Search results for: molecular mobility

Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Abas Mohsenzadeh, Tariq Bashir, Waseen Tahir, Ulf Stigh, Mikael Skrifvars, Kim Bolton

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The area of artificial muscles has received significant attention from many research domains including soft robotics, biomechanics and smart textiles in recent years. Poly(vinylidene fluoride) (PVDF) has been used to form artificial muscles since it contracts upon heating when under load. In this study, PVDF fibers were produced by melt spinning technique at different solid state draw ratios and then actuation mechanism for PVDF tie molecules within the semicrystalline region of PVDF polymer has been investigated using molecular dynamics simulations. Tie molecules are polymer chains that link two (or more) crystalline regions in semicrystalline polymers. The changes in fiber length upon heating have been investigated using a novel simulation technique. The results show that conformational changes of the tie molecules from the longer all-trans conformation at low temperature (β structure) to the shorter conformation (α structure) at higher temperature accrue by increasing the temperature. These results may be applied to understand the actuation observed for PVDF upon heating.

Keywords: poly(vinylidene fluoride), molecular dynamics, simulation, actuators, tie molecules, semicrystalline

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Authors: Iram Batool, Aamer Saeed, Irfan Zia Qureshi, Ayesha Razzaq, Saima Kalsoom

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Heterocyclic compounds analogues and their derivatives have attracted strong interest in medicinal chemistry due to their biological and pharmacological properties. A series of new thiazolopyrimidine carboxylates were conveniently synthesized by one-pot three-component reaction of ethyl acetoacetate, 2-aminothiazole and benzaldehyde substituted with electron-donating and electron-withdrawing groups in order to find some more potent antidiabetic and antibacterial drugs. The structures of synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopy. An in vitro antidiabetic effect was evaluated in adult male BALB/c mice and antibacterial activities were tested against Micrococcus luteus, Salmonella typhimurium, Bacillus subtilis, Bordetella bronchiseptica and Escherichia coli. Some of the tested compounds proved to possess good to excellent activities more than the reference drugs. An in silico molecular docking was also performed on synthesized compounds. The current study is expected to provide useful insights into the design of antidiabetic and antibacterial drugs and understanding the mechanism by which such drugs interact with RNA and diabetes target and exert their biochemical action.

Keywords: antidiabetic, antibacterial, MOE docking, thiazolopyrimidine

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Authors: Dorothea Voß, Tobias Esser, Michael Huber, Jakob Albert

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The growing world population and the associated increase in demand for energy and consumer goods, as well as increasing waste production, requires the development of sustainable processes. In addition, the increasing environmental awareness of our society is a driving force for the requirement that processes must be as resource and energy efficient as possible. In this context, the use of polyoxometalate catalysts (POMs) has emerged as a promising approach for the development of green processes. POMs are bifunctional polynuclear metal-oxo-anion cluster characterized by a strong Brønsted acidity, a high proton mobility combined with fast multi-electron transfer and tunable redox potential. In addition, POMs are soluble in many commonly known solvents and exhibit resistance to hydrolytic and oxidative degradation. Due to their structure and excellent physicochemical properties, POMs are efficient acid and oxidation catalysts that have attracted much attention in recent years. Oxidation processes with molecular oxygen are worth mentioning here. However, the fact that the POM catalysts are homogeneous poses a challenge for downstream processing of product solutions and recycling of the catalysts. In this regard, nanofiltration membranes have gained increasing interest in recent years, particularly due to their relative sustainability advantage over other technologies and their unique properties such as increased selectivity towards multivalent ions. In order to establish an efficient downstream process for the highly selective separation of homogeneous POM catalysts from aqueous solutions using nanofiltration membranes, a laboratory-scale membrane system was designed and constructed. By varying various process parameters, a sensitivity analysis was performed on a model system to develop an optimized method for the recovery of POM catalysts. From this, process-relevant key figures such as the rejection of various system components were derived. These results form the basis for further experiments on other systems to test the transferability to serval separation tasks with different POMs and products, as well as for recycling experiments of the catalysts in processes on laboratory scale.

Keywords: downstream processing, nanofiltration, polyoxometalates, homogeneous catalysis, green chemistry

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Authors: Drashti G. Daraji, Rosa E. Moo-Puc, Hitesh D. Patel

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Substituted 2-Thioimidazole analogues have been synthesized and confirmed by advanced spectroscopic techniques. Among them, ten compounds have been selected and evaluated for their in vitro anti-cancer activity at the National Cancer Institute (NCI) for testing against a panel of 60 different human tumor cell lines derived from nine neoplastic cancer types. Furthermore, synthesized compounds were tested for their in vitro antiprotozoal activity, and none of them exhibited significant potency against antiprotozoans. It was observed that the tested all compounds seem effective on the UACC-62 melanoma cancer cell line as compared to other cancer cell lines and also exhibited the least potent in the Non-Small Cell Lung Cancer cell line in one-dose screening. In silico studies of these derivatives were carried out by molecular docking techniques and Absorption, Distribution, Metabolism, and Excretion (ADME) using Schrödinger software to find potent B-Raf kinase inhibitor (PDB ID: 3OG7). All the compounds have been performed for docking study; Compound D4 has a good docking score for melanoma cancer as compared with other.

