Search results for: molecular interactions

Authors: Qin Ou, Yanghui Xu, Xintu Wang, Kim Maren Lompe, Gang Liu, Jan Peter Van Der Hoek

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Microplastics (MPs) can undergo the photooxidation process under ultraviolet (UV) exposure, which determines their transformation and fate in environments. The presence of dissolved organic matter (DOM) can interact with MPs and take participate in the photo-degradation of MPs. As an important DOM component, dissolved black carbon (DBC), widely distributed in aquatic environments, can accelerate or inhibit the sunlight-driven photo-transformation of environmental pollutants. However, the role and underlying mechanism of DBC in the photooxidation of MPs are not clear. Herein, the DBC (< 0.45 µm) was extracted from wood biochar and fractionated by molecular weight (i.e., <3 KDa, 3 KDa−30 KDa, 30 KDa−0.45 µm). The effects of DBC chemical composition (i.e., molecular weight and chemical structure) in DBC-mediated photo-transformation of polystyrene (PS) MPs were investigated. The results showed that DBC initially inhibited the photo-degradation of MPs due to light shielding. Under UV exposure for 6−24 h, the presence of 5 mg/L DBC decreased the carbonyl index of MPs compared to the control. This inhibitory effect of DBC was found to decrease with increasing irradiation time. Notably, DBC initially decreased but then increased the hydroxyl index with aging time, suggesting that the role of DBC may shift from inhibition to acceleration. In terms of the different DBC fractions, the results showed that the smallest fraction of DBC (<3 KDa) significantly accelerated the photooxidation of PS MPs since it acted as reactive oxygen species (ROS) generators, especially in promoting the production of ¹O₂ and ³DBC* and •OH. With the increase in molecular weight, the acceleration effect of DBC on the degradation of MPs was decreased due to the increase of light shielding and possible decrease of photosensitization ability. This study thoroughly investigated the critical role of DBC chemical composition in the photooxidation process, which helps to assess the duration of aging and transformation of MPs during long-term weathering in natural waters.

Keywords: microplastics, photo-degradation, dissolved black carbon, molecular weight, photosensitization

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Authors: Daniela Panico

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Framed by language socialization and family language policy theories, the present study explores the ways the language choice patterns of bilingual siblings contribute to the shaping of the language environment and the language practices of Italian/English families residing in Sydney. The main source of data is video recordings of naturally occurring parent-children and child-to-child interactions during everyday routines (i.e., family mealtimes and siblings playtime) in the home environment. Recurrent interactional practices are analyzed in detail through a conversational analytical approach. This presentation focuses on the interactional trajectories developing during the negotiation of language choices between all family members and between siblings in face-to-face interactions. Fine-grained analysis is performed on language negotiation sequences of multiparty bilingual conversations in order to uncover the sequential patterns through which a) the children respond to the parental strategies aiming to minority language maintenance, and b) the siblings influence each other’s language use and choice (e.g., older siblings positioning themselves as language teachers and language brokers, younger siblings accepting the role of apprentices). The findings show that, along with the parents, children are active socializing agents in the family and, with their linguistic behavior, they contribute to the establishment of a bilingual or a monolingual context in the home. Moreover, by orienting themselves towards the use of one or the other language in family talk, bilingual siblings are a major internal micro force in the language ecology of a bilingual family and can strongly support language maintenance or language shift processes in such domain. Overall, the study provides insights into the dynamic ways in which family language policy is interactionally negotiated and instantiated in bilingual homes as well as the challenges of intergenerational language transmission.

Keywords: bilingual siblings, family interactions, family language policy, language maintenance

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Authors: Abhishikta Ghosh Roy

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Breast cancer is the most common malignancy among women globally, including India. Human breast cancer results from the genetic and environmental interaction. The present study attempts to understand the molecular heterogeneity of BRCA1 and BRCA2 genes, as well as to understand the association of various lifestyle and reproductive variables for the Breast Cancer risk. The study was conducted amongst 110 patients and 128 controls with total DNA sequencing of flanking and coding regions of BRCA1 BRCA2 genes that revealed ten Single Nucleotide Polymorphisms (SNPs) (6 novels). The controls selected for the study were age, sex and ethnic group matched. After written and informed consent biological samples were collected from the subjects. After detailed molecular analysis, significant (p < 0.005) molecular heterogeneity is revealed in terms of SNPs in BRCA1 (4 Exonic & 1 Intronic) and BRCA2 (2exonic and 3 Intronic) genes. The augmentation study investigated significant (p < 0.05) association with positive family history, early age at menarche, irregular menstrual periods, menopause, prolong contraceptive use, nulliparity, history of abortions, consumption of alcohol and smoking for breast cancer risk. To the best of authors knowledge, this study is the first of its kind, envisaged that the identification of the SNPs and modification of the lifestyle factors might aid to minimize the risk among the Bengalee Hindu females.

