Search results for: laboratory molecular diagnostics

Authors: Boda Sreenivas, Lyathakula Ravindranath, Kanugula Srishailam, Byru Venkatram Reddy

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Extensive research into the optimized structure and molecular properties of 3-Flouro-2-methylbenzoicacid(FMB), 3-Chloro-2-methoxybenzoicacid (CMB), and 3-Bromo-2-methylbenzoicacid (BMB) was carried out using FT-IR, FT-Raman and UV-Visible spectra, as well as theoretically using the DFT approach with B3LYPfunctional in conjunction with 6-311++G(d,p) basis set. The optimized structure was determined by evaluating torsional scans about free rotation bonds. Structure parameters, harmonic vibrational frequencies, potential energy distribution(PED), and infrared and Raman intensities were computed. The computational results from the DFT approach, such asFT-IR, FT-Raman, and UV-Visible spectra, were compared with the experimental results and found good agreement. Observed and calculated frequencies agreed with an rms error of 8.42, 6.60, and 6.95 cm-1 for FMB, CMB, and BMB, respectively. Unambiguous vibrational assignments were made for all fundamentals using PED and eigenvectors. The electronic HOMO-LUMO, H-bonding, and strong conjugative interactions across different molecular entities are discussed using experimental and simulated Ultraviolet-Visible spectra. The title molecules' molecular properties such as dipole moment, mean polarizability, and first-order hyperpolarizability, were calculated to study their non-linear optical (NLO) behavior. The chemical reactivity descriptors and mapped electrostatic surface potential (MESP) were also evaluated. Natural bond orbital (NBO) analysis was used to examine the stability of molecules resulting from hyperconjugative interactions and charge delocalization.

Keywords: ftir/raman spectra, DFT, NLO, homo-lumo, NBO, halogenated benzoic acids

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Authors: Mohamed Moussaoui

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A series of thirty-one potential inhibitors targeting the epidermal growth factor receptor kinase (EGFR), derived from quinazoline, underwent 3D-QSAR analysis using CoMFA and CoMSIA methodologies. The training and test sets of quinazoline derivatives were utilized to construct and validate the QSAR models, respectively, with dataset alignment performed using the lowest energy conformer of the most active compound. The best-performing CoMFA and CoMSIA models demonstrated impressive determination coefficients, with R² values of 0.981 and 0.978, respectively, and Leave One Out cross-validation determination coefficients, Q², of 0.645 and 0.729, respectively. Furthermore, external validation using a test set of five compounds yielded predicted determination coefficients, R² test, of 0.929 and 0.909 for CoMFA and CoMSIA, respectively. Building upon these promising results, eighteen new compounds were designed and assessed for drug likeness and ADMET properties through in silico methods. Additionally, molecular docking studies were conducted to elucidate the binding interactions between the selected compounds and the enzyme. Detailed molecular dynamics simulations were performed to analyze the stability, conformational changes, and binding interactions of the quinazoline derivatives with the EGFR kinase. These simulations provided deeper insights into the dynamic behavior of the compounds within the active site. This comprehensive analysis enhances the understanding of quinazoline derivatives as potential anti-cancer agents and provides valuable insights for lead optimization in the early stages of drug discovery, particularly for developing highly potent anticancer therapeutics

Keywords: 3D-QSAR, CoMFA, CoMSIA, ADMET, molecular docking, quinazoline, molecular dynamic, egfr inhibitors, lung cancer, anticancer

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Authors: M. Dehestani, F. Kamali, M. Klantari Pour, L. Zeidabadi-Nejad

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Chemical bonding between polyethylene glycol (PEG) with pharmaceutical proteins called pegylation is one of the most effective methods of improving the pharmacological properties. The covalent attachment of polyethylene glycol (PEG) to proteins will increase their pharmacologic properties. For the formation of a combination of pegylated protein should first be activated PEG and connected to the protein. Interferons(IFNs) are a family of cytokines which show antiviral effects in front of the biological and are responsible for setting safety system. In this study, the nature and properties of the interaction between active positions of IFNs and polyethylene glycol have been investigated using molecular dynamics simulation. The main aspect of this theoretical work focuses on the achievement of valuable data on the reaction pathways of PEG-IFNs and the transition state energy. Our results provide a new perspective on the interactions, chemical properties and reaction pathways between IFNs and PEG.

