with x=0.2, 0.25, and 0.5 exhibited a secondary PM-FM transition between 200 K and 208 K. Cation ordering was quantitatively assessed, indicating a higher ordering in Ni2+-rich samples (x=0.75 and 0.8) at over 96%, whereas the sample with x=0.25 showed minimal ordering. Furthermore, the out-of-phase component of the AC susceptibility displayed frequency-dependent transitions between 65 K and 110 K, suggesting the presence of superparamagnetic domains across all samples.

Keywords: double perovskite oxides, magnetic transitions, cation ordering, squid magnetometry

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