Search results for: reactive molecular dynamics

Authors: Omaima G. Allam, O. A. Hakeim, K. Haggag, N. S. Elshemy

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In the midst of the two decades the use of microwave dielectric warming in the field of science has transformed into a powerful methodology to redesign compound procedures. The potential benefit of the application of these modern methods of treatment emphasize so as to reach to optimum treatment conditions and the best results, especially hydrophobicity, moisture content and increase dyeing processing while maintaining the physical and chemical properties of each textile. Moreover, polyester fibres are sometimes spun together with natural fibres to produce a cloth with blended properties. So that at the present task, the polyester/viscose mix fabrics (60 /40) were pretreated with 4 g/l of KOH for 2 min in microwave irradiation with a liquor ratio 1:25. Subsequently fabrics were inundated with different concentrations of sericin (10, 30, 50 g/l). Treated fabrics were coloured with the commercial dyes samples: Reactive Red 84(Dye 1). C. I. Acid Blue 203(Dye 2) and C.I. Reactive violet 5 (Dye 3). Colour value was specified as well as fastness properties. Likewise, the physical properties of untreated and treated fabrics such as moisture content %, tensile strength, elongation % and were evaluated. The untreated and treated fabrics are described by infrared spectroscopy (FTIR) and scanning electron microscopy.

Keywords: polyester viscose blends fabric, sericin, dyes, colour value

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Authors: Kianoosh Ahadi, Mustafa Ergil

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In this study, the event of vibrations caused by vortexes and the distribution of induced hydrodynamic forces due to vortexes on the sliding gate valves has been investigated. For this reason, a sliding valve with the help of computational fluid dynamics (CFD) software was simulated in two-dimensional )2D(, where the flow and turbulence equations were solved for three different valve openings (full, half, and 16.7 %) models. The variety of vortexes formed within the vicinity of the valve structure was investigated based on time where the trend of fluctuations and their occurrence regions have been detected. From the gathered solution dataset of the numerical simulations, the pressure coefficient (CP), the lift force coefficient (CL), the drag force coefficient (CD), and the momentum coefficient due to hydrodynamic forces (CM) were examined, and relevant figures were generated were from these results, the vortex-induced vibrations were analyzed.

Keywords: induced vibrations, computational fluid dynamics, sliding gate valves, vortexes

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Authors: Myunggon Yoon, Jung-Ho Moon

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In this paper, we present a transfer function representation of a general one-dimensional combustor. The input of the transfer function is a heat rate perturbation of a burner and the output is a flow velocity perturbation at the burner. This paper considers a general combustor model composed of multiple cans with different cross sectional areas, along with a non-zero flow rate.

Keywords: combustor, dynamics, thermoacoustics, transfer function

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Authors: Alpana Tiwari, N. K. Gaur

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We have incorporated the translational rotational (TR) coupling effects in the framework of three body force shell model (TSM) to develop an extended TSM (ETSM). The dynamical matrix of ETSM has been applied to compute the phonon frequencies of orientationally disordered mixed crystal (ND4Br)x(KBr)1-x in (q00), (qq0) and (qqq) symmetry directions for compositions 0.10≤x≤0.50 at T=300K.These frequencies are plotted as a function of wave vector k. An unusual acoustic mode softening is found along symmetry directions (q00) and (qq0) as a result of translation-rotation coupling.

Keywords: orientational glass, phonons, TR-coupling, lattice dynamics

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Authors: Vanessa Roulet, Marc Turini, Juliane Hey, Stéphanie Bord-Romeu, Emilie Bonzom, Mahmoud Badawi, Mohammed-Amine Chakir, Valérie Simon, Vanessa Viotti, Jérémie Gautier, Françoise Le Boulaire, Catherine Coignard, Claire Vincent, Sandrine Greaume, Isabelle Voisin