Keywords: interaction, interferons, molecular dynamics simulation, polyethylene glycol

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Authors: Sireethorn Nimitvilai, Ussanee Poolvivatchaikarn, Nuchanart Tomeun

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Objective: To determine the simple laboratory parameters to predict disease severity among COVID-19 patients in resource-limited settings. Material and methods: A retrospective cohort study was conducted at Nakhonpathom Hospital, a 722-bed tertiary care hospital, with an average of 50,000 admissions per year, during April 15 and May 15, 2021. Eligible patients were adults aged ≥ 15 years who were hospitalized with COVID-19. Baseline characteristics, comorbid conditions ad laboratory findings at admission were collected. Predictive factors for severe COVID-19 infection were analyzed. Result: There were 207 patients (79 male and 128 female) and the mean age was 46.7 (16.8) years. Of these, 39 cases (18.8%) were severe and 168 (81.2%) cases were non-severe. Factors associated with severe COVID-19 were neutrophil to lymphocyte ratio ≥ 4 (OR 8.1, 95%CI 2.3-20.3, P < 0.001) and C-reactive protein to albumin ratio ≥ 10 (OR 3.49, 95%CI 1.3-9.1, p 0.01). Conclusions: Complete blood counts, C-reactive protein and albumin are simple, inexpensive, widely available tests and can be used to predict severe COVID-19 in resource-limited settings.

Keywords: COVID-19, predictor of severity, resource-limiting settings, simple laboratory parameters

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Authors: Mahdi Asghari

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The cavitation phenomenon is the formation and production of micro-bubbles and eventually the bursting of the micro-bubbles inside the liquid fluid, which results in localized high pressure and temperature, causing physical and chemical fluid changes. This pressure and temperature are predicted to be 2000 atmospheres and 5000 °C, respectively. As a result of small bubbles bursting from this process, temperature and pressure increase momentarily and locally, so that the intensity and magnitude of these temperatures and pressures provide the energy needed to break the molecular bonds of heavy compounds such as fuel oil. In this paper, we study the theory of cavitation and the methods of cavitation production by acoustic and hydrodynamic methods and the necessary mechanical equipment and reactors for industrial application of the hydrodynamic cavitation method to break down the molecular bonds of the fuel oil and convert it into useful and economical products.

Keywords: Cavitation, Hydrodynamic Cavitation, Cavitation Reactor, Fuel Oil

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Authors: A. Vinod Kumar, G. Sunny Deol, Rakesh Kumar, B. Chandra

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Application of fiber reinforcement in road construction is gaining some interest in enhancing soil strength. In this paper, the natural Geotextile material obtained from gunny bags was used due to vast local availability material. Construction of flexible pavement on weaker soil such as clay soils are a significant problem in construction as well as in design due to its expansive characteristics. Jute Geotextile (JGT) was used on a foundation layer of flexible pavement on rural roads. This problem will be conquered by increasing the subgrade strength by decreasing sub-base layer thickness by improving their overall pavement strength characteristics which ultimately reduces the cost of construction and leads to economically design. The California Bearing Ratio (CBR), unconfined compressive strength (UCS) and triaxial laboratory tests were conducted on two different soil samples CI and MI. Weaker soil is reinforced with JGT, JGT+Bitumen; JGT+polythene sheet was varied with heights while performing the laboratory tests. Subgrade strength evaluation was investigated by conducting soak CBR test in the laboratory for clayey and silt soils. Laboratory results reveal that reinforced soak CBR value of clayey soil (CI) observed was 10.35%, and silty soil (MI) was 15.6%. This study intends to develop new technique for reinforcing weaker soil with JGT varying parameters for the need of low volume flexible pavements. It was observed that the performance of JGT is inferior when used with bitumen and polyethylene sheets.

Keywords: CBR, Jute geotextile, low volume road, weaker soil

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Authors: A. Rezaei, M. Huisman, W. Van Paepegem

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Atomic interactions in molecular systems are mainly studied by particle mechanics. Nevertheless, researches have also put on considerable effort to simulate them using continuum methods. In early 2000, simple equivalent finite element models have been developed to study the mechanical properties of carbon nanotubes and graphene in composite materials. Afterward, many researchers have employed similar structural simulation approaches to obtain mechanical properties of nanostructured materials, to simplify interface behavior of fiber-reinforced composites, and to simulate defects in carbon nanotubes or graphene sheets, etc. These structural approaches, however, are limited to small deformations due to complicated local rotational coordinates. This article proposes a method for the finite element simulation of molecular mechanics. For ease in addressing the approach, here it is called Structural Finite Element Molecular Modeling (SFEMM). SFEMM method improves the available structural approaches for large deformations, without using any rotational degrees of freedom. Moreover, the method simulates molecular conformation, which is a big advantage over the previous approaches. Technically, this method uses nonlinear multipoint constraints to simulate kinematics of the atomic multibody interactions. Only truss elements are employed, and the bond potentials are implemented through constitutive material models. Because the equilibrium bond- length, bond angles, and bond-torsion potential energies are intrinsic material parameters, the model is independent of initial strains or stresses. In this paper, the SFEMM method has been implemented in ABAQUS finite element software. The constraints and material behaviors are modeled through two Fortran subroutines. The method is verified for the bond-stretch, bond-angle and bond-torsion of carbon atoms. Furthermore, the capability of the method in the conformation simulation of molecular structures is demonstrated via a case study of a graphene sheet. Briefly, SFEMM builds up a framework that offers more flexible features over the conventional molecular finite element models, serving the structural relaxation modeling and large deformations without incorporating local rotational degrees of freedom. Potentially, the method is a big step towards comprehensive molecular modeling with finite element technique, and thereby concurrently coupling an atomistic domain to a solid continuum domain within a single finite element platform.