Keywords: anticancer activity, cancer cell line, 2-thio imidazole, one-dose assay, molecular docking

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Authors: Jadwiga Fila, Mateusz Jezowski, Pawel Poszytek

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The outbreak of the global COVID-19 pandemic started the times of crisis full of uncertainty, especially in the field of transnational cooperation projects based on the international mobility of their participants. This is notably the case of Erasmus+ Program for higher education, which is the flagship European initiative boosting cooperation between educational institutions, businesses, and other actors, enabling students and staff mobility, as well as strategic partnerships between different parties. The aim of this abstract is to study whether competences 4.0 are able to empower Erasmus+ project leaders in sustaining their international cooperation in times of global crisis, widespread online learning, and common project disruption or cancellation. The concept of competences 4.0 emerged from the notion of the industry 4.0, and it relates to skills that are fundamental for the current labor market. For the aim of the study presented in this abstract, four main 4.0 competences were distinguished: digital, managerial, social, and cognitive competence. The hypothesis for the study stipulated that the above-mentioned highly-developed competences may act as a protective shield against the pandemic challenges in terms of projects’ sustainability and continuation. The objective of the research was to assess to what extent individual competences are useful in managing projects in times of crisis. For this purpose, the study was conducted, involving, among others, 141 Polish higher education project leaders who were running their cooperation projects during the peak of the COVID-19 pandemic (Mar-Nov 2020). The research explored the self-perception of the above-mentioned competences among Erasmus+ project leaders and the contextual data regarding the sustainability of the projects. The quantitative character of data permitted validation of scales (Cronbach’s Alfa measure), and the use of factor analysis made it possible to create a distinctive variable for each competence and its dimensions. Finally, logistic regression was used to examine the association of competences and other factors on project status. The study shows that the project leaders’ competence profile attributed the highest score to digital competence (4.36 on the 1-5 scale). Slightly lower values were obtained for cognitive competence (3.96) and managerial competence (3.82). The lowest score was accorded to one specific dimension of social competence: adaptability and ability to manage stress (1.74), which proves that the pandemic was a real challenge which had to be faced by project coordinators. For higher education projects, 10% were suspended or prolonged because of the COVID-19 pandemic, whereas 90% were undisrupted (continued or already successfully finished). The quantitative analysis showed a positive relationship between the leaders’ levels of competences and the projects status. In the case of all competences, the scores were higher for project leaders who finished projects successfully than for leaders who suspended or prolonged their projects. The research demonstrated that, in the demanding times of the COVID-19 pandemic, competences 4.0, to a certain extent, do play a significant role in the successful management of Erasmus+ projects. The implementation and sustainability of international educational projects, despite mobility and sanitary obstacles, depended, among other factors, on the level of leaders’ competences.

Keywords: Competences 4.0, COVID-19 pandemic, Erasmus+ Program, international education, project sustainability

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Authors: Ertuğ Yıldırım, Dile Kara, Salih Zeki Yıldız

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Metal containing polymers (MCPs) are macro molecules usually containing metal-ligand coordination units and are a multidisciplinary research field mainly based at the interface between coordination chemistry and polymer science. The progress of this area has also been reinforced by the growth of several other closely related disciplines including macro molecular engineering, crystal engineering, organic synthesis, supra molecular chemistry and colloidal and material science. Schiff base ligands are very effective in constructing supra molecular architectures such as coordination polymers, double helical and triple helical complexes. In addition, Schiff base derivatives incorporating a fluorescent moiety are appealing tools for optical sensing of metal ions. MCPs are well-known systems in which the combinations of local parameters are possible by means of fluoro metric techniques. Generally, without incorporation of the fluorescent groups with polymers is unspecific, and it is not useful to analyze their fluorescent properties. Therefore, it is necessary to prepare a new type epoxy polymers with fluorescent groups in terms of metal sensing prop and the other photo chemical applications. In the present study metal containing polymers were prepared via poly functional monomeric Schiff base metal chelate complexes in the presence of dis functional monomers such as diglycidyl ether Bisphenol A (DGEBA). The synthesized complexes and polymers were characterized by FTIR, UV-VIS and mass spectroscopies. The preparations of epoxy polymers have been carried out at 185 °C. The prepared composites having sharp and narrow excitation/emission properties are expected to be applicable in various systems such as heat-resistant polymers and photo voltaic devices. The prepared composite is also ideal for various applications, easily prepared, safe, and maintain good fluorescence properties.

Keywords: Schiff base ligands, crystal engineering, fluorescence properties, Metal Containing Polymers (MCPs)

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Authors: K. Żak, S. Przetocka, R. Kitel, K. Guzik, B. Musielak, S. Malicki, G. Dubin, T. A. Holak

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Studies on tumor genesis revealed a number of factors that may potentially serve as molecular targets for immunotherapies. One of such promising targets are PD1 and PDL1 proteins. PD1 (Programmed cell death protein 1) is expressed by activated T cells and plays a critical role in modulation of the host's immune response. One of the PD1 ligands -PDL1- is expressed by macrophages, monocytes and cancer cells which exploit it to avoid immune attack. The notion of the mechanisms used by cancer cells to block the immune system response was utilized in the development of therapies blocking PD1-PDL1 interaction. Up to date, human PD1-PDL1 complex has not been crystallized and structure of the mouse-human complex does not provide a complete view of the molecular basis of PD1-PDL1 interactions. The purpose of this study is to obtain crystal structure of the human PD1-PDL1 complex which shall allow rational design of small molecule inhibitors of the interaction. In addition, the study presents results of binding small-molecules to PD1 and fragment docking towards PD1 protein which will facilitate the design and development of small–molecule inhibitors of PD1-PDL1 interaction.