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Background: Beckman Coulter, Inc. has recently developed fully automated assays for the detection of HBsAg on a new immunoassay platform. The objective of this European multicenter study was to evaluate the performance of the ACCESS HBsAg and ACCESS HBsAg Confirmatory assays† on the recently CE-marked DxI 9000 ACCESS Immunoassay Analyzer. Methods: The clinical specificity of the ACCESS HBsAg and HBsAg Confirmatory assays was determined using HBsAg-negative samples from blood donors and hospitalized patients. The clinical sensitivity was determined using presumed HBsAg-positive samples. Sample HBsAg status was determined using a CE-marked HBsAg assay (Abbott ARCHITECT HBsAg Qualitative II, Roche Elecsys HBsAg II, or Abbott PRISM HBsAg assay) and a CE-marked HBsAg confirmatory assay (Abbott ARCHITECT HBsAg Qualitative II Confirmatory or Abbott PRISM HBsAg Confirmatory assay) according to manufacturer package inserts and pre-determined testing algorithms. False initial reactive rate was determined on fresh hospitalized patient samples. The sensitivity for the early detection of HBV infection was assessed internally on thirty (30) seroconversion panels. Results: Clinical specificity was 99.95% (95% CI, 99.86 – 99.99%) on 6047 blood donors and 99.71% (95%CI, 99.15 – 99.94%) on 1023 hospitalized patient samples. A total of six (6) samples were found false positive with the ACCESS HBsAg assay. None were confirmed for the presence of HBsAg with the ACCESS HBsAg Confirmatory assay. Clinical sensitivity on 455 HBsAg-positive samples was 100.00% (95% CI, 99.19 – 100.00%) for the ACCESS HBsAg assay alone and for the ACCESS HBsAg Confirmatory assay. The false initial reactive rate on 821 fresh hospitalized patient samples was 0.24% (95% CI, 0.03 – 0.87%). Results obtained on 30 seroconversion panels demonstrated that the ACCESS HBsAg assay had equivalent sensitivity performances compared to the Abbott ARCHITECT HBsAg Qualitative II assay with an average bleed difference since first reactive bleed of 0.13. All bleeds found reactive in ACCESS HBsAg assay were confirmed in ACCESS HBsAg Confirmatory assay. Conclusion: The newly developed ACCESS HBsAg and ACCESS HBsAg Confirmatory assays from Beckman Coulter have demonstrated high clinical sensitivity and specificity, equivalent to currently marketed HBsAg assays, as well as a low false initial reactive rate. †Pending achievement of CE compliance; not yet available for in vitro diagnostic use. 2023-11317 Beckman Coulter and the Beckman Coulter product and service marks mentioned herein are trademarks or registered trademarks of Beckman Coulter, Inc. in the United States and other countries. All other trademarks are the property of their respective owners.

Keywords: dxi 9000 access immunoassay analyzer, hbsag, hbv, hepatitis b surface antigen, hepatitis b virus, immunoassay

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Authors: Neha Kanodia, M. Kamil

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Properties of mono layers of Pluronic F127 at air/water interface have been investigated by using Langmuir trough method. Pluronic F127 is a triblock copolymer of poly (ethyleneoxide) (PEO groups)– poly (propylene oxide) (PO groups)–poly(ethylene oxide) (PEO groups). Surface pressure versus mean molecular area isotherms is studied. The isotherm of the mono layer showed the characteristics of a pancake-to-brush transition upon compression of the mono layer. The effect of adding surfactant (SDS) to polymer and the effect of increasing loading on polymer was also studied. The effect of repeated compression and expansion cycle (or hysteresis curve) is investigated to know about stability of the film formed. Static elasticity of mono layer gives information about molecular arrangement, phase structure and phase transition.

Keywords: surface-pressure, mean molecular area isotherms, hysteresis, static elasticity

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Authors: Annis Lai Chu Fung

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While aggression had high stability throughout developmental stages and across generations, it should be the top priority of researchers and frontline helping professionals to develop prevention and intervention programme for aggressive children and children at risk of developing aggressive behaviours. Although there is a substantial amount of anti-bullying programmes, they gave disappointingly small effect sizes. The neglectful practical significance could be attributed to the overly simplistic categorisation of individuals involved as bullies or victims. In the past three decades, the distinction between reactive and proactive aggression has been well-proved. As children displaying reactively aggressive behaviours have distinct social-information processing pattern with those showing proactively aggressive behaviours, it is critical to identify the unique needs of the two subtypes accordingly when designing an intervention. The onset of reactive aggression and proactive aggression was observed at earliest in 4.4 and 6.8 years old respectively. Such findings called for a differential early intervention targeting these high-risk children. However, to the best of the author’s knowledge, the author was the first to establish an evidence-based intervention programme against reactive and proactive aggression. With the largest samples in the world, the author, in the past 10 years, explored three different approaches and their effectiveness against aggression quantitatively and qualitatively with longitudinal design. The three approaches presented are (a) cognitive-behavioral approach, (b) moral education, with Chinese marital arts and ethics as the medium, and (c) bioneurological measures (omega-3 supplementation). The studies adopted a multi-informant approach with repeated measures before and after the intervention, and follow-up assessment. Participants were recruited from primary and secondary schools in Hong Kong. In the cognitive-behavioral approach, 66 reactive aggressors and 63 proactive aggressors, aged from 11 to 17, were identified from 10,096 secondary-school children with questionnaire and subsequent structured interview. Participants underwent 10 group sessions specifically designed for each subtype of aggressor. Results revealed significant declines in aggression levels from the baseline to the follow-up assessment after 1 year. In moral education through the Chinese martial arts, 315 high-risk aggressive children, aged 6 to 12 years, were selected from 3,511 primary-school children and randomly assigned into four types of 10-session intervention group, namely martial-skills-only, martial-ethics-only, both martial-skills-and-ethics, and physical fitness (placebo). Results showed only the martial-skills-and-ethics group had a significant reduction in aggression after treatment and 6 months after treatment comparing with the placebo group. In the bioneurological approach, 218 children, aged from 8 to 17, were randomly assigned to the omega-3 supplement group and the placebo group. Results revealed that compared with the placebo group, the omega-3 supplement group had significant declines in aggression levels at the 6-month follow-up assessment. All three approaches were effective in reducing proactive and reactive aggression. Traditionally, intervention programmes against aggressive behaviour often adapted the cognitive and/or behavioural approach. However, cognitive-behavioural approach for children was recently challenged by its demanding requirement of cognitive ability. Traditional cognitive interventions may not be as beneficial to an older population as in young children. The present study offered an insightful perspective in aggression reduction measures.