Keywords: finite element, large deformation, molecular mechanics, structural method

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Authors: Bakhtishod Matmuratov, Sakhiba Madraximova, Rakhmat Esanov, Alimjan Matchanov

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Studies have been performed to obtain complexes of glycyrrhizic acid and kinetins in a 2:1 ratio. The complex of glycyrrhizic acid and kinetins in a 2:1 ratio was considered evidence of the formation of a molecular complex by determining the molecular masses using chromato-mass spectroscopy and analyzing the IR spectra.

Keywords: monoammonium salt of glycyrrhizic acid, glycyrrhizic acid, supramolecular complex, isomolar series, IR spectroscopy

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Authors: Mohammed N. Al Kindi, Mazin Al Khabouri, Khalsa Al Lamki, Tommasso Pappuci, Giovani Romeo, Nadia Al Wardy

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Hereditary hearing loss is a heterogeneous group of complex disorders with an overall incidence of one in every five hundred newborns presented as syndromic and non-syndromic forms. Cadherin-related 23 (CDH23) is one of the listed deafness causative genes. CDH23 is found to be expressed in the stereocilia of hair cells and the retina photoreceptor cells. Defective CDH23 has been associated mostly with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic (USH1D) or non-syndromic SNHL (DFNB12). An Omani family diagnosed clinically with severe-profound sensorineural hearing loss was genetically analysed by whole exome sequencing technique. A novel homozygous missense variant, c.A7451C (p.D2484A), in exon 53 of CDH23 was detected. One hundred and thirty control samples were analysed where all were negative for the detected variant. The variant was analysed in silico for pathogenicity verification using several mutation prediction software. The variant proved to be a pathogenic mutation and is reported for the first time in Oman and worldwide. It is concluded that in silico mutation prediction analysis might be used as a useful molecular diagnostics tool benefiting both genetic counseling and mutation verification. The aspartic acid 2484 alanine missense substitution might be the main disease-causing mutation that damages CDH23 function and could be used as a genetic hearing loss marker for this particular Omani family.

Keywords: Cdh23, d2484a, in silico, Oman

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Authors: M. Shahina, K. Fakruddin, C. M. Subhan, S. Rangappa

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In this work, two mixtures with equal concentrations of 1) 4ꞌ-(6-(4-(pentylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(hexyloxy) benzylidene) amino) phenyl 4-butoxy benzoate and 2) 4ꞌ - (6-(4-(hexylamino) methyl)-3-hydroxyphenoxy) hexyloxy) biphenyl-4-carbonitrile+-4-((4-(octyloxy) benzylidene) amino) phenyl 4-butoxy benzoate, have been prepared. The transition temperature and optical texture are observed by using thermal microscopy. Density and birefringence studies are carried out on the above liquid crystalline mixtures. Using density and refractive indices data, the molecular polarizabilities are evaluated by using well-known Vuks and Neugebauer models. The molecular polarizability is also evaluated theoretically by Lippincott δ function model. The results reveal that the polarizability values are same in both experimental and theoretical methods.

Keywords: liquid crystals, optical textures, transition temperature, birefringence, polarizability

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Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck, Jason Stanley, Leroy Whilby

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major threat to fruit and vegetable industries in the United States. The establishment of pest fruit fly in the agricultural industries and produce severe ecological and economic impacts on agricultural diversification and trade. Detection and identification of these agricultural pests in a timely manner will facilitate the possibility of eradication from newly invaded areas. Identification of larval stages to species level is difficult, but is required to determine pest loads and their pathways into the United States. The aim of this study is the New World genus, Anastrepha which includes pests of major economic importance. Mitochondrial cytochrome c oxidase I (COI) gene sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level. During phylogenetics analysis numerous nuclear mitochondrial pseudogenes (numts) were discovered in different specimens. The numts are nonfunctional copies of the mtDNA present in the nucleus and are easily coamplified with the mitochondrial COI gene copy by using conserved universal primers. This is problematic for DNA Barcoding, which attempts to characterize all living organisms by using the COI gene. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed.