Keywords: PD1, PDL1, cancer, small molecule, drug discovery

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Authors: Ritwik Saha, Anindita Chaudhuri

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The psychological dimension of work-based mobility of the contemporary time in the context of the ever-changing socio-economic process mounting the interest to address the consequential issues of quality of life and well-being of the migrant section of society. The negotiation with the fluidity of the job market and the changing psychosocial dimensions within and between psychosocial relations may disentangle the resilience as well as the mechanism of diligence toward migrant (marginal) life. The work-based mobility and its associated phenomena have highly impacted the migrant’s quality of life especially the marginalized (socioeconomically weak) ones along with their family members staying away from them. The subjective experiences of the journey of their migrant life and reconstruction of the psychosocial being in terms of existence and well-being at the host place are the minimal addressed issues in migrant literature. Hence this gap instigates to bring forth the issue with the present study exploring the phenomenal aspects of lived experiences, resilience, and sense-making of the well-being of migrant living by the marginalized migrant people engaging in unorganized space. In doing so qualitative research method was followed, and semi-structured interviews were used for data collection from the four selected migrant groups (Fuchkawala, Bhunjawala, Bhari - drinking water supplier, Construction worker) as they migrated to Kolkata and its metropolis area from different states of India, Five participants from each group (20 participants in total) age range between 20 to 45 were interviewed physically and participants’ observatory notes were taken to capture their lived experiences, audio recordings were transcribed and analyzed systematically following Charmaz’s three-layer coding of grounded theory. Being truthful to daily industry, the strong desire to build children’s future, the mastering mechanism to dual existence, use of traditional social network these four themes emerges after analysis of the data. However, incorporating fate as their usual way of life and making sense of well-being through their assertion is another evolving aspect of migrant life.

Keywords: lived experiences, marginal living, resilience, sense-making process, well-being

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Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

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Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

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Authors: Max Plotnikov, Arkadius Schier

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To counteract climate change, the European Commission adopted the European Green Deal (EDG) in 2019. Some of the main objectives of the EDG are climate neutrality by 2050, decarbonization, sustainable mobility, and the shift from a linear economy to a circular economy in the European Union. The mobility turnaround envisages, among other things, the switch from classic internal combustion vehicles to electromobility. The aforementioned goals are therefore accompanied by increased demand for lithium-ion batteries (LIBs) and the associated logistics. However, this inevitably gives rise to challenges that need to be addressed. Depending on whether the LIB is transported by road, rail, air, or sea, there are different regulatory frameworks in the European Union that relevant players in the value chain must adhere to. LIBs are classified as Dangerous Goods Class 9, and against this backdrop, there are various restrictions that need to be adhered to when transporting them for various actors. Currently, the exchange of information in the value chain between the various actors is almost entirely paper-based. Especially in the transport of dangerous goods, this often leads to a delay in the transport or to incorrect data. The exchange of information with the authorities is particularly essential in this context. A solution for the digital exchange of information is currently being developed. Electronic freight transport information (eFTI) enables fast and secure exchange of information between the players in the freight transport process. This concept is to be used within the supply chain from 2025. Another initiative that is expected to improve the monitoring of LIB in this context, among other things, is the battery pass. In July 2023, the latest battery regulation was adopted in the Official Journal of the European Union. This battery pass gives different actors static as well as dynamic information about the batteries depending on their access rights. This includes master data such as battery weight or battery category or information on the state of health or the number of negative events that the battery has experienced. The integration of the battery pass with the eFTI platform will be investigated for synergy effects in favor of the actors for battery transport.

Keywords: battery logistics, battery passport, data sharing, eFTI, sustainability

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Authors: Jiahui Song

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The use of electric fields with high intensity (~ 100kV/cm or higher) and ultra short pulse durations (nanosecond range) has been a recent development. Most of the studies of electroporation have ignored possible thermal effects because of the small duration of the applied voltage pulses. However, it has been predicted membrane temperature gradients ranging from 0.2×109 to 109 K/m. This research focuses on thermal effects that drive for electroporative enhancements, even though the actual temperature values might not have changed appreciably from their equilibrium levels. The dynamics of pore formation with the application of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations of a lipid layer with constant electric field strength of 0.5 V/nm at 25 °C and 47 °C are implemented to simulate the appropriate thermal effects. The GROMACS provides the force fields for the lipid membranes, which is taken to comprise of dipalmitoyl-phosphatidyl-choline (DPPC) molecules. The water model mimicks the aqueous environment surrounding the membrane. Velocities of water and membrane molecules are generated randomly at each simulation run according to a Maxwellian distribution. The high background electric field is typically used in MD simulations to probe electroporation. It serves as an accelerated test of the pore formation process since low electric fields would take inordinately long simulation time. MD simulation shows no pore is formed in a 1-ns snapshot for a DPPC membrane set at a temperature of 25°C after a 0.5 V/nm electric field is applied. A nano-sized pore is clearly seen in a 0.75-ns snapshot on the same geometry, but with the membrane surfaces kept at temperatures of 47°C. And the pore increases at 1 ns. The MD simulation results suggest the possibility that the increase in temperature can result in different degrees of electrically stimulated bio-effects. The results points to the role of thermal effects in facilitating and accelerating the electroporation process.