Keywords: intervention, outcome effectiveness, proactive aggression, reactive aggression

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Authors: Majid Etaati, Hamid Majedi

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Relational planning approach proposed by Patsy Healey goes beyond the physical proximity and emphasizes social proximity. This approach stresses the importance of nodes and flows between nodes. Current plans in European cities have incrementally incorporated this approach, but urban plans in Iran have still stayed very detailed and rigid. In response to the weak evaluation results of the comprehensive planning approach in Qazvin, the local authorities applied the City Development Strategy (CDS) to cope with new urban challenges. The paper begins with an explanation of relational planning and suggests that Healey gives urban planners about spatial strategies and then it surveys relational factors in CDS of Qazvin. This study analyzes the extent which CDS of Qazvin have highlighted nodes, flows, and dynamics. In the end, the study concludes that there is a relational understanding of urban dynamics in the plan, but it is weak.

Keywords: relational, dynamics, city development strategy, urban planning, Qazvin

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Authors: Sergei Zhevnenko

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Сontinuous layer of tantalum boride is formed on the surface as a result of reactive wetting of oxidized tantalum by copper melt with boron at a temperatures above 1150 °C. An increase in the wetting temperature above 1400 °C leads to a change in the formation mechanism of tantalum borides, they are formed in the nanosized flakes. In the presented work, we studied the process of copper-based in-situ composite formation, strengthened by the particles of tantalum borides. We investigated the structure of the formed particles, the conditions, and the kinetics of their formation. Dissolving boride particles do not have time to mix uniformly in the melt upon sufficiently rapid cooling and form a macrostructure, partly repeating the shape of the metallic tantalum. This allows to set different gradient structures in the copper alloy. Such macrostructures have been obtained. Boride particles and microstructures were studied by scanning and transmission electron microscopy, and regions with particles were investigated by nanoindentation. In this work, we also measured the kinetics of impregnation of porous tantalum with copper-boron melt and studied the structures of the composite, in which the melt filling the interpore space is saturated with boride particles.

Keywords: copper, tantalum borides, in-situ composites, wetting, imbibition

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Authors: Dino Carpentras, Paul J. Maher, Caoimhe O'Reilly, Michael Quayle

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Opinion dynamics is a sub-field of agent-based modeling that focuses on people’s opinions and their evolutions over time. Despite the rapid increase in the number of publications in this field, it is still not clear how to apply these models to real-world scenarios. Indeed, there is no agreement on how people update their opinion while interacting. Furthermore, it is not clear if different topics will show the same dynamics (e.g., more polarized topics may behave differently). These problems are mostly due to the lack of experimental validation of the models. Some previous studies started bridging this gap in the literature by directly measuring people’s opinions before and after the interaction. However, these experiments force people to express their opinion as a number instead of using natural language (and then, eventually, encoding it as numbers). This is not the way people normally interact, and it may strongly alter the measured dynamics. Another limitation of these studies is that they usually average all the topics together, without checking if different topics may show different dynamics. In our work, we collected data from 200 participants on 5 unpolarized topics. Participants expressed their opinions in natural language (“agree” or “disagree”). We also measured the certainty of their answer, expressed as a number between 1 and 10. However, this value was not shown to other participants to keep the interaction based on natural language. We then showed the opinion (and not the certainty) of another participant and, after a distraction task, we repeated the measurement. To make the data compatible with opinion dynamics models, we multiplied opinion and certainty to obtain a new parameter (here called “continuous opinion”) ranging from -10 to +10 (using agree=1 and disagree=-1). We firstly checked the 5 topics individually, finding that all of them behaved in a similar way despite having different initial opinions distributions. This suggested that the same model could be applied for different unpolarized topics. We also observed that people tend to maintain similar levels of certainty, even when they changed their opinion. This is a strong violation of what is suggested from common models, where people starting at, for example, +8, will first move towards 0 instead of directly jumping to -8. We also observed social influence, meaning that people exposed with “agree” were more likely to move to higher levels of continuous opinion, while people exposed with “disagree” were more likely to move to lower levels. However, we also observed that the effect of influence was smaller than the effect of random fluctuations. Also, this configuration is different from standard models, where noise, when present, is usually much smaller than the effect of social influence. Starting from this, we built an opinion dynamics model that explains more than 80% of data variance. This model was also able to show the natural conversion of polarization from unpolarized states. This experimental approach offers a new way to build models grounded on experimental data. Furthermore, the model offers new insight into the fundamental terms of opinion dynamics models.