Keywords: tephritid, Anastrepha fraterculus, COI, numts

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Authors: Noureddine Benharkat, Abdelkader Chouaih, Nourdine Boukabcha

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A thiourea derivative compound was synthesized and subjected to structural analysis using single-crystal X-ray diffraction (XRD). The crystallographic data unveiled its crystallization in the P21/c space group within the monoclinic system. Examination of the dihedral angles indicated a notable non-planar structure. To support and interpret these resulats, density functional theory (DFT) calculations were conducted utilizing the B3LYP functional along with a 6–311 G (d, p) basis set. Additionally, to assess the contribution of intermolecular interactions, Hirshfeld surface analysis and 2D fingerprint plots were employed. Various types of interactions, whether weak intramolecular or intermolecular, within a molecule can significantly impact its stability. The distinctive signature of non-covalent interactions can be detected solely through electron density analysis. The NCI-RDG analysis was employed to investigate both repulsive and attractive van der Waals interactions while also calculating the energies associated with intermolecular interactions and their characteristics. Additionally, a molecular docking study was studied to explain the structure-activity relationship, revealing that the title compound exhibited an affinity energy of -6.8 kcal/mol when docked with B-DNA (1BNA).

Keywords: computational chemistry, density functional theory, crystallography, molecular docking, molecular structure, powder x-ray diffraction, single crystal x-ray diffraction

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Authors: Sumit Sharma, Rakesh Chandra, Pramod Kumar, Navin Kumar

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Molecular dynamics (MD) simulation has been used to study the effect of carbon nanofiber (CNF) volume fraction (Vf) and aspect ratio (l/d) on mechanical properties of CNF reinforced polypropylene (PP) composites. Materials Studio 5.5 has been used as a tool for finding the modulus and damping in composites. CNF composition in PP was varied by volume from 0 to 16%. Aspect ratio of CNF was varied from l/d=5 to l/d=100. To the best of the knowledge of the authors, till date there is no study, either experimental or analytical, which predict damping for CNF-PP composites at the nanoscale. Hence, this will be a valuable addition in the area of nanocomposites. Results show that with only 2% addition by volume of CNF in PP, E11 increases 748%. Increase in E22 is very less in comparison to the increase in E11. With increase in CNF aspect ratio (l/d) till l/d=60, the longitudinal loss factor (η11) decreases rapidly. Results of this study have been compared with those available in literature.

Keywords: carbon nanofiber, elasticity, mechanical properties, molecular dynamics

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Authors: Alya Harichane, Abderraouf Achour, Abdelbaki Benmounah

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The main difficulty encountered in the formulation of high-performance concrete (HPC) consists in choosing the most efficient cement-superplasticizer pair allowing to obtain maximum water reduction, good workability of the concrete in the fresh state, and very good mechanical resistance in the hardened state. The aim of this work is to test the efficiency of three polycarboxylate ether-based superplasticizers (PCE) marketed in Algeria with CEMI 52.5 R cement and to study the effect of chemical structure of PCE on zeta potential, rheological and mechanical properties of cement pastes. The property of the polymers in cement was tested by a Malvern Zetasizer 2000 apparatus and VT 550 viscometer. Results showed that the zeta potential and its rheological properties are related to the molecular weight and the density carboxylic of PCE. The PCE with a moderate molecular weight and the highest carboxylic groups had the best dispersion (high value of zeta potential) and lowest viscosity. The effect of the chemical structure of PCEs on mechanical properties is evaluated by the formulation of cement mortar with these PCEs. The result shows that there is a correlation between the zeta potential of polymer and the compressive strength of cement paste.

Keywords: molecular weight, polycarboxylate-ether superplasticizer, rheology, zeta potential

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Authors: Chaudhari S. G., Saxena, S.

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We systematically and quantitatively investigated the effect of glucose as a model of natural molecular crowding agent on the structure and thermodynamics of Watson-Crick base paired three duplexes (named as D1, D2 and D3) of different base compositions and lengths. Structural analyses demonstrated that duplexes (D1 and D2) folded into B-form with different cations in the absence and presence of glucose while duplex (D3) folded into mixed A and B-form. Moreover, we demonstrated that the duplex was more stable in the absence of glucose, and marginally destabilized in its presence because glucose act as a weak structure breaker on the tetrahedral network of water. In the absence of glucose, the values of ΔG°25 for duplex (D1) were -13.56, -13.76, -12.46, and -12.36 kcal/mol, for duplex (D2) were -13.64, -12.93, -12.86, and -12.30 kcal/mol, for duplex (D3) were -10.05, -11.76, -9.91, -9.70 kcal/mol in the presence of Na+, K+, Na+ + Mg++ and K+ + Mg++ respectively. At high concentration of glucose (1:10000), there was increase in ΔG°25 for duplex (D1) -12.47, -12.37, -11.96, -11.55 kcal/mol, for duplex (D2) -12.37, -11.47, -11.98, -11.01 kcal/mol and for duplex (D3) -8.47, -9.17, -9.16, -8.66 kcal/mol. Our results provide the information that structure and stability of DNA duplex depends on the structure of molecular crowding agent present in its close vicinity. In this study, I have taken the hydration of simple sugar as an essential model for understanding interactions between hydrophilic groups and interfacial water molecules and its effect on hydrogen bonded DNA duplexes. On the basis of these relatively simple building blocks I hope to gain some insights for understanding more generally the properties of sugar–water–salt systems with DNA duplexes.