Keywords: high-intensity, ultra-short, electroporation, thermal effects, molecular dynamics

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

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The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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Authors: Balazs Patczai, Katalin Gocze, Gabriella Kiss, Dorottya Szabo, Tibor Mintal

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Introduction: Running has become increasingly popular on a global scale in the past decades. Amateur athletes are taking their sport to a new level in an attempt to surpass their performance goals. The aim of our study was to assess the musculoskeletal condition of amateur runners and the prevalence of injuries with a special focus on stress fracture risk. Methods: The cross sectional analysis included ankle mobility, hamstring and lower back flexibility, the use of Renne’s test for iliotibial band syndrome, functional tests for trunk and rotary stability, and measurements of bone density. Data was collected at 2 major half-marathon events in Hungary. Results: Participants (n=134) mean age was 41.76±8.57 years (males: 40.67±8.83, females: 42.08±8.56). Measures of hamstring and lower back flexibility fell into the category of good for both genders (males: 7.13±6.83cm, females: 10.17±6.67cm). No side asymmetry nor gender differences were characteristic in the case of ankle mobility. Trunk stability was significantly better for males than in females (p=0.004). Markers of bone health were in the low normal range for females and were significantly better for males (T-score: p=0.003, T-ratio: p=0.014, Z-score: p=0.034, Z-ratio: p=0.011). 5.2% of females had a previous stress fracture and 24.1% experienced irregular menstrual cycles during the past year. As for the knowledge on the possible association of energy deficiency, menstrual disturbances and their effect on bone health, Only 8.6% of females have heard of the female athlete triad either during their studies or from a health professional. Discussion: The overall musculoskeletal state was satisfactory for both genders both physically and functionally. More attention and effort should be placed on primary and secondary prevention of amateur runners. Very few active women are well informed about the effects of low energy availability and menstrual dysfunction and the negative impact these have on bone health.

Keywords: bone health, flexibility, running, stress fracture

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Authors: Sibani Bisoyi, Ute Zschieschang, Alexander Hoyer, Hagen Klauk

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Abstract— Organic thin-film transistors (TFTs) have great potential to be used for various applications such as flexible displays or sensors. For some of these applications, the TFTs must be able to withstand temperatures in excess of 100 °C, for example to permit the integration with devices or components that require high process temperatures, or to make it possible that the devices can be subjected to the standard sterilization protocols required for biomedical applications. In this work, we have investigated how the thermal stability of low-voltage small-molecule semiconductor dinaphtho[2,3-b:2’,3’-f]thieno[3,2-b]thiophene (DNTT) TFTs is affected by the encapsulation of the TFTs and by the ambient in which the thermal stress is performed. We also studied to which extent the thermal stability of the TFTs depends on the channel length. Some of the TFTs were encapsulated with a layer of vacuum-deposited Teflon, while others were left without encapsulation, and the thermal stress was performed either in nitrogen or in air. We found that the encapsulation with Teflon has virtually no effect on the thermal stability of our TFTs. In contrast, the ambient in which the thermal stress is conducted was found to have a measurable effect, but in a surprising way: When the thermal stress is carried out in nitrogen, the mobility drops to 70% of its initial value at a temperature of 160 °C and to close to zero at 170 °C, whereas when the stress is performed in air, the mobility remains at 75% of its initial value up to a temperature of 160 °C and at 60% up to 180 °C. To understand this behavior, we studied the effect of the thermal stress on the semiconductor thin-film morphology by scanning electron microscopy. While the DNTT films remain continuous and conducting when the heating is carried out in air, the semiconductor morphology undergoes a dramatic change, including the formation of large, thick crystals of DNTT and a complete loss of percolation, when the heating is conducted in nitrogen. We also found that when the TFTs are heated to a temperature of 200 °C in air, all TFTs with a channel length greater than 50 µm are destroyed, while TFTs with a channel length of less than 50 µm survive, whereas when the TFTs are heated to the same temperature (200 °C) in nitrogen, only the TFTs with a channel smaller than 8 µm survive. This result is also linked to the thermally induced changes in the semiconductor morphology.

Keywords: organic thin-film transistors, encapsulation, thermal stability, thin-film morphology

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Authors: Sorin Muraru

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Computational generation of carbon nanostructures is still a very demanding process. This work provides an alternative to manual molecular modeling through an algorithm meant to automate the design of such structures. Specifically, carbon nanochimneys are obtained through the bonding of a carbon nanotube with the smaller edge of an open carbon nanocone. The methods of connection rely on mathematical, geometrical and chemical properties. Non-hexagonal rings are used in order to perform the correct bonding of dangling bonds. Once obtained, they are useful for thermal transport, gas storage or other applications such as gas separation. The carbon nanochimneys are meant to produce a less steep connection between structures such as the carbon nanotube and graphene sheet, as in the pillared graphene, but can also provide functionality on its own. The method relies on connecting dangling bonds at the edges of the two carbon nanostructures, employing the use of two different types of auxiliary structures on a case-by-case basis. The code is implemented in Python 3.7 and generates an output file in the .pdb format containing all the system’s coordinates. Acknowledgment: This work was supported by a grant of the Executive Agency for Higher Education, Research, Development and innovation funding (UEFISCDI), project number PN-III-P1-1.1-TE-2016-24-2, contract TE 122/2018.