Keywords: experimental validation, micro-dynamics rule, opinion dynamics, update rule

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p > 0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: kidney cancer, molecular biomarker, expression analysis, mutation screening

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Authors: Dino Carpentras, Alejandro Dinkelberg, Michael Quayle

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Within agent-based modeling, opinion dynamics is the field that focuses on modeling people's opinions. In this prolific field, most of the literature is dedicated to the exploration of the two 'degrees of freedom' and how they impact the model’s properties (e.g., the average final opinion, the number of final clusters, etc.). These degrees of freedom are (1) the interaction rule, which determines how agents update their own opinion, and (2) the network topology, which defines the possible interaction among agents. In this work, we show that the third degree of freedom exists. This can be used to change a model's output up to 100% of its initial value or to transform two models (both from the literature) into each other. Since opinion dynamics models are representations of the real world, it is fundamental to understand how people’s opinions can be measured. Even for abstract models (i.e., not intended for the fitting of real-world data), it is important to understand if the way of numerically representing opinions is unique; and, if this is not the case, how the model dynamics would change by using different representations. The process of measuring opinions is non-trivial as it requires transforming real-world opinion (e.g., supporting most of the liberal ideals) to a number. Such a process is usually not discussed in opinion dynamics literature, but it has been intensively studied in a subfield of psychology called psychometrics. In psychometrics, opinion scales can be converted into each other, similarly to how meters can be converted to feet. Indeed, psychometrics routinely uses both linear and non-linear transformations of opinion scales. Here, we analyze how this transformation affects opinion dynamics models. We analyze this effect by using mathematical modeling and then validating our analysis with agent-based simulations. Firstly, we study the case of perfect scales. In this way, we show that scale transformations affect the model’s dynamics up to a qualitative level. This means that if two researchers use the same opinion dynamics model and even the same dataset, they could make totally different predictions just because they followed different renormalization processes. A similar situation appears if two different scales are used to measure opinions even on the same population. This effect may be as strong as providing an uncertainty of 100% on the simulation’s output (i.e., all results are possible). Still, by using perfect scales, we show that scales transformations can be used to perfectly transform one model to another. We test this using two models from the standard literature. Finally, we test the effect of scale transformation in the case of finite precision using a 7-points Likert scale. In this way, we show how a relatively small-scale transformation introduces both changes at the qualitative level (i.e., the most shared opinion at the end of the simulation) and in the number of opinion clusters. Thus, scale transformation appears to be a third degree of freedom of opinion dynamics models. This result deeply impacts both theoretical research on models' properties and on the application of models on real-world data.

Keywords: degrees of freedom, empirical validation, opinion scale, opinion dynamics

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Authors: Alok Shiomurti Tripathi, Ajay Kumar Timiri, Papiya Mitra Mazumder, Anil Chandewar

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The present study evaluates the possible drug interaction between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ) induced in diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction by molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg/kg, ip) and confirms it by assessing the blood and urine biochemical parameters on 28th day of its induction. Selected DN animals were used for the drug interaction between GLIM (0.5mg/kg, p.o.) and SIL (2.5 mg/kg, p.o.) after 29th and 70th day of protocol. Drug interaction were assessed by evaluating the plasma drug concentration using HPLC-UV and also determine the change in the biochemical parameter in blood and urine. Mechanism of the interaction was postulated by molecular modeling study using Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in the blood and urine biochemical parameter in STZ treated groups. The concentration of SIL increased significantly (p<0.001) in rat plasma when co administered with GLIM after 70th day of protocol. Molecular modelling study revealed few important interactions with rat serum albumin and CYP2C9.GLIM has strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL. Whereas, for CYP2C9, GLIM has strong hydrogen bond with polar contacts and hydrophobic interactions than SIL. Present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals and mechanism has been supported by molecular modeling studies.