Keywords: breast cancer, BRCA, lifestyle, India

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Authors: Ashish Kumar Agrahari, Amit Kumar

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Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

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Authors: Jian-Li Shao

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Using Molecular Dynamic (MD) simulations, we simulated the microjet from the metal surface under decaying shock loading. The microjetting processes under release melting conditions are presented in detail, and some properties on the microjet mass and velocity are revealed. The phased increase of microjet mass with shock pressure is found. For all cases, the ratio of the maximal jetting velocity to the surface velocity approximately keeps a constant for liquid state. In addition, the temperature of the microjet can be always above the melting point. When introducing slow decaying profiles, the microjet mass begins to increase with the decay rate, which is dominated by the deformation of the bubble during pull-back. When the decay rate becomes fast enough, the microspall occurs as expected, meanwhile, the microjet appears to reduce because of the shock energy reduction.

Keywords: microjetting, shock, metal, molecular dynamics

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Authors: Abdela Bulbula

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Background: Marek’s disease virus is a devastating infection, causing high morbidity and mortality in chickens in Ethiopia. Methods: The current study was conducted from March to November, 2021 with the general objective of performing antemortem and postmortem, isolation, and molecular detection of Marek’s disease virus from outbreak cases in southwestern Ethiopia. Accordingly, based on outbreak information reported from the study sites namely, Bedelle, Yayo, and Bonga towns in southwestern Ethiopia, 50 sick chickens were sampled. The backyard and intensive farming systems of chickens were included in the sampling and priorities were given for chickens that showed clinical signs that are characteristics of Marek’s disease. Results: By clinical examinations, paralysis of legs and wings, gray eye, loss of weight, difficulty in breathing, and depression were recorded on all chickens sampled for this study and death of diseased chickens was observed. In addition, enlargement of the spleen and gross lesions of the liver and heart were recorded during postmortem examination. The death of infected chickens was observed in both vaccinated and non-vaccinated flocks. Out of 50 pooled feather follicle samples, Marek’s disease virus was isolated from 14/50 (28%) by cell culture method and out of six tissue samples, the virus was isolated from 5/6(83.30%). By Real time polymerization chain reaction technique, which was targeted to detect the Meq gene, Marek’s disease virus was detected from 18/50 feather follicles which accounts for 36% of sampled chickens. Conclusion: In general, the current study showed that the circulating Marek’s disease virus in southwestern Ethiopia was caused by the oncogenic Gallid herpesvirus-2 (Serotype-1). Further research on molecular characterization of revolving virus in current and other regions is recommended for effective control of the disease through vaccination.

Keywords: Ethioi, Marek's disease, isolation, molecular

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Authors: S. Roy, R. Rekha, K. Sriram, G. Subhadra, R. Johana

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Cardiovascular disease remains a leading cause of death in most industrialized countries. Many chemical drugs are available in the market which targets different receptor proteins related to cardiovascular diseases. Of late the traditional herbal drugs are safer when compared to chemical drugs because of its side effects. However, many herbal remedies used in treating cardiovascular diseases have not undergone scientific assessment to prove its pharmacological activities. There are many natural compounds, nature derived and Natural product mimic compounds are available which are in the market as approved drug. In the most of the cases drug activity at the molecular level are not known. Here we have categorized those compounds with our experimental compounds in different classes based on the structural similarity and physicochemical properties, using a tool, Chemmine and has attempted to understand the mechanism of the action of a experimental compound, which are clustered with Simvastatin, Lovastatin, Mevastatin and Pravastatin. Target protein molecule for Simvastatin, Lovastatin, Mevastatin and Pravastatin is HMG-CoA reductase, so we concluded that the experimental compound may be able to bind to the same target. Molecular docking and atomic interaction studies with simvastatin and our experimental compound were compared. A pharmacophore modeling was done based on the experimental compound and HMG-CoA reductase inhibitor.

Keywords: molecular docking, physicochemical properties, pharmacophore modeling structural similarity, pravastatin

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Authors: Ruswanto Ruswanto, Richa Mardianingrum, Tita Nofianti, Nur Rahayuningsih

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Tuberculosis (TB) is a chronic disease as a result of Mycobacterium tuberculosis. It can affect all age groups, and hence, is a global health problem that causes the death of millions of people every year. One of the drugs used in tuberculosis treatment is isonicotinohydrazide. In this study, N'-benzoylisonicotinohydrazide derivative compounds (a-l) were prepared using acylation reactions between isonicotinohydrazide and benzoyl chloride derivatives, through the reflux method. Molecular docking studies suggested that all of the compounds had better interaction with Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) than isonicotinohydrazide. It can be concluded that N'-benzoylisonicotinohydrazide derivatives (a-l) could be used as anti-tuberculosis candidates. From the docking results revealed that all of the compounds interact well with InhA, with compound g (N'-(3-nitrobenzoyl)isonicotinohydrazide) exhibiting the best interaction.

Keywords: anti-tuberculosis , docking, InhA, N'-benzoylisonicotinohydrazide, synthesis

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Authors: Manasa Kalla, Narasimha Raju Chebrolu, Ashok Chatterjee

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We have studied the quantum transport properties of a single molecular transistor in the presence of an external magnetic field using the Keldysh Green function technique. We also used the Anderson-Holstein-Caldeira-Leggett Model to describe the single molecular transistor that consists of a molecular quantum dot (QD) coupled to two metallic leads and placed on a substrate that acts as a heat bath. The phonons are eliminated by the Lang-Firsov transformation and the effective Hamiltonian is used to study the effect of an external magnetic field on the spectral density function, Tunneling Current, Differential Conductance and Spin polarization. A peak in the spectral function corresponds to a possible excitation. In the presence of a magnetic field, the spin-up and spin-down states are degenerate and this degeneracy is lifted by the magnetic field leading to the splitting of the central peak of the spectral function. The tunneling current decreases with increasing magnetic field. We have observed that even the differential conductance peak in the zero magnetic field curve is split in the presence electron-phonon interaction. As the magnetic field is increased, each peak splits into two peaks. And each peak indicates the existence of an energy level. Thus the number of energy levels for transport in the bias window increases with the magnetic field. In the presence of the electron-phonon interaction, Differential Conductance in general gets reduced and decreases faster with the magnetic field. As magnetic field strength increases, the spin polarization of the current is increasing. Our results show that a strongly interacting QD coupled to metallic leads in the presence of external magnetic field parallel to the plane of QD acts as a spin filter at zero temperature.

Keywords: Anderson-Holstein model, Caldeira-Leggett model, spin-polarization, quantum dots

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Authors: Marianna Maiaru, Gregory M. Odegard

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During the processing of high-performance thermoset polymer matrix composites, chemical reactions occur during elevated pressure and temperature cycles, causing the constituent monomers to crosslink and form a molecular network that gradually can sustain stress. As the crosslinking process progresses, the material naturally experiences a gradual shrinkage due to the increase in covalent bonds in the network. Once the cured composite completes the cure cycle and is brought to room temperature, the thermal expansion mismatch of the fibers and matrix cause additional residual stresses to form. These compounded residual stresses can compromise the reliability of the composite material and affect the composite strength. Composite process modeling is greatly complicated by the multiscale nature of the composite architecture. At the molecular level, the degree of cure controls the local shrinkage and thermal-mechanical properties of the thermoset. At the microscopic level, the local fiber architecture and packing affect the magnitudes and locations of residual stress concentrations. At the macroscopic level, the layup sequence controls the nature of crack initiation and propagation due to residual stresses. The goal of this research is use molecular dynamics (MD) and finite element analysis (FEA) to predict the residual stresses in composite laminates and the corresponding effect on composite failure. MD is used to predict the polymer shrinkage and thermomechanical properties as a function of degree of cure. This information is used as input into FEA to predict the residual stresses on the microscopic level resulting from the complete cure process. Virtual testing is subsequently conducted to predict strength allowables. Experimental characterization is used to validate the modeling.

Keywords: molecular dynamics, finite element analysis, processing modeling, multiscale modeling

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Authors: Naveed Ahmad, Farooq Ahmad, Abdul Aal

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The effect of iron contents on the rheological behavior of sPP/iron composites in the melt phase was investigated using a series of syndiotactic polypropylene/iron (sPP/iron) composite samples. Using the Advanced Rheometric Expansion System, studies with small amplitude oscillatory shear were conducted (ARES). It was discovered that the plateau modulus rose along with the iron loading. Also it was found that both entanglement molecular weight and packing length decrease with increase in iron loading.. This finding demonstrates how iron content in polymer/iron composites affects chain parameters and dimensions, which in turn affects the entire chain dynamics.

Keywords: plateau modulus, packing lenght, polymer/iron composites, rheology, entanglement molecular weight

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Authors: Sayanti Kar, Amitava Ghosh, Pritam Aitch, Gupinath Bhandari

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An extensive seasonal analysis of wastewater had been done from outfalls of river Ganga in Howrah, Hooghly, 24 PGS (N) District, West Bengal, India during 2017. The morphological parameters of Bitter gourd (Momordica charantia L.) were estimated under wastewater treatment. An approach to study the activity within the range of low molecular weight peptide 3-0.5 kDa were taken through its extraction and purification by ion exchange resin column, cation, and anion exchanger. HPLC analysis had been done for both in wastewater treated and untreated plants. The antioxidant activity by using DPPH and germination percentage in control and treated plants were also determined in relation to wastewater effect. The inhibition of growth and its parameters were maximum in pre-monsoon in comparing to post-monsoon and monsoon season. The study also helped to explore the effect of wastewater on the peptidome of Bitter gourd (Momordica charantia L.). Some of these low molecular weight peptide(s) (3-0.5 kDa) also inhibited during wastewater treatment. Expression of particular peptide(s) or absence of some peptide(s) in chromatogram indicated the adverse effects on plants which may be the indication of stressful condition. Pre monsoon waste water was found to create more impact than other two.

Keywords: bitter gourd (Momordica charantia l.), low molecular weight peptide, river ganga, waste water

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Authors: J. L. Chukwuneke, C. H. Achebe, S. N. Omenyi

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This research work presents the surface thermodynamics approach to M-TB/HIV-Human sputum interactions. This involved the use of the Hamaker coefficient concept as a surface energetics tool in determining the interaction processes, with the surface interfacial energies explained using van der Waals concept of particle interactions. The Lifshitz derivation for van der Waals forces was applied as an alternative to the contact angle approach which has been widely used in other biological systems. The methodology involved taking sputum samples from twenty infected persons and from twenty uninfected persons for absorbance measurement using a digital Ultraviolet visible Spectrophotometer. The variables required for the computations with the Lifshitz formula were derived from the absorbance data. The Matlab software tools were used in the mathematical analysis of the data produced from the experiments (absorbance values). The Hamaker constants and the combined Hamaker coefficients were obtained using the values of the dielectric constant together with the Lifshitz equation. The absolute combined Hamaker coefficients A132abs and A131abs on both infected and uninfected sputum samples gave the values of A132abs = 0.21631x10-21Joule for M-TB infected sputum and Ã132abs = 0.18825x10-21Joule for M-TB/HIV infected sputum. The significance of this result is the positive value of the absolute combined Hamaker coefficient which suggests the existence of net positive van der waals forces demonstrating an attraction between the bacteria and the macrophage. This however, implies that infection can occur. It was also shown that in the presence of HIV, the interaction energy is reduced by 13% conforming adverse effects observed in HIV patients suffering from tuberculosis.

Keywords: absorbance, dielectric constant, hamaker coefficient, lifshitz formula, macrophage, mycobacterium tuberculosis, van der waals forces

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Authors: Hermann Kuehnle

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Developments in ICT totally reshape manufacturing as machines, objects and equipment on the shop floors will be smart and online. Interactions with virtualizations and models of a manufacturing unit will appear exactly as interactions with the unit itself. These virtualizations may be driven by providers with novel ICT services on demand that might jeopardize even well established business models. Context aware equipment, autonomous orders, scalable machine capacity or networkable manufacturing unit will be the terminology to get familiar with in manufacturing and manufacturing management. Such newly appearing smart abilities with impact on network behavior, collaboration procedures and human resource development will make distributed manufacturing a preferred model to produce. Computing miniaturization and smart devices revolutionize manufacturing set ups, as virtualizations and atomization of resources unwrap novel manufacturing principles. Processes and resources obey novel specific laws and have strategic impact on manufacturing and major operational implications. Mechanisms from distributed manufacturing engaging interacting smart manufacturing units and decentralized planning and decision procedures already demonstrate important effects from this shift of focus towards collaboration and interoperability.

Keywords: autonomous unit, networkability, smart manufacturing unit, virtualization

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Authors: Sehrish Jalal, Choon-Mee Kim, Dong-Min Kim

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Background: Many pathogens causing hemorrhagic fevers of medical and veterinary importance have been identified and isolated from rodents in the Republic of Korea (ROK). Objective: We investigated the prevalence of emerging viruses causing hemorrhagic fevers, such as hemorrhagic fever with renal syndrome (HFRS), severe fever with thrombocytopenia syndrome (SFTS) and flaviviruses, from wild rodents. Methods: Striped field mice, Apodemus agrarius, (n=39) were captured during 2014-2015 in the south-west of ROK. Using molecular methods, lung samples were evaluated for SFTS virus, HFRS virus and flavivirus, and seropositivity was evaluated in the blood. Results: A high positive rate of Hantavirus (46.2%) was detected in A.agrarius lungs by reverse transcription-nested polymerase chain reaction (RT-N-PCR). The monthly prevalence of HFRS virus was 16.7% in October, 86.7% in November and 25% in August of the following year (p < 0.001). Moreover, 17.9% of blood samples were serologically positive for Hantavirus antibodies. The most prevalent strain in A. agrarius was Hantaan virus. All samples were positive for neither SFTS nor flavivirus. Conclusion: Hantan virus was detected in 86.7% of A. agrarius in November (autumn), and thus, virus shedding from A. agrarius can increase the risk of humans contracting HFRS. These findings may help to predict and prevent disease outbreaks in ROK.

Keywords: hemorrhagic fever virus, molecular diagnostic technique, rodents, Korea

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Authors: Olatunde Sunday Eludoyin, Charles Obiechina Olisa

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The study examined the spatial interactions between earthworm abundance (EA) and tree growth characteristics in ecological belts of Western Niger Delta, Nigeria. Eight 20m x 20m quadrat were delimited in the natural vegetation in each of the rainforest (RF), mangrove (M), fresh water swamp (FWS), and guinea savanna (GS) ecological belts to gather data about the tree species (TS) characteristics which included individual number of tree species (IN), diversity (Di), density (De) and richness (Ri). Three quadrats of 1m x 1m were delineated in each of the 20m x 20m quadrats to collect earthworm species the topsoil (0-15cm), and subsoil (15-30cm) and were taken to laboratory for further analysis. Descriptive statistics and inferential statistics were used for data analysis. Findings showed that a total of 19 earthworm species was found, with 58.5% individual species recorded in the topsoil and 41.5% recorded in the subsoil. The total population ofEudriliuseugeniae was predominantly highest in both topsoil (38.4%) and subsoil (27.1%). The total population of individual species of earthworm was least in GS in the topsoil (11.9%) and subsoil (8.4%). A total of 40 different species of TS was recorded, of which 55.5% were recorded in FWS, while RF was significantly highest in the species diversity(0.5971). Regression analysis revealed that Ri, IN, DBH, Di, and De of trees explained 65.9% of the variability of EA in the topsoil, while 46.9 % of the variability of earthworm abundance was explained by the floristic parameters in the subsoil.Similarly, correlation statistics revealed that in the topsoil, EA is positively and significantly correlated with Ri (r=0.35; p<0.05), IN (r=0.523; p<0.05) and De (r=0.469; p<0.05) while DBH was negatively and significantly correlated with earthworm abundance (r=-0.437; p<0.05). In the subsoil, only Ri and DBH correlated significantly with EA. The study concluded that EA in the study locations was highly influenced by tree growth species especially Ri, IN, DBH, Di, and De. The study recommended that the TSabundance should be improved in the study locations to ensure the survival of earthworms for ecosystem functions.

Keywords: interactions, earthworm abundance, tree growth, ecological zones, western niger delta

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Authors: M. Sadique, S. Ainane, Y. F. Yap, P. Rostron, E. Al Hajri

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The presence of sand in production lines in the oil and gas industries causes material degradation due to erosion-corrosion. The material degradation caused by erosion-corrosion in pipelines can result in a high cost of monitoring and maintenance and in major accidents. The process of erosion-corrosion consists of erosion, corrosion, and their interactions. Investigating and understanding how the erosion-corrosion process affects the degradation process in certain materials will allow for a reduction in economic loss and help prevent accidents. In this study, material loss due to erosion-corrosion of mild steel under impingement of sand-laden water at 90˚ impingement angle is investigated using a submerged impingement jet (SIJ) test. In particular, effects of jet velocity and sand loading on TWL due to erosion-corrosion, weight loss due to pure erosion and erosion-corrosion interactions, at a temperature of 29-33 °C in sea water environment (3.5% NaCl), are analyzed. The results show that the velocity and sand loading have a great influence on the removal of materials, and erosion is more dominant under all conditions studied. Changes in the surface characteristics of the specimen after impingement test are also discussed.

Keywords: erosion-corrosion, flow velocity, jet impingement, sand loading

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Authors: Anukriti Verma, Bhawna Rathi, Shivani Sharda

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Reactive Arthritis (ReA) is a disorder that causes inflammation in joints due to certain infections at distant sites in the body. ReA begins with stiffness, pain, and inflammation in these areas especially the ankles, knees, and hips. It gradually causes several complications such as conjunctivitis in the eyes, skin lesions in hand, feet and nails and ulcers in the mouth. Nowadays the diagnosis of ReA is based upon a differential diagnosis pattern. The parameters for differentiating ReA from other similar disorders include physical examination, history of the patient and a high index of suspicion. There are no standard lab tests or markers available for ReA hence the early diagnosis of ReA becomes difficult and the chronicity of disease increases with time. It is reported that enteric disorders such as Inflammatory Bowel Disease (IBD) that is inflammation in gastrointestinal tract namely Crohn’s Disease (CD) and Ulcerative Colitis (UC) are reported to be linked with ReA. Several microorganisms are found such as Campylobacter, Salmonella, Shigella and Yersinia causing IBD leading to ReA. The aim of our study was to perform the in-silico analysis in order to find interactions between microorganisms and human host causing IBD leading to ReA. A systems biology approach for metabolic network reconstruction and simulation was used to find the essential genes of the reported microorganisms. Interactomics study was used to find the interactions between the pathogen genes and human host. Genes such as nhaA (pathogen), dpyD (human), nagK (human) and kynU (human) were obtained that were analysed further using the functional, pathway and network analysis. These genes can be used as putative drug targets and biomarkers in future for early diagnosis, prevention, and treatment of IBD leading to ReA.

Keywords: drug targets, inflammatory bowel disease, reactive arthritis, systems biology

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Authors: Shajaratuldur Ismail, Nurlidia Mansor, Zakaria Man

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Thermoplastic starch (TPS) plasticized by 1-ethyl-3-methylimidazolium acetate [Emim][OAc] were obtained through gelatinization process. The gelatinization process occurred in the presence of water and [Emim][OAc] as plasticizer at high temperature (90˚C). The influence of [Emim][OAc] and water on the gelatinization and interactions with starch have been studied over a range of compositions. The homogenous mass was obtained for the samples containing 35, 40 and 43.5 % of water contents which showed that water plays important role in gelatinization process. Detailed IR spectroscopy analysis showed decrease in hydrogen bonding intensity and strong interaction between acetate anion in [Emim][OAc] and starch hydroxyl groups in the presence of [Emim][OAc]. Starch-[Emim][OAc]-water mixture at 10-3-8.7 presented homogenous mass, less hydrogen bonding intensity and strong interaction between acetate anion in [Emim][OAc] and starch hydroxyl groups.

Keywords: starch, ionic liquid, 1-ethyl-3-methylimidazolium acetate, plasticizer, gelatinization, IR spectroscopy

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Authors: Kuei-Hao Li, Eden Huang

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Motivation suggests the willingness one person has towards taking action. Learners’ motivation has frequently been regarded as the most crucial factor in successful language acquisition. Without sufficient motivation, learners cannot achieve long-term learning goals despite remarkable abilities. Therefore, the study aims to investigate motivation of interaction tasks designed by the researchers for college EFL learners in Travel English class in virtual reality environment, integrating CUE model, Cognition, Usage and Expansion in the course. Thirty college learners were asked to join the virtual language learning website designed by the researchers. Data was collected via feedback questionnaire, interview, and learner interactions. The findings indicated that the course in the CUE model in language learning website of virtual reality environment was effective at motivating EFL learners and improving their oral communication and social interactions in the learning process. Some pedagogical implications are also provided in helping both language instructors and EFL learners in virtual reality environment.

Keywords: motivation, virtual reality, virtual language learning, second language acquisition

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

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

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

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Authors: Chen Zheng, Lin Zhou, Bao Xie, Xiao Du, Nianbin Shao

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Power generated by large-scale photovoltaic plants (LSPVPs) is usually transmitted to the grid through several transformers and long distance overhead lines. Impedance of transformers and transmission lines results in complex interactions between the plant and the grid and among different inverters. In accordance with the topological structure of LSPV in reality, an equivalent model containing different inverters was built and then interactions between the plant and the grid and among different inverters were studied. Based on the vector composition principle of voltage at the point of common coupling (PCC), the mathematic function of PCC voltage in regard to the total power and grid impedance was deduced, from which the uttermost total power to guarantee the system stable is obtained. Taking the influence of different inverters numbers and the length of transmission lines to the system stability into account, the stability criterion of LSPV containing different inverters was derived. The result of simulation validated the theory analysis in the paper.

Keywords: LSPVPs, stability analysis, grid impedance, different types of inverter, PCC voltage

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Authors: Ritesh K. Shukla

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

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

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Authors: Wenya Shu, Ilinca Stanciulescu

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Carbon nanotubes (CNTs) possess attractive properties, such as high stiffness and strength, and high thermal and electrical conductivities, making them promising filler in multifunctional nanocomposites. Although CNTs can be efficient reinforcements, the expected level of mechanical performance of CNT-polymers is not often reached in practice due to the poor mechanical behavior of the CNT-polymer interfaces. It is believed that the interactions of CNT and polymer mainly result from the Van der Waals force. The interface debonding is a fracture and delamination phenomenon. Thus, the cohesive zone modeling (CZM) is deemed to give good capture of the interface behavior. The detailed, cohesive zone modeling provides an option to consider the CNT-matrix interactions, but brings difficulties in mesh generation and also leads to high computational costs. Homogenized models that smear the fibers in the ground matrix and treat the material as homogeneous are studied in many researches to simplify simulations. But based on the perfect interface assumption, the traditional homogenized model obtained by mixing rules severely overestimates the stiffness of the composite, even comparing with the result of the CZM with artificially very strong interface. A mechanical model that can take into account the interface debonding and achieve comparable accuracy to the CZM is thus essential. The present study first investigates the CNT-matrix interactions by employing cohesive zone modeling. Three different coupled CZM laws, i.e., bilinear, exponential and polynomial, are considered. These studies indicate that the shapes of the CZM constitutive laws chosen do not influence significantly the simulations of interface debonding. Assuming a bilinear traction-separation relationship, the debonding process of single CNT in the matrix is divided into three phases and described by differential equations. The analytical solutions corresponding to these phases are derived. A homogenized model is then developed by introducing a parameter characterizing interface sliding into the mixing theory. The proposed mechanical model is implemented in FEAP8.5 as a user material. The accuracy and limitations of the model are discussed through several numerical examples. The CZM simulations in this study reveal important factors in the modeling of CNT-matrix interactions. The analytical solutions and proposed homogenized model provide alternative methods to efficiently investigate the mechanical behaviors of CNT/polymer composites.

Keywords: carbon nanotube, cohesive zone modeling, homogenized model, interface debonding

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Authors: Abu Salim Mustafa

Abstract:

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

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

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Authors: Sihem Bazid, Meriem El Kolli, Aicha Medjahed

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Proteins and polysaccharides are the two types of biopolymers most frequently used in the food industry to control the mechanical properties and structural stability and organoleptic properties of the products. The textural and structural properties of these two types of blend polymers depend on their interaction and their ability to form organized structures. From an industrial point of view, a better understanding of mixtures protein / polysaccharide is an important issue since they are already heavily involved in processed food. It is in this context that we have chosen to work on a model system composed of a fibrous protein mixture (gelatin)/anionic polysaccharide (sodium carboxymethylcellulose). Gelatin, one of the most popular biopolymers, is widely used in food, pharmaceutical, cosmetic and photographic applications, because of its unique functional and technological properties. Sodium Carboxymethylcellulose (NaCMC) is an anionic linear polysaccharide derived from cellulose. It is an important industrial polymer with a wide range of applications. The functional properties of this anionic polysaccharide can be modified by the presence of proteins with which it might interact. Another factor may also manage the interaction of protein-polysaccharide mixtures is the triple helix of the gelatin. Its complex synthesis method results in an extracellular assembly containing several levels. Collagen can be in a soluble state or associate into fibrils, which can associate in fiber. Each level corresponds to an organization recognized by the cellular and metabolic system. Gelatin allows this approach, the formation of gelatin gel has triple helical folding of denatured collagen chains, this gel has been the subject of numerous studies, and it is now known that the properties depend only on the rate of triple helices forming the network. Chemical modification of this system is quite controlled. Observe the dynamics of the triple helix may be relevant in understanding the interactions involved in protein-polysaccharides mixtures. Gelatin is central to any industrial process, understand and analyze the molecular dynamics induced by the triple helix in the transitions gelatin, can have great economic importance in all fields and especially the food. The goal is to understand the possible mechanisms involved depending on the nature of the mixtures obtained. From a fundamental point of view, it is clear that the protective effect of NaCMC on gelatin and conformational changes of the α helix are strongly influenced by the nature of the medium. Our goal is to minimize the maximum the α helix structure changes to maintain more stable gelatin and protect against denaturation that occurs during such conversion processes in the food industry. In order to study the nature of interactions and assess the properties of mixtures, polarimetry was used to monitor the optical parameters and to assess the rate of helicity gelatin.

Keywords: gelatin, sodium carboxymethylcellulose, interaction gelatin-NaCMC, the rate of helicity, polarimetry

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Authors: Rashini Maduka, C. R. Wijesinghe, A. R. Weerasinghe

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Drug-drug interactions (DDIs) can happen when two or more drugs are taken together. Today DDIs have become a serious health issue due to adverse drug effects. In vivo and in vitro methods for identifying DDIs are time-consuming and costly. Therefore, in-silico-based approaches are preferred in DDI identification. Most machine learning models for DDI prediction are used chemical and biological drug properties as features. However, some drug features are not available and costly to extract. Therefore, it is better to make automatic feature engineering. Furthermore, people who have diabetes already suffer from other diseases and take more than one medicine together. Then adverse drug effects may happen to diabetic patients and cause unpleasant reactions in the body. In this study, we present a model with a graph convolutional autoencoder and a graph decoder using a dataset from DrugBank version 5.1.3. The main objective of the model is to identify unknown interactions between antidiabetic drugs and the drugs taken by diabetic patients for other diseases. We considered automatic feature engineering and used Known DDIs only as the input for the model. Our model has achieved 0.86 in AUC and 0.86 in AP.

Keywords: drug-drug interaction prediction, graph embedding, graph convolutional networks, adverse drug effects

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

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

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

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

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

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

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Authors: Harish Rajak, Preeti Patel

Abstract:

The application of histone deacetylase inhibitors is a well-known strategy in prevention of cancer which shows acceptable preclinical antitumor activity due to its ability of growth inhibition and apoptosis induction of cancer cell. Molecular docking were performed using Histone Deacetylase protein (PDB ID:1t69) and prepared series of hydroxamic acid based HDACIs. On the basis of docking study, it was predicted that compound 1 has significant binding interaction with HDAC protein and three hydrogen bond interactions takes place, which are essential for antitumor activity. On docking, most of the compounds exhibited better glide score values between -8 to -10 which is close to the glide score value of suberoylanilide hydroxamic acid. The pharmacophore hypotheses were developed using e-pharmacophore script and phase module. The 3D-QSAR models provided a good correlation between predicted and actual anticancer activity. Best QSAR model showed Q2 (0.7974), R2 (0.9200) and standard deviation (0.2308). QSAR visualization maps suggest that hydrogen bond acceptor groups at carbonyl group of cap region and hydrophobic groups at ortho, meta, para position of R9 were favorable for HDAC inhibitory activity. We established structure activity correlation using docking, pharmacophore modeling and atom based 3D QSAR model for hydroxamic acid based HDACIs.

Keywords: HDACIs, QSAR, e-pharmacophore, docking, suberoylanilide hydroxamic acid

Procedia PDF Downloads 268