Keywords: carbon nanochimneys, computational, carbon nanotube, carbon nanocone, molecular modeling, carbon nanostructures

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Authors: Pejman Hosseinioun, Ali Safari, Hamed Sarbazi

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Graphene is a one-atom-thick sheet of carbon with numerous impressive properties. It is a promising material for future high-speed nanoelectronics due to its intrinsic superior carrier mobility and very high saturation velocity. These exceptional carrier transport properties suggest that graphene field effect transistors (G-FETs) can potentially outperform other FET technologies. In this paper, detailed discussions are introduced for Graphene Transistors Based Microwave Amplifiers.

Keywords: graphene, microwave FETs, microwave amplifiers, transistors

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Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

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Authors: P. M. Fonseca Alfonso, E. A. Murillo Ruiz, M. Diaz Lagos

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Understanding the physicochemical properties and mineralogy of fly ash from a particular source is essential for to protect the environment and considering its possible applications, specifically, in the production of geopolymeric materials that solidify/stabilize heavy metals ions. The results of the characterization of three fly ash samples are shown in this paper. The samples were produced in the TERMOPAIPA IV thermal power plant in the State of Boyaca, Colombia. The particle size distribution, chemical composition, mineralogy, and molecular structure of three samples were analyzed using laser diffraction, X-ray fluorescence, inductively coupled plasma mass spectrometry, X-ray diffraction, and infrared spectroscopy respectively. The particle size distribution of the three samples probably ranges from 0.128 to 211 μm. Approximately 59 elements have been identified in the three samples. It is noticeable that the ashes are made up of aluminum and silicon compounds. Besides, the iron phase in low content was also found. According to the results found in this study, the fly ash samples type F has a great potential to be used as raw material for the manufacture of geopolymers with potential use in the stabilization/solidification of heavy metals; mainly due to the presence of amorphous aluminosilicates typical of this type of ash, which react effectively with alkali-activator.

Keywords: fly ash, geopolymers, molecular structure, physicochemical properties.

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Authors: Jos Olijve

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Introduction and Purpose: Endotoxins are found in the outer membrane of gram-negative bacteria and have profound in vitro and in vivo responses. They can trigger strong immune responses and negatively affect various cellar activities particular cells expressing toll-like receptors. They are therefore unwanted contaminants of biomaterials sourced from natural raw materials, and their activity must be as low as possible. Collagen and gelatin are natural extracellular matrix components and have, due to their low allergenic potential, suitable biological properties, and tunable physical characteristics, high potential in biomedical applications. The purpose of this study was to determine the influence of autoclave sterilization of gelatin on physical properties and endotoxin level compared to surfactant purified gelatin. Methods: Type A gelatin from Sigma-Aldrich (G1890) with endotoxin level of 35000 endotoxin units (EU) per gram gelatin and type A gelatins from Rousselot Gent with endotoxin activity of 30000 EU per gram were used. A 10 w/w% G1890 gelatin solution was autoclave sterilized during 30 minutes at 121°C and 1 bar over pressure. The physical properties and the endotoxin level of the sterilized G1890 gelatin were compared to a type A gelatin from Rousselot purified with Triton X100 surfactant. The Triton X100 was added to a concentration of 0.5 w/w% which is above the critical micellar concentration. The gelatin surfactant mixtures were kept for 30-45 minutes under constant stirring at 55-60°C. The Triton X100 was removed by active carbon filtration. The endotoxin levels of the gelatins were measured using the Endozyme recombinant factor C method from Hyglos GmbH (Germany). Results and Discussion: Autoclave sterilization significantly affect the physical properties of gelatin. Molecular weight of G1890 decreased from 140 to 50kDa, and gel strength decreased from 300 to 40g. The endotoxin level of the gelatin reduced after sterilization from 35000 EU/g to levels of 400-500 EU/g. These endotoxin levels are however still far above the upper endotoxin level of 0.05 EU/ml, which resembles 5 EU/g gelatin based on a 1% gelatin solution, to avoid cell proliferation alteration. Molecular weight and gel strength of Rousselot gelatin was not altered after Triton X100 purification and remained 150kDa and 300g respectively. The endotoxin levels of Triton X100 purified Rousselot gelatin was < 5EU/g gelatin. Conclusion: Autoclave sterilization of gelatin is, in comparison to Triton X100 purification, not efficient to inactivate endotoxin levels in gelatin to levels below the upper limit to avoid cell proliferation alteration. Autoclave sterilization gave a significant decrease in molecular weight and gel strength which makes autoclave sterilized gelatin, in comparison to Triton X100 purified gelatin, not suitable for 3D printing.

Keywords: endotoxin, gelatin, molecular weight, sterilization, Triton X100

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Authors: Guido Lorenzi, Massimo Santarelli, Carlos Augusto Santos Silva