Keywords: diabetic nephropathy, glimepiride, sildenafil citrate, pharmacokinetics, homology modeling, schrodinger

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Authors: Hiroyuki Aoki, Toru Asada, Tomomi Tanii

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The properties of a spin-cast film of a polymer material are different from those in the bulk material because the polymer chains are frozen in an un-equilibrium state due to the rapid evaporation of the solvent. However, there has been little information on the un-equilibrated conformation and dynamics in a spin-cast film at the single chain level. The real-space observation of individual chains would provide direct information to discuss the morphology and dynamics of single polymer chains. The recent development of super-resolution fluorescence microscopy methods allows the conformational analysis of single polymer chain. In the current study, the conformation of a polymer chain in a spin-cast film by the super-resolution microscopy. Poly(methyl methacrylate) (PMMA) with the molecular weight of 2.2 x 10^6 was spin-cast onto a glass substrate from toluene and chloroform. For the super-resolution fluorescence imaging, a small amount of the PMMA labeled by rhodamine spiroamide dye was added. The radius of gyration (Rg) was evaluated from the super-resolution fluorescence image of each PMMA chain. The mean-square-root of Rg was 48.7 and 54.0 nm in the spin-cast films prepared from the toluene and chloroform solutions, respectively. On the other hand, the chain dimension in a bulk state (a thermally annealed 10- μm-thick sample) was observed to be 43.1 nm. This indicates that the PMMA chain in the spin-cast film takes an expanded conformation compared to the unperturbed chain and that the chain dimension is dependent on the solvent quality. In a good solvent, the PMMA chain has an expanded conformation by the excluded volume effect. The polymer chain is frozen before the relaxation from an un-equilibrated expanded conformation to an unperturbed one by the rapid solvent evaporation.

Keywords: chain conformation, polymer thin film, spin-coating, super-resolution optical microscopy

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Authors: Tsutomu Iwayama, Takayuki Hama

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Si ion implantation was widely used to synthesize specimens of SiO2 containing supersaturated Si and subsequent high temperature annealing induces the formation of embedded luminescent Si nanocrystals. In this work, the potentialities of excimer UV-light (172 nm, 7.2 eV) irradiation and rapid thermal annealing (RTA) to enhance the photoluminescence and to achieve low temperature formation of Si nanocrystals have been investigated. The Si ions were introduced at acceleration energy of 180 keV to fluence of 7.5 x 1016 ions/cm2. The implanted samples were subsequently irradiated with an excimer-UV lamp. After the process, the samples were rapidly thermal annealed before furnace annealing (FA). Photoluminescence spectra were measured at various stages at the process. We found that the luminescence intensity is strongly enhanced with excimer-UV irradiation and RTA. Moreover, effective visible photoluminescence is found to be observed even after FA at 900 oC, only for specimens treated with excimer-UV lamp and RTA. We also prepared specimens of Si nanocrystals embedded in a SiO2 by reactive pulsed laser deposition (PLD) in an oxygen atmosphere. We will make clear the similarities and differences with the way of preparation.

Keywords: Ion implantation, photoluminescence, pulsed laser deposition, rapid thermal anneal, Si nanocrystals

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Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

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Authors: Nurul Bin Ibrahim

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Advancements in neural networks have offered valuable insights into Fluid Dynamics, notably in addressing turbulence-related challenges. In this research, we introduce multiple applications of models of neural networks, namely Feed-Forward and Recurrent Neural Networks, to explore the relationship between jet formations and stratified turbulence within stochastically excited Boussinesq systems. Using machine learning tools like TensorFlow and PyTorch, the study has created models that effectively mimic and show the underlying features of the complex patterns of jet formation and stratified turbulence. These models do more than just help us understand these patterns; they also offer a faster way to solve problems in stochastic systems, improving upon traditional numerical techniques to solve stochastic differential equations such as the Euler-Maruyama method. In addition, the research includes a thorough comparison with the Statistical State Dynamics (SSD) approach, which is a well-established method for studying chaotic systems. This comparison helps evaluate how well neural networks can help us understand the complex relationship between jet formations and stratified turbulence. The results of this study underscore the potential of neural networks in computational physics and fluid dynamics, opening up new possibilities for more efficient and accurate simulations in these fields.

Keywords: neural networks, machine learning, computational fluid dynamics, stochastic systems, simulation, stratified turbulence

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Authors: Rizwan H. Khan, Saima Nusrat

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Despite the fact that amyloid associated neurodegenerative diseases and non-neuropathic systemic amyloidosis have allured the research endeavors, as no curative drugs have been proclaimed up till now except for symptomatic cure. Therapeutic compounds which can diminish or disaggregate such toxic oligomers and fibrillar species have been examined and more are on its way. In the present study, we had reported an extensive biophysical, microscopic and computational study, revealing that L-3, 4-dihydroxyphenylalanine (L-Dopa) possess undeniable potency to inhibit heat induced human lysozyme (HL) amyloid fibrillation and also retain the fibril disaggregating potential. L-Dopa interferes in the amyloid fibrillogenesis process by interacting hydrophobically and also by forming hydrogen bonds with the amino acid residues found in amyloid fibril forming prone region of HL as elucidated by molecular docking results. L-Dopa also disaggregates the mature amyloid fibrils into some unorganised species. Thus, L-Dopa and related compounds can work as a promising inhibitor for the therapeutic advancement prospective against systemic amyloidosis.

Keywords: amyloids, disaggregation, human lysozyme, molecular docking

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Authors: Jeongyeon Park, Yeo Jun Yoon, Jiyoung Seo, In Seok Moon, Hae Jun Lee, Kiwon Song

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Cold Atmospheric Pressure Plasma (CAPP) is defined as a partially ionized gas with electrically charged particles at room temperature and atmospheric pressure. CAPP generates reactive oxygen species (ROS) and reactive nitrogen species (RNS), and has potential as a new apoptosis-promoting cancer therapy. With an annular type dielectric barrier discharge (DBD) CAPP-generating device combined with a helium (He) gas feeding system, we showed that CAPP selectively induced apoptosis in various cancer cells while it promoted proliferation of the adipose tissue-derived stem cell (ASC). The apoptotic effect of CAPP was highly selective toward p53-mutated cancer cells. The intracellular ROS was mainly responsible for apoptotic cell death in CAPP-treated cancer cells. CAPP induced apoptosis even in doxorubicin-resistant cancer cell lines, demonstrating the feasibility of CAPP as a potent cancer therapy. With the same device and exposure conditions to cancer cells, CAPP stimulated proliferation of the ASC, a kind of mesenchymal stem cell that is capable of self-renewing and differentiating into adipocytes, chondrocytes, osteoblasts and neurons. CAPP-treated ASCs expressed the stem cell markers and differentiated into adipocytes as untreated ASCs. The increase of proliferation by CAPP in ASCs was offset by a NO scavenger but was not affected by ROS scavengers, suggesting that NO generated by CAPP is responsible for the activated proliferation in ASCs. Usually, cancer stem cells are reported to be resistant to known cancer therapies. When we applied CAPP of the same device and exposure conditions to cancer cells to liver cancer stem cells (CSCs) that express CD133 and epithelial cell adhesion molecule (EpCAM) cancer stem cell markers, apoptotic cell death was not examined. Apoptotic cell death of liver CSCs was induced by the CAPP generated from a device with an air-based flatten type DBD. An exposure of liver CSCs to CAPP decreased the viability of liver CSCs to a great extent, suggesting plasma be used as a promising anti-cancer treatment. To validate whether CAPP can be a promising anti-cancer treatment or an adjuvant modality to eliminate remnant tumor in cancer surgery of vestibular schwannoma, we applied CAPP to mouse schwannoma cell line SC4 Nf2 ‑/‑ and human schwannoma cell line HEI-193. A CAPP treatment leads to anti-proliferative effect in both cell lines. We are currently studying the molecular mechanisms of differential physiological effect of CAPP; the proliferation of ASCs and apoptosis of various cancer cells and CSCs.

Keywords: cold atmospheric pressure plasma, apoptosis, proliferation, cancer cells, adult stem cells

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Authors: Sanghoon Bae, Hanju Cha

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Failed fuel detector (FFD) in research reactor is a very crucial instrument to detect the anomaly from failed fuels in the early stage around primary cooling system (PCS) outlet prior to the decay tank. FFD is considered as a mandatory sensor to ensure the integrity of fuel assemblies and mitigate the consequence from a failed fuel accident. For the effective function of FFD, the location of them should be determined by contemplating the effect from coolant flow around two outlets. For this, the analysis on computational flow dynamics (CFD) should be first performed how the coolant outlet flow including radioactive materials from failed fuels are mixed and discharged through the outlet plenum within certain seconds. The analysis result shows that the outlet flow is well mixed regardless of the position of failed fuel and ultimately illustrates the effect of detector location.

Keywords: computational flow dynamics (CFD), failed fuel detector (FFD), fresh fuel assembly (FFA), spent fuel assembly (SFA)

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: Sandra Sasikumar, Noorjahan AI, Aurine Anthony

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The background of this article is the frequently unacknowledged effects of corporal punishment in a child's life as they change into adulthood, how it may permutate into various dynamics and combinations and manifest in major areas like fear of intimacy and reactive and ineffective defending styles, which may eventually lead to much more interpersonal problems and in extreme cases psychopathology. Even though such studies require a longitudinal research design, there is a wealth of information on corporal punishment in the literature. Defense styles, or the coping mechanisms that individuals use to deal with stress and difficult emotions, can also be affected by corporal punishment. Individuals who have experienced corporal punishment may develop maladaptive defense styles, such as repression or denial, that can make it difficult for them to process and cope with their emotions. The fear of intimacy, or the fear of getting close to others, is another potential effect of corporal punishment. Individuals who have experienced physical discipline may develop a fear of physical touch, making it difficult for them to form close relationships. This fear can also lead to other mental health issues, such as anxiety and depression. It is important to note that not everyone who experiences corporal punishment will develop these issues, and other factors can contribute to the development of these problems. However, corporal punishment can have a significant impact on an individual's mental and emotional well-being.

Keywords: corporal punishment, fear of intimacy, defense styles, attachment

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Eszter J. Tóth, Alexandra Hoffmann, Csaba Vágvölgyi, Tamás Papp

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Members of the genera Curvularia and Bipolaris are closely related melanin producing filamentous fungi; both of them have the teleomorph states in genus Cochliobolus. While Bipolaris species infect only plants and may cause serious agriculture damages, some Curvularia species was recovered from opportunistic human infections. The human pathogenic species typically cause phaeohyphomycoses, i.e. mould infections caused by melanised fungi, which can manifest as invasive mycoses with frequent involvement of the central nervous system in immunocompromised patients or as local infections (e.g. keratitis, sinusitis, and cutaneous lesions) in immunocompetent people. Although their plant-fungal interactions have been intensively studied, there is only little information available about the human pathogenic feature of these fungi. The aim of this study was to investigate the neutrophil granulocytes’ response to hyphal forms of Curvularia and Bipolaris in comparison with the response to Aspergillus. In the present study Curvularia lunata SZMC 23759 and Aspergillus fumigatus SZMC 23245 both isolated from human eye infection, and Bipolaris zeicola BRIP 19582b isolated from plant leaf were examined. Neutrophils were isolated from heparinised venous blood of healthy donors with dextran sedimentation followed by centrifugation over Ficoll and hypotonic lysis of erythrocytes. Viability and purity of the cells were checked with trypan blue and Wright staining, respectively. Infection of neutrophils was carried out with germinated conidia in a ratio of 5:1. Production of hydrogen peroxide, superoxide anion, and nitrogen monoxide was measured both intracellularly and extracellularly in response to the germinated spores with or without the supernatant and after serum treatment. ROS and NOS production of neutrophils in interaction with the three fungi were compared. It is already known that Aspergillus species induce ROS production of neutrophils only after serum treatment. Although, in case of C. lunata, serum opsonisation also induced an intensive production of reactive species, lower level of production was measured in the lack of serum as well. After interaction with the plant pathogenic B. zeicola, amount of reactive species found to be similar with and without serum treatment. The presence of germination supernatant decreased the reactive species production in case of each fungus. Interaction with Curvularia, Bipolaris and Aspergillus species induced different response of neutrophils. It seems that recognition of C. lunata and B. zeicola is independent of serum opsonisation, albeit it increases the level of the produced reactive species in response for C. lunata. The study was supported by the grant LP2016-8/2016.

Keywords: Curvularia, neutrophils, NOS, ROS, serum opsonisation

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Nadeem Bashir, Ghulam Mustafa Peerzada

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The present study pertains to the nonlinear behavior of acetaminophen based uncatalyzed Belousov-Zhabotinsky (BZ) oscillator and its dynamics in the presence of Ferroin as the catalyst. The role of free metal ions as catalysts was examined and the results compared with corresponding complexed catalysts. Free metal ions were found to be sluggish with respect to the evolution of the oscillatory regime as compared to complexed ones. Effect of change of the ligand moiety of the catalyst complex on the oscillatory parameters was monitored. Since ethanol potentiates the hepatotoxicity caused by acetaminophen in-vivo, it is thought to understand this interaction by virtue of causing perturbation of the acetaminophen based oscillator with different concentrations of the ethanol with and without ferroin as the catalyst. Another dimension to the ethanol effect was added by perturbation of the system with ethanol at different stages of the reaction so as to get an idea whether it is acetaminophen or some reactive intermediate generated in the reaction system which reacts with ethanol. Further, the ferroin-catalyzed oscillator is taken as a prototype inorganic model of the acetaminophen-ethanol syndrome, as ferroin and HOBr were inorganic replacements to Cyt P450 and NADPH in the alcohol metabolism.

Keywords: Belousov-Zhabotinsky reaction, ferroin, Paracetamol-Ethanol syndrome, kinetics

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Authors: Ewelina Nowak, Anna Wisla-Swider, Gohar Khachatryan, Krzysztof Danel

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Complexes of ionic liquids with different heterocyclic-rings were synthesized by ion exchange reactions with pure salmon DNA. Ionic liquids (ILs) like 1-hexyl-3-methylimidazolium chloride, 1-butyl-4-methylpyridinium chloride and 1-ethyl-1-methylpyrrolidinium bromide were used. The ILs were built into helical state and confirmed by IR spectrometric techniques. Patterns of UV-Vis, photoluminescence, IR, and CD spectra indicated inclusion of small molecules into DNA structure. Molecular weight and radii of gyrations values of ILs-DNA complexes chains were established by HPSEC–MALLS–RI method. Modification DNA with 1-ethyl-1-methylpyrrolidinium bromide gives more uniform material and leads to elimination of high molecular weight chains. Thus, the incorporation DNA double helical structure with both 1-hexyl-3-methylimidazolium chloride and 1-butyl-4-methylpyridinium chloride exhibited higher molecular weight values. Scanning electron microscopy images indicate formation of nanofibre structures in all DNA complexes. Fluorescence depends strongly on the environment in which the chromophores are inserted and simultaneously on the molecular interactions with the biopolymer matrix. The most intensive emission was observed for DNA-imidazole ring complex. Decrease in intensity UV-Vis peak absorption is a consequence of a reduction in the spatial order of polynucleotide strands and provides different π–π stacking structure. Changes in optical properties confirmed by spectroscopy methods make DNA-ILs complexes potential biosensor applications.

Keywords: biopolymers, biosensors, cationic surfactant, DNA, DNA-gels

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Authors: Javad Sarvestan, Zdenek Svoboda

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Force-time (F-T) curvature characteristics are globally referenced as the main indicators of athletic jump performance. Nevertheless, to the best of authors’ knowledge, no investigation tried to deeply study the relationship between F-T curve variables and real-game jump performance among elite volleyball players. To this end, this study was designated to investigate the association between F-T curve variables, including movement timings, force, velocity, power, rate of force development (RFD), modified reactive strength index (RSImod), and net impulse with spike jump height during real-game circumstances. Twelve young elite volleyball players performed 3 countermovement jump (CMJ) and 3 spike jump in real-game circumstances with 1-minute rest intervals to prevent fatigue. Shapiro-Wilk statistical test illustrated the normality of data distribution, and Pearson’s product correlation test portrayed a significant correlation between CMJ height and peak RFD (0.85), average RFD (r=0.81), RSImod (r=0.88) and concentric net impulse (r=0.98), and also significant correlation between spike jump height and peak RFD (0.73), average RFD (r=0.80), RSImod (r=0.62) and concentric net impulse (r=0.71). Multiple regression analysis also reported that these factors have a strong contribution in predicting of CMJ (98%) and spike jump (77%) heights. Outcomes of this study confirm that the RFD, concentric net impulse, and RSImod values could precisely monitor and track the volleyball attackers’ explosive strength, muscular stretch-shortening cycle function efficiency, and ultimate spike jump height. To this effect, volleyball coaches and trainers are advised to have an in-depth focus on their athletes’ progression or the impacts of strength trainings by observing and chasing the F-T curve variables such as RFD, net impulse, and RSImod.

Keywords: net impulse, reactive strength index, rate of force development, stretch-shortening cycle

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Authors: A. Kudrev

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The duplex Poly(A)-Poly(U) denaturation in an aqueous solutions in mixtures with the tetracationic MeTMPyP4 (Me = 2H, Zn(II); TMPyP4 is 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin), was investigated by monitoring the changes in the UV-Vis absorbance spectrum with increasing temperatures from 20°С to 70°С (рН 7.0, I=0.15M). The absorbance data matrices were analyzed with a versatile chemometric procedure that provides the melting profile (distribution of species) and the pure spectrum for each chemical species present along the heating experiment. As revealed by the increase of Tm, the duplex structure was stabilized by these porphyrins. The values of stabilization temperature ΔTm in the presence of these porphyrins are relatively large, 1.2-8.4 °C, indicating that the porphyrins contribute differently in stabilizing the duplex Poly(A)-Poly(U) structure. Remarkable is the fact that the porphyrin TMPyP4 was less effective in the stabilization of the duplex structure than the metalloporphyrin Zn(X)TMPyP4 which suggests that metallization play an important role in porphyrin-RNA binding. Molecular Dynamics Simulations has been used to illustrate melting of the duplex dsRNA bound with a porphyrin molecule.

Keywords: melting, Poly(A)-Poly(U), TMPyP4, Zn(X)TMPyP4

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