Keywords: natural molecular crowding, DNA Duplex, structure of DNA, bioengineering and life sciences

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Authors: M. Patterson, R. Bond, K. Cowan, M. Mulvenna, C. Reid, F. McMahon, P. McGowan, H. Cormican

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This paper outlines the design of a simulator to allow for the optimisation of clinical workflows through a pathology laboratory and to improve the laboratory’s efficiency in the processing, testing, and analysis of specimens. Often pathologists have difficulty in pinpointing and anticipating issues in the clinical workflow until tests are running late or in error. It can be difficult to pinpoint the cause and even more difficult to predict any issues which may arise. For example, they often have no indication of how many samples are going to be delivered to the laboratory that day or at a given hour. If we could model scenarios using past information and known variables, it would be possible for pathology laboratories to initiate resource preparations, e.g. the printing of specimen labels or to activate a sufficient number of technicians. This would expedite the clinical workload, clinical processes and improve the overall efficiency of the laboratory. The simulator design visualises the workflow of the laboratory, i.e. the clinical tests being ordered, the specimens arriving, current tests being performed, results being validated and reports being issued. The simulator depicts the movement of specimens through this process, as well as the number of specimens at each stage. This movement is visualised using an animated flow diagram that is updated in real time. A traffic light colour-coding system will be used to indicate the level of flow through each stage (green for normal flow, orange for slow flow, and red for critical flow). This would allow pathologists to clearly see where there are issues and bottlenecks in the process. Graphs would also be used to indicate the status of specimens at each stage of the process. For example, a graph could show the percentage of specimen tests that are on time, potentially late, running late and in error. Clicking on potentially late samples will display more detailed information about those samples, the tests that still need to be performed on them and their urgency level. This would allow any issues to be resolved quickly. In the case of potentially late samples, this could help to ensure that critically needed results are delivered on time. The simulator will be created as a single-page web application. Various web technologies will be used to create the flow diagram showing the workflow of the laboratory. JavaScript will be used to program the logic, animate the movement of samples through each of the stages and to generate the status graphs in real time. This live information will be extracted from an Oracle database. As well as being used in a real laboratory situation, the simulator could also be used for training purposes. ‘Bots’ would be used to control the flow of specimens through each step of the process. Like existing software agents technology, these bots would be configurable in order to simulate different situations, which may arise in a laboratory such as an emerging epidemic. The bots could then be turned on and off to allow trainees to complete the tasks required at that step of the process, for example validating test results.

Keywords: laboratory-process, optimization, pathology, computer simulation, workflow

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Authors: I. Schäfer, B. Kohn, M. Volkmann, E. Müller

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Introduction: Blood-feeding arthropods transmit parasitic, bacterial, or viral pathogens to domestic animals and wildlife. Vector-borne infections are gaining significance due to the increase of travel, import of domestic animals from abroad, and the changing climate in Europe. Aims of the study: The main objective of this retrospective study was to assess the prevalence of vector-borne infections in cats in which a ‘Feline Travel Profile’ had been conducted. Material and Methods: This retrospective study included test results from cats for which a ‘Feline Travel Profile’ established by LABOKLIN had been requested by veterinarians between April 2012 and December 2019. This profile contains direct detection methods via polymerase chain reaction (PCR) for Hepatozoon spp. and Dirofilaria spp. as well as indirect detection methods via immunofluorescence antibody test (IFAT) for Ehrlichia spp. and Leishmania spp. This profile was expanded to include an IFAT for Rickettsia spp. from July 2015 onwards. The prevalence of the different vector-borne infectious agents was calculated. Results: A total of 602 cats were tested using the ‘Feline Travel Profile’. Positive test results were as follows: Rickettsia spp. IFAT 54/442 (12.2%), Ehrlichia spp. IFAT 68/602 (11.3%), Leishmania spp. IFAT 21/602 (3.5%), Hepatozoon spp. PCR 51/595 (8.6%), and Dirofilaria spp. PCR 1/595 cats (0.2%). Co-infections with more than one pathogen could be detected in 22/602 cats. Conclusions: 170/602 cats (28.2%) were tested positive for at least one vector-borne pathogen. Infections with multiple pathogens could be detected in 3.7% of the cats. The data emphasizes the importance of considering vector-borne infections as potential differential diagnoses in cats.