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The growth of non-dispatchable renewable energy sources in the European electricity generation mix is promoting the research of technically feasible and cost-effective solutions to make use of the excess energy, produced when the demand is low. The increasing intermittent renewable capacity is becoming a challenge to face especially in Europe, where some countries have shares of wind and solar on the total electricity produced in 2015 higher than 20%, with Denmark around 40%. However, other consumption sectors (mainly transportation) are still considerably relying on fossil fuels, with a slow transition to other forms of energy. Among the opportunities for different mobility concepts, electric (EV) and biofuel-powered vehicles (BPV) are the options that currently appear more promising. The EVs are targeting mainly the light duty users because of their zero (Full electric) or reduced (Hybrid) local emissions, while the BPVs encourage the use of alternative resources with the same technologies (thermal engines) used so far. The batteries which are applied to EVs are based on ions of Lithium because of their overall good performance in energy density, safety, cost and temperature performance. Biofuels, instead, can be various and the major difference is in their physical state (liquid or gaseous). In this study gaseous biofuels are considered and, more specifically, Synthetic Natural Gas (SNG) produced through a process of Power-to-Gas consisting in an electrochemical upgrade (with Solid Oxide Electrolyzers) of biogas with CO2 recycling. The latter process combines a first stage of electrolysis, where syngas is produced, and a second stage of methanation in which the product gas is turned into methane and then made available for consumption. A techno-economic comparison between the two alternatives is possible, but it does not capture all the different aspects involved in the two routes for the promotion of a more sustainable mobility. For this reason, a more comprehensive methodology, i.e. Life Cycle Assessment, is adopted to describe the environmental implications of using excess electricity (directly or indirectly) for new vehicle fleets. The functional unit of the study is 1 km and the two options are compared in terms of overall CO2 emissions, both considering Cradle to Gate and Cradle to Grave boundaries. Showing how production and disposal of materials affect the environmental performance of the analyzed routes is useful to broaden the perspective on the impacts that different technologies produce, in addition to what is emitted during the operational life. In particular, this applies to batteries for which the decommissioning phase has a larger impact on the environmental balance compared to electrolyzers. The lower (more than one order of magnitude) energy density of Li-ion batteries compared to SNG implies that for the same amount of energy used, more material resources are needed to obtain the same effect. The comparison is performed in an energy system that simulates the Western European one, in order to assess which of the two solutions is more suitable to lead the de-fossilization of the transport sector with the least resource depletion and the mildest consequences for the ecosystem.

Keywords: electrical energy storage, electric vehicles, power-to-gas, life cycle assessment

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Authors: Godwin Dennison, C. E. Boulind, O. Gould, B. de Lacy Costello, J. Allison, P. White, P. Ewings, A. Wicaksono, N. J. Curtis, A. Pullyblank, D. Jayne, J. A. Covington, N. Ratcliffe, N. K. Francis

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Background: Colorectal symptoms are common but only infrequently represent serious pathology, including colorectal cancer (CRC). A large number of invasive tests are presently performed for reassurance. We investigated the feasibility of urinary volatile organic compound (VOC) testing as a potential triage tool in patients fast-tracked for assessment for possible CRC. Methods: A prospective, multi-centre, observational feasibility study was performed across three sites. Patients referred on NHS fast-track pathways for potential CRC provided a urine sample which underwent Gas Chromatography Mass Spectrometry (GC-MS), Field Asymmetric Ion Mobility Spectrometry (FAIMS) and Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) analysis. Patients underwent colonoscopy and/or CT colonography and were grouped as either CRC, adenomatous polyp(s), or controls to explore the diagnostic accuracy of VOC output data supported by an artificial neural network (ANN) model. Results: 558 patients participated with 23 (4.1%) CRC diagnosed. 59% of colonoscopies and 86% of CT colonographies showed no abnormalities. Urinary VOC testing was feasible, acceptable to patients, and applicable within the clinical fast track pathway. GC-MS showed the highest clinical utility for CRC and polyp detection vs. controls (sensitivity=0.878, specificity=0.882, AUROC=0.884). Conclusion: Urinary VOC testing and analysis are feasible within NHS fast-track CRC pathways. Clinically meaningful differences between patients with cancer, polyps, or no pathology were identified therefore suggesting VOC analysis may have future utility as a triage tool. Acknowledgment: Funding: NIHR Research for Patient Benefit grant (ref: PB-PG-0416-20022).

Keywords: colorectal cancer, volatile organic compound, gas chromatography mass spectrometry, field asymmetric ion mobility spectrometry, selected ion flow tube mass spectrometry

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Authors: Rosario Rivera Rubite, Ching-I Peng, Che-Wei Lin, Mark Hughes, Yoshiko Kono, Kuo-Fang Chung

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The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.

Keywords: conservation, endemic , herbarium , limestone, phylogenetics, taxonomy

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Authors: Hyeon Su Kim, Sungjin Park, Hae Ryung Chang, Hae Rim Jung, Young Zoo Ahn, Yon Hui Kim, Seungyoon Nam

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Ependymoma, one of the most common parenchymal spinal cord tumor, represents 3-6% of all CNS tumor. Especially intracranial ependymomas, which are more frequent in childhood, have a more poor prognosis and more malignant than spinal ependymomas. Although there are growing needs to understand pathogenesis, detailed molecular understanding of pathogenesis remains to be explored. A cancer cell is composed of complex signaling pathway networks, and identifying interaction between genes and/or proteins are crucial for understanding these pathways. Therefore, we explored each ependymoma in terms of differential expressed genes and signaling networks. We used Microsoft Excel™ to manipulate microarray data gathered from NCBI’s GEO Database. To analyze and visualize signaling network, we used web-based PATHOME algorithm and Cytoscape. We show HOX family and NEFL are down-regulated but SCL family is up-regulated in cerebrum and posterior fossa cancers over a spinal cancer, and JAK/STAT signaling pathway and Chemokine signaling pathway are significantly different in the both intracranial ependymoma comparing to spinal ependymoma. We are considering there may be an age-dependent mechanism under different histological pathogenesis. We annotated mutation data of each gene subsequently in order to find potential target genes.

Keywords: systems biology, ependymoma, deg, network analysis

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Authors: Md. Alauddin, Md. Ruhul Amin, Md. Omar Faruque, Muhammad Ali Siddiquee, Zakir Hossain Howlader, Mohammad Asaduzzaman

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Diabetes and hypertension are the major lifestyle related diseases. The α-amylase and angiotensin converting enzymes (ACE) are the key enzymes that regulate diabetes and hypertension. The aim was to develop a drug for the treatment of diabetes and hypertension. The Rice Bran (RB) sample (Oryza sativa; BRRI-Dhan-84) was collected from the Bangladesh Rice Research Institute (BRRI), and rice bran proteins were isolated and hydrolyzed by hydrolyzing enzyme alcalase and trypsin. In vivo experiment suggested that rice bran bioactives has an effect on regulating the expression of several key gluconeogenesis and lipogenesis-regulating genes, such as glucose-6-phosphatase, phosphoenolpyruvate carboxykinase, and fatty acid synthase. The above genes have a connection of regulating the glucose level, lipids profile as well as act as an anti-inflammatory agent. A molecular docking, bioinformatics and in vitro experiments were performed. We found rice bran protein hydrolysates significantly (<0.05) influence the peptide concentration in the case of trypsin, alcalase, and (trypsin + alcalase) digestion. The in vitro analysis found that protein hydrolysate significantly (<0.05) reduced diabetic and hypertension as well as oxidative stress. A molecular docking study showed that the YY and IP peptide have a significantly strong binding affinity to the active site of the ACE enzyme and α-amylase with -7.8Kcal/mol and -6.2Kcal/mol, respectively. The Molecular dynamics (MD) simulation and Swiss ADME data analysis showed that less toxicity risk, good physicochemical properties, pharmacokinetics, and drug-likeness with drug scores 0.45 and 0.55 of YY and IP peptides, respectively. Thus, rice bran bioactive could be a good candidate for the treatment of diabetes and hypertension.

Keywords: anti-hypertensive and anti-hyperglycemic, anti-oxidative, bioinformatics, in vitro study, rice bran proteins and peptides

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Authors: Zhong-Dan Tu, Wang-Xi Fan, Yi-Chen Huang, Jen-Taut Yeh

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Novel ultrahigh molecular weight polyethylene (UHMWPE)/cellulose nanofiber (CNF) (F100CNFy) and UHMWPE/modified cellulose nanofiber (MCNF) (F100MCNFxy) as-prepared nanocomposite fibers were prepared by spinning F100CNFy and F100MCNFxy gel solutions, respectively. Cellulose nanofibers were successfully prepared by proper acid treatment of cotton fibers using sulfuric acid solutions. The best prepared CNF is with specific surface areas around 120 m2/g and a nanofiber diameter of 20 nm. Modified cellulose nanofiber was prepared by grafting maleic anhydride grafted polyethylene (PE-g-MAH) onto cellulose nanofibers. The achievable draw ratio (Dra) values of each F100MCNFxy as-prepared fiber series specimens approached a maximal value as their MCNF contents reached the optimal value at 0.05 phr. In which, the maximum Dra value obtained for F100MCNFx0.05 as-prepared fiber specimen prepared at the optimal MCNF content reached another maximum value as the weight ratio of PE-g-MAH to CNF approach an optimal value at 6. Similar to those found for the achievable drawing properties of the as-prepared fibers, the orientation factor, tensile strength (σ f) and initial modulus (E) values of drawn F100MCNF6y fiber series specimens with a fixed draw ratio reach a maximal value as their MCNF contents approach the optimal value, wherein the σ f and E values of the drawn F100MCNFxy fiber specimens are significantly higher than those of the drawn F100 fiber specimens and corresponding drawn F100CNFy fiber specimens prepared at the same draw ratios and CNF contents but without modification. To understand the interesting ultradrawing, thermal, orientation and tensile properties of F100CNFy and F100MCNFxy fiber specimens, Fourier transform infra-red, specific surface areas, and transmission electron microcopic analyses of the original and modified CNF nanofillers were performed in this study.

Keywords: ultradrawing, cellulose nanofibers, ultrahigh molecular weight polyethylene, nanocomposite fibers

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Authors: Fatimah A. Alhomaid

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The present study was planned to investigate the role of molecular changes and immunohistochemical in early detection of liver cancer in Saudi patients. our results were carried out on 54 patients liver cancer. We obtained our data from laboratory in King Khalid University Hospital. The specimens were taken (54) patients with liver cancer 34 male and 14 female and 2 control. The average age of varied from 37-85 years. The tumor was diagnosed as grade I in tow patients (male and female) and grade 2 in 45 patients (28 male and 17 female) while the grade 3 in 4 patients (all males). The specimens were processed for haematoxylin and eosin staining, immunohistochemical technique and flow cytometry analysis. Our study noted that most patients had adenocarcinoma which characterized by presence of signet-ring cells were very clear in advanced patients with adenocarcinoma. Our sections in adenocarcinoma in grade 2 and stage 3 had an increase in signet ring cells,an increase in the acini of glands and an increase in number of lymphocytes which spread to the muscular layer. With advancing the disease, there were haemorrhage in blood and increase in lymphocytes and increase in the number of nuclei in the tubular glands. Our study was carried on 48 patients, immunohistochemical diagnosis (CK20, PCNA, P53) and the analysis of DNA content by flow cytometry technique. Our study indicated that the presence of correlation between the immunohistochemical analysis for P53 and the grades. The reaction of P53 appeared as strong in nucleus in grades &stage 3 and appeared in other sections as dark brown pigment. Our study indicated that the absence of correlation between the immunohistochemical analysis for PCAN and the grades. In our sections there were strong reaction in the more 80% of nuclei in grade 1& stage 2. Our study indicated that the presence of correlation between the immunohistochemical analysis for CK20 and the grades. Our results indicated the presence of positive reaction in cytoplasm varied from weak to moderate in grade 3 & stage 4. Concerning the Flow cytometry technique our results indicated that the presence of correlation between the DNA and different stages of liver cancer.

Keywords: cancer, CK20, DNA, cytometry analysis, liver, immunohistochemical, molecular changes, PCNA, p53

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Authors: Arpita Roy, Navneeta Bharadvaja

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Cancer is an uncontrolled growth of abnormal cells in the body. It is one of the most serious diseases on which extensive research work has been going on all over the world. Structure-based drug designing is a computational approach which helps in the identification of potential leads that can be used for the development of a drug. Plumbagin is a naphthoquinone derivative from Plumbago zeylanica roots and belongs to one of the largest and diverse groups of plant metabolites. Anticancer and antiproliferative activities of plumbagin have been observed in animal models as well as in cell cultures. Plumbagin shows inhibitory effects on multiple cancer-signaling proteins; however, the binding mode and the molecular interactions have not yet been elucidated for most of these protein targets. In this investigation, an attempt to provide structural insights into the binding mode of plumbagin against four cancer receptors using molecular docking was performed. Plumbagin showed minimal energy against targeted cancer receptors, therefore suggested its stability and potential towards different cancers. The least binding energies of plumbagin with COX-2, TACE, and CDK6 are -5.39, -4.93, -and 4.81 kcal/mol, respectively. Comparison studies of plumbagin with different receptors showed that it is a promising compound for cancer treatment. It was also found that plumbagin obeys the Lipinski’s Rule of 5 and computed ADMET properties which showed drug likeliness and improved bioavailability. Since plumbagin is from a natural source, it has reduced side effects, and these results would be useful for cancer treatment.

Keywords: cancer, receptor, plumbagin, docking

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Authors: Md. Baki Billah, Suraiya Parveen, Shuvra Kanti Dey

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Bangladesh is earning a lot of foreign currency by exporting shrimp, but this industry is facing a tremendous problem due to the infection of white spot syndrome virus (WSSV). This study was undermined to develop rapid detection method of WSSV. A total of shrimp samples 240 collected from the 12 shrimp farms of different coastal regions (Satkhira, Khulna, and Bagerhat) were analyzed by conventional PCR using VP28 and VP664 gene-specific primers. In satkhira, Bagerhat and Khulna 39, 41 and 29 samples were found WSSV positive respectively. Real-time PCR using 71-bp amplicon for VP664 gene correlated well with conventional PCR data. The prevalence rates of WSSV among the collected 240 samples were Satkhira 38%, Khulna 47% and Bagerhat 50%. Molecular analysis of the VP28 gene sequences of WSSV revealed that Bangladeshi strains phylogenetically affiliated to the strains belong to India. This work concluded that WSSV infections are widely distributed in the coastal regions cultured shrimp in Bangladesh. Physico-chemical parameters were within the range of fish culture.

Keywords: coastal regions of Bangladesh, PCR, shrimp, white spot syndrome virus

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Authors: Eleni Stefanidou, Nikolaos Katsenios, Ioanna Karamichali, Aspasia Efthimiadou, Panagiotis Madesis

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The excessive use of pesticides and fertilizers has significant environmental and human health-related negative effects. In the frame of the development of sustainable agriculture practices, especially in the context of extreme environmental changes (climate change), it is important to develop alternative practices to increase productivity and biotic and abiotic stress tolerance. Beneficial bacteria, such as symbiotic bacteria in legumes (rhizobia) and symbiotic or free-living Plant Growth Promoting Rhizobacteria (PGPR), which could act as "plant probiotics", can promote plant growth and significantly increase the resistance of crops under adverse environmental conditions. In this study, we explored the symbiotic relationships between Faba bean (Vicia faba L.) cultivars with different PGPR bacteria, aiming to identify the possible influence on yield and biotic-abiotic phytoprotection benefits. Transcriptomic analysis of root and whole plant samples was executed for two Vicia faba L. cultivars (Polikarpi and Solon) treated with selected PGPR bacteria (6 treatments: B. subtilis + Rhizobium-mixture, A. chroococcum + Rhizobium-mixture, B. subtilis, A. chroococcum and Rhizobium-mixture). Preliminary results indicate a significant yield (Seed weight and Total number of pods) increase in both varieties, ranging around 25%, in comparison to the control, especially for the Solon cultivar. The increase was observed for all treatments, with the B. subtilis + Rhizobium-mixture treatment being the highest performing. The correlation of the physiological and morphological data with the transcriptome analysis revealed molecular mechanisms and molecular targets underlying the observed yield increase, opening perspectives for the use of nitrogen-fixing bacteria as a natural, more ecological enhancer of legume crop productivity.

Keywords: plant probiotics, PGPR, legumes, sustainable agriculture

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