Keywords: arthopod-transmitted infections, feline vector-borne infections, Germany, laboratory diagnostics

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Authors: Nwadioha Samuel Iheanacho, Abah Paul, Odimayo Simidele Michael

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Background: The World Health Assembly through the Global Health Sector Strategy on viral hepatitis calls for the elimination of viral hepatitis as a public health threat by 2030. All hands are on deck to actualize this goal through an effective and active vaccination and monitoring tool. Aim: To combine the Epidemiologic with Laboratory Hepatitis B Virus vaccination monitoring tools. Method: Laboratory results analysis of subjects recruited during the World Hepatitis week from July 2020 to July 2021 was done after obtaining their epidemiologic data on Hepatitis B virus risk factors, in the Medical Microbiology Laboratory of Benue State University Teaching Hospital, Nigeria. Result: A total of 500 subjects comprising males 60.0%(n=300/500) and females 40.0%(n=200/500) were recruited. A fifty-three percent majority was of the age range of 26 to 36 years. Serologic profiles were as follows, 15.0%(n=75/500) HBsAg; 7.0% (n=35/500) HBeAg; 8.0% (n=40/500) Anti-Hbe; 20.0% (n=100/500) Anti-HBc and 38.0% (n=190/500) Anti-HBs. Immune responses to vaccination were as follows, 47.0%(n=235/500) Immune naïve {no serologic marker + normal ALT}; 33%(n=165/500) Immunity by vaccination {Anti-HBs + normal ALT}; 5%(n=25/500) Immunity to previous infection {Anti-HBs, Anti-HBc, +/- Anti-HBe + normal ALT}; 8%(n=40/500) Carriers {HBsAg, Anti-HBc, Anti-HBe +normal ALT} and 7% (35/500) Anti-HBe serum- negative infections {HBsAg, HBeAg, Anti-HBc +elevated ALT}. Conclusion: The present 33.0% immunity by vaccination coverage in Central Nigeria was much lower than the 41.0% national peak in 2013, and a far cry from the global expectation of attainment of a Global Health Sector Strategy on the elimination of viral hepatitis as a public health threat by 2030. Therefore, more creative ideas and collective effort are needed to attain this goal of the World Health Assembly.

Keywords: Hepatitis B, vaccination status, laboratory tools, resource-limited settings

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Authors: Nicolas Spitz, Nicolas Coniglio, Mohamed El Mansori, Alex Montagne, Sabeur Mezghani

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Nowadays buildings' construction is performed by pouring concrete into molds referred to as formworks that are usually prefabricated metallic modules. Defects such as stripping may possibly form during the removal of the formwork if the interfacial bonding between the concrete and the formwork is high. A new pull-off tensile test was developed in our laboratory to simulate small-scale formwork removals. The concrete-to-formwork adherence force was measured on bare and coated formworks with different surface signatures. The used concrete was a mixture largely used on building sites and contains CEM I Portland cement and calcareous filler. The concrete surface appearance and the type of failures at the concrete-formwork interface have been investigated. The originality of this near-to-surface test was to compare the laboratory-measured adherence forces to the on-site observations. Based upon the small-scale laboratory test results, functional formwork specifications with low adherence to concrete was proposed in terms of superficial signature characteristics.

Keywords: concrete-formwork adherence, interfacial bonding, skin formwork functionality, small-scale pull-off tensile test

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Authors: Maria Konstadinou, Etienne Alderlieste, Anderson Peccin da Silva, Ben Arntz, Leonard van der Bijl, Wouter Verschueren

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The shear strength and compression properties of stiff Boom clay from Belgium at the depth of about 30 m has been investigated by means of cone penetration and laboratory testing. The latter consisted of index classification, constant rate of strain, direct, simple shear, and unconfined compression tests. The Boom clay samples exhibited strong swelling tendencies. The suction pressure was measured via different procedures and has been compared to the expected in-situ stress. The undrained shear strength and OCR profile determined from CPTs is not compatible with the experimental measurements, which gave significantly lower values. The observed response can be attributed to the presence of pre-existing discontinuities, as shown in microscale CT scans of the samples. The results of this study demonstrate that the microstructure of the clay prior to testing has an impact on the mechanical behaviour and can cause inconsistencies in the comparison of the laboratory test results with in-situ data.

Keywords: boom clay, laboratory testing, overconsolidation ratio, stress-strain response, swelling, undrained shear strength

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

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The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory

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Authors: Mahdi Golriz

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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

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Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld

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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.

Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups

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Authors: Santina Sahibon, Sivasooriar Sivaneson, Martin Giddy, Nelson Nheu, Siti Sazeelah, Choo Kok Ming, Thuhairah Abdul Rahman, Fatmawati Binti Kamal

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Introduction: Establishing population-based reference intervals (RI) are essential when evaluating laboratory test results and for method verification. Our laboratory initiated an exercise to establish RI for routine coagulation profile as part of the method verification procedure and to determine any differences in RI between three analyzers planned to be used in the laboratory. Methodology: 145 blood samples were collected and analysed for activated partial thromboplastin time (aPTT), prothrombin time (PT), international normalized ratio (INR), and fibrinogen] using three coagulation analysers which were CA104, CA660, and CS-2500 (Sysmex, USA). RI was established at 2.5th and 97.5th percentiles. Results: The RI for aPTT between C104, C660 and CS-2500 are (RI: 20.5-30.2 sec), (RI: 21.5-29.2 sec) and (RI: 22.7-30.3 sec) respectively. The RI for PT were (RI: 7.5-10.3 sec), (RI: 9.2- 11.1 sec) and (RI: 9.8-11.9 sec) for C104, CA660 and CS-2500 respectively. INR had an RI of (RI: 0.87- 1.16), (RI: 0.89-1.10) and (0.90-1.11) respectively on CA104, C660 and CS-2500. Fibrinogen RI was (RI: 2.04-4.62 g/L) and (2.05-4.76 g/L) on the CA660 and CS-2500, respectively. Conclusion: The RI was similar across the analytical platforms for aPTT, INR, and fibrinogen. However, CA104 showed lower RI compared to the other two analysers for PT. This highlights the potential variability in results between instruments that need to be addressed when verifying RI.

Keywords: coagulation, reference interval, APTT, PT, INR, fibrinogen

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Authors: Kinga Wieczorek, Elzbieta Kukier, Remigiusz Pomykala, Beata Lachtara, Renata Szewczyk, Krzysztof Kwiatek, Jacek Osek

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The MICRORISK project (Research cooperation in assessment of microbiological hazard and risk in the food chain) was funded by the European Commission under the FP7 PEOPLE 2012 IRSES call within the International Research Staff Exchange Scheme of Marie Curie Action and realized during years from 2014 to 2015. The main aim of the project was to establish a cooperation between the European Union (EU) and the third State in the area important from the public health point of view. The following organizations have been engaged in the activity: National Veterinary Research Institute (NVRI) in Pulawy, Poland (coordinator), French Agency for Food, Environmental and Occupational Health & Safety (ANSES) in Maisons Alfort, France, National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), Kharkov and State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE) Kijev Ukraine. The results of the project showed that Ukraine used microbiological criteria in accordance with Commission Regulation (EC) No 2073/2005 of 15 November 2005 on microbiological criteria for foodstuffs. Compliance concerns both the criteria applicable at the stage of food safety (retail trade), as well as evaluation criteria and process hygiene in food production. In this case, the Ukrainian legislation also provides application of the criteria that do not have counterparts in the food law of the European Union, and are based on the provisions of Ukrainian law. Partial coherence of the Ukrainian and EU legal requirements in terms of microbiological criteria for food and feed concerns microbiological parameters such as total plate count, coliforms, coagulase-positive Staphylococcus spp., including S. aureus. Analysis of laboratory methods used for microbiological hazards control in food production chain has shown that most methods used in the EU are well-known by Ukrainian partners, and many of them are routinely applied as the only standards in the laboratory practice or simultaneously used with Ukrainian methods. The area without any legislation, where the EU regulation and analytical methods should be implemented is the area of Shiga toxin producing E. coli, including E. coli O157 and staphylococcal enterotoxin detection. During the project, the analysis of the existing Ukrainian and EU data concerning the prevalence of the most important food-borne pathogens on different stages of food production chain was performed. Particularly, prevalence of Salmonella spp., Campylobacter spp., L. monocytogenes as well as clostridia was examined. The analysis showed that poultry meat still appears to be the most important food-borne source of Campylobacter and Salmonella in the UE. On the other hand, L. monocytogenes were seldom detected above the legal safety limit (100 cfu/g) among the EU countries. Moreover, the analysis revealed the lack of comprehensive data regarding the prevalence of the most important food-borne pathogens in Ukraine. The results of the MICRORISK project are networking activities among researches originations participating in the tasks will help with a better recognition of each other regarding very important, from the public health point of view areas such as microbiological hazards in the food production chain and finally will help to improve food quality and safety for consumers.

Keywords: cooperation, European Union, food chain safety, food law, microbiological risk, Microrisk, Poland, Ukraine

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Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad

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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.

Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation

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Authors: Sangwoo Oh, Jaewoo Kim, Dongmin Seo, Jaewon Park, Yongha Hwang, Sungkyu Seo

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Plasmonics has been regarded one of the most powerful bio-sensing modalities to evaluate bio-molecular interactions in real-time. However, most of the plasmonic sensing methods are based on labeling metallic nanoparticles, e.g. gold or silver, as optical modulation markers, which are non-recyclable and expensive. This plasmonic modulation can be usually achieved through various nano structures, e.g., nano-hole arrays. Among those structures, plasmonic lens has been regarded as a unique plasmonic structure due to its light focusing characteristics. In this study, we introduce a custom designed plasmonic lens array for bio-sensing, which was simulated by finite-difference-time-domain (FDTD) approach and fabricated by top-down approach. In our work, we performed the FDTD simulations of various plasmonic lens designs for bacteria sensor, i.e., Samonella and Hominis. We optimized the design parameters, i.e., radius, shape, and material, of the plasmonic lens. The simulation results showed the change in the peak intensity value with the introduction of each bacteria and antigen i.e., peak intensity 1.8711 a.u. with the introduction of antibody layer of thickness of 15nm. For Salmonella, the peak intensity changed from 1.8711 a.u. to 2.3654 a.u. and for Hominis, the peak intensity changed from 1.8711 a.u. to 3.2355 a.u. This significant shift in the intensity due to the interaction between bacteria and antigen showed a promising sensing capability of the plasmonic lens. With the batch processing and bulk production of this nano scale design, the cost of biological sensing can be significantly reduced, holding great promise in the fields of clinical diagnostics and bio-defense.

Keywords: plasmonic lens, FDTD, fabrication, bacteria sensor, salmonella, hominis

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Authors: Maznieda Mahjom, Rohaida Ismail, Masita Arip, Mohd Shaiful Azlan, Nor’Ashikin Othman, Hafizah Abdullah, nor Zahrin Hasran, Joshita Jothimanickam, Syaqilah Shawaluddin, Nadia Mohamad, Raheel Nazakat, Tuan Mohd Amin, Mizanurfakhri Ghazali, Rosmanajihah Mat Lazim

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COVID-19 outbreak is particularly detrimental to the mental health of everyone as well as leaving a long devastating crisis in the healthcare sector. Daily increment of COVID-19 cases and close contact, necessitating the testing of a large number of samples, thus increasing the workload and burden to laboratory personnel. This study aims to determine the prevalence of personal-, work- and client-related burnout as well as to measure the concentration of salivary cortisol among laboratory personnel in the main laboratories in Klang Valley, Malaysia. This cross-sectional study was conducted in late 2021 and recruited a total of 404 respondents from three laboratories in Klang Valley, Malaysia. The level of burnout was assessed using Copenhagen Burnout Inventory (CBI) comprising three sub-dimensions of personal-, work- and client-related burnout. The cut-off score of 50% and above indicated possible burnout. Meanwhile, salivary cortisol was measured using a competitive enzyme immunoassay kit (Salimetrics, State College, PA, USA). Normal levels of salivary cortisol concentration in adults are within 0.094 to 1.551 μg/dl (morning) and can be none detected to 0.359 μg/dl (evening). The prevalence of personal-, work- and client-related burnout among laboratory personnel were 36.1%, 17.8% and 7.2% respectively. Meanwhile, the abnormal morning and evening cortisol concentration recorded were 29.5% and 21.8% excluding 6.9%-7.4% missing data. While the IgA level is normal for most of the respondents, which recorded at 95.53%. Laboratory personnel were at risk of suffering burnout during the COVID-19 pandemic. Thus, mental health programs need to be addressed at the department and hospital level by regularly screening healthcare workers and designing an intervention program. It is also vital to improve the coping skills of laboratory personnel by increasing the awareness of good coping skill techniques. The training must be in an innovative way to ensure that the lab personnel can internalise the technique and practise it in real life.

Keywords: burnout, COVID-19, laborotary personnel, salivary cortisol

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Authors: Moustafa Osman Mohammed

Abstract:

This paper introduces Luhmann’s autopoietic social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. A specific type of autopoietic system is explained in the three existing groups of the ecological phenomena: interaction, social and medical sciences. This hypothesis model, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for the exchange of photon energy with molecular without any changes in topology. The external forces in the systems environment might be concomitant with the natural fluctuations’ influence (e.g. radioactive radiation, electromagnetic waves). The cantilever sensor deploys insights to the future chip processor for prevention of social metabolic systems. Thus, the circuits with resonant electric and optical properties are prototyped on board as an intra–chip inter–chip transmission for producing electromagnetic energy approximately ranges from 1.7 mA at 3.3 V to service the detection in locomotion with the least significant power losses. Nowadays, therapeutic systems are assimilated materials from embryonic stem cells to aggregate multiple functions of the vessels nature de-cellular structure for replenishment. While, the interior actuators deploy base-pair complementarity of nucleotides for the symmetric arrangement in particular bacterial nanonetworks of the sequence cycle creating double-stranded DNA strings. The DNA strands must be sequenced, assembled, and decoded in order to reconstruct the original source reliably. The design of exterior actuators have the ability in sensing different variations in the corresponding patterns regarding beat-to-beat heart rate variability (HRV) for spatial autocorrelation of molecular communication, which consists of human electromagnetic, piezoelectric, electrostatic and electrothermal energy to monitor and transfer the dynamic changes of all the cantilevers simultaneously in real-time workspace with high precision. A prototype-enabled dynamic energy sensor has been investigated in the laboratory for inclusion of nanoscale devices in the architecture with a fuzzy logic control for detection of thermal and electrostatic changes with optoelectronic devices to interpret uncertainty associated with signal interference. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other and forms its unique spatial structure modules for providing the environment mutual contribution in the investigation of mass temperature changes due to pathogenic archival architecture of clusters.

Keywords: autopoiesis, nanoparticles, quantum photonics, portable energy, photonic structure, photodynamic therapeutic